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About the Sandbox

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An infrastructure project for health data science training and research in Denmark

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The National Health Data Science Sandbox project kicked off in 2021 with 5 years of funding via the Data Science Research Infrastructure initiative from the Novo Nordisk Foundation. Health data science experts at five Danish universities are contributing to the Sandbox with coordination from the Center for Health Data Science under lead PI Professor Anders Krogh. Data scientists hosted in the research groups of each PI are building infrastructure and training modules on Computerome and UCloud, the primary academic high performance computing (HPC) platforms in Denmark. If you have any questions or would like to get in touch with one of our data scientists, please contact us here.

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Our computational ‘sandbox’ allows data scientists to explore datasets, tools and analysis pipelines in the same high performance computing environments where real research projects are conducted. Rather than a single, hefty environment, we’re deploying modularized topical environments tailored for independent use on each HPC platform. We aim to support three key user groups based at Danish universities:

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Activity developing independent training modules and hosting workshops has centered on UCloud, while collaborative construction of a flexible Course Platform has been completed on Computerome for use by the Sandbox and independent educators. Publicly sourced datasets are being used in training modules on UCloud, while generation of synthetic data is an ongoing project at Computerome. Sandbox resources are under active construction, so check out our other pages for the current status on HPC Access, Datasets, and Modules. We run workshops using completed training modules on a regular basis and provide active support for Sandbox-hosted courses through a slack workspace. See our Contact page for more information.

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Partner with the Sandbox

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The Sandbox welcomes proposals for new courses, modules, and prototyping projects from researchers and educators. We’d like to partner with lecturers engaged with us in developing needed materials collaboratively - we would love to have input from subject experts or help promote exciting new tools and analysis methods via modules! Please contact us with your ideas at nhds_sandbox@sund.ku.dk.

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We thank the Novo Nordisk Foundation for funding support. If you use the Sandbox for research or reference it in text or presentations, please acknowledge the Health Data Science Sandbox project and its funder the Novo Nordisk Foundation (grant number NNF20OC0063268).

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Computerome

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Accessing the Sandbox on Computerome

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We do not currently support independent use of Sandbox materials on Computerome. Access is supported via courses collaborating with the Sandbox and run on Computerome’s Course Platform. Check here for more info.

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The below instructions are provided as reference for course participants.

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To set up a user account on Computerome, you will need to provide administrators with your name, email address, and phone number for two-factor authentication. Once approved as a user, you will receive your username and server address (URL) by email, and you will receive an initial course-platform password by text.

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On Computerome, the Sandbox environment is deployed as a virtual machine with a Linux desktop as user interface. This environment can be accessed through VMware Horizon using two different methods: (A) a desktop client (which you install on your computer) or (B) a web-based client (for those without install privileges on their computer). Please follow the appropriate instructions (A versus B) depending on your access preference.

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!!! note “Sign-In Instructions” 1. On FIRST login, enter the provided server address (URL) in a browser window to access the environment using your provided credentials. The URL will take you to a VMware Horizon access portal where you can * (A) choose to install the desktop client (left: ‘Install VMware Horizon Client’). You will then open this client for all subsequent logins instead of using the server address, and can login starting from step 2. * (B) access the environment via browser (right: ‘VMware Horizon HTML Access’). You will always use the server address in your browswer to access this entry point if this is your chosen method of access.

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2. Select the cloud icon
+  *  (A) which is linked to the server URL. This option appears when you have successfully installed and opened the VMware Horizon client.
+  *  (B) which is linked to the Sandbox course. This option appears after you have selected VMware Horizon HTML Access.
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+3. Enter your username and your course-platform password. 
+  *  On the first sign-in, this will be the course-platform password texted to you. You will then be prompted to create your own permanent password to replace this password which you will use for all future sign-ins.
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+4. When prompted, enter the one-time password texted to you from DTU (NOT the same password as the course-platform password).
+  *  (A) If it is your first login / you logged off at last access, press any key when greeted with the blue time status screen. This will allow you to select your own user account in a dialog box.
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+5. Sign-in using your course-platform password again after choosing the correct language for the environment in the upper right corner of the screen (this is important for the keyboard and typing your password). Danish (the da option) is default, so those with English keyboards will need to switch to English (the en option) at every login.
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+6. Congratulations, you have entered the Sandbox environment. Relevant links for courses should be present on your desktop.
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!!! warning “Exit Instructions” To exit the environment, you have two options with different outcomes. You can log off and kill all running processes, or you can disconnect and your processes will continue running. “Power off” is disabled for users as this will shut down your virtual machine, local settings and user files may be lost, and the virtual machine will need to be manually restarted for your account.

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1. To exit and kill all running processes, select the power icon in the upper right corner, then select your name and choose "log off" in the pop up window.
+2. To exit and preserve running processes,
+    *  (A) hover at the top of the screen for a few seconds until your VMware Client menu is accessible, choose "Connection", and select "Disconnect".
+    *  (B) close the browser tab where you are accessing the Sandbox environment.
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+ + + + + \ No newline at end of file diff --git a/access/UCloud.html b/access/UCloud.html new file mode 100644 index 0000000..2831603 --- /dev/null +++ b/access/UCloud.html @@ -0,0 +1,929 @@ + + + + + + + + + +Introduction to NGS data analysis - UCloud + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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UCloud

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Accessing the Sandbox on UCloud

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User accounts on UCloud are enabled by university login credentials using WAYF (Where Are You From). Access the WAYF login portal here, and then find your affiliated Danish university using the search bar. After login, we suggest setting up Two Factor Authentication by clicking on the icon in the top-right corner of the screen. Once you are an approved user of UCloud, you can access the Sandbox environment via different ‘Sandbox’ apps linked to topical modules that you deploy using your own storage and computing resources - just go to Apps once you have signed into UCloud and search ‘Sandbox’ to find what we have deployed. Each app page has its own Documentation link that will direct you to Sandbox-based usage guidelines which may be customized to the app’s particular tools and scope. Apps will have different ‘courses’ that you can initially choose which make a personal copy of training materials in your workspace for you to edit.

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Each Danish university has its usage relationship with UCloud as governed by their local front office of DeiC - check with your university IT support / DeiC representatives about requesting computational resources. For example, the University of Copenhagen has previously allotted an initial chunk of free UCloud compute hours to staff (from PhD students to professors as well as non-academic staff). If you have further questions about getting compute resources, please contact Sandbox staff.

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Extensive documentation on the general use of UCloud (how to use apps and run jobs, etc.) is available in the UCloud user guide.

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Click on the images to view them in full size.

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Example: how to open a Sandbox app

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Step 1

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Log onto UCloud at the address http://cloud.sdu.dk using university credentials.

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Step 2

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When you are logged in, choose the project from the dashboard (highlighted in red) from which you would like to utilize compute resources. Every user has their personal workspace (My workspace). You can also provision your own project (check with your local DeiC office if you’re new to UCloud) or you can be invited to someone else’s project. If you’ve previously selected a project, it will be launched by default. If it’s your first time, you’ll be in your workspace. If you’ve joined one of our courses or workshops, your instructor will let you know which to choose.

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For this example, we select Sandbox_workshop.

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Screenshot of your dashboard

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Dashboard: your workspace
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On the left side, you can see the structure of the project (content changes when you select a different project):

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  • Files: all folders/files you have access to. You can navigate through folders, download, upload, or share files with collaborators. You might have varying rights across folders, mostly depending on whether they are yours or have been shared with you
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  • Apps: gain access to the apps catalog on ucloud. We refer to apps as the software applications that can be deployed on the cloud. It’s recommended to explore the featured ones. Use the search bar to find the sandbox apps
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Don’t forget to accept the invitation to access new projects. Remember to switch projects to access other files and resources. Test switching among projects and observe how the dashboard changes.

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At the bottom left corner, you will find your user ID, which you may need to provide once the course starts or for future collaborations, such as being added to other people’s projects. You can also find it on UCloud docs.

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In the dashboard, you will also find news, your favorite apps, recent runs, resources, and other notifications between other applications: - Resource allocations: indicate your currently allocated resources (e.g., KU employees have access to 1000kr in computing). - Grant applications: apply for more resources (computing or storage if you run out of them)

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Step 3

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Then click on Apps in the left panel to investigate what tools and environments you can use (green circle). The easiest way to find Sandbox resources is to search via the toolbar (red circle). In this example, we’ll select the Genomics Sandbox (which will bring you to the submission screen).

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Screenshot of apps dashboard

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Dashboard: all apps
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Mark them as favorites so they appear on your dashboard.

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Step 4

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Click on the app button to get into the settings window. First, we recommend reading the documentation of the app (highlighted in green). Then, you can configure the app as shown below, or be provided with a configuration file made available in a workshop’s project folders (import parameters) which will take care of everything for you.

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Screenshot of how to configure your job

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Dashboard jobs: configuration step
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In this example, we configure our session by:

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  2. selecting the time (in hours) we want to use a node for (it can be modified afterward)
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  4. choosing the course “Introduction to NGS Data Analysis”
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The first 3 steps set up our computing resources for the period we want to work and can be customized as needed. However, only step 2 can be modified after submitting the job. For some of the Sandbox apps, you might want to select folders (Home and the Notebooks/Data from the module to avoid downloading it every time you start a new job). If you are in doubt, read the documentation specific to the app you are interested in.

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Select the version of the app (if in doubt, use the latest one). This allows you to run specific versions of software.

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There are different types of apps, and therefore, interfaces. Some, like RStudio or Jupyter Notebooks, have their own graphical user interface, whereas others are command-line interfaces. Lastly, you can also deploy a virtual desktop and virtual machine, which allow you to spin up a virtual computer.

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Step 5

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Wait to go through the queue. When the session starts, the timer begins to count down. In a couple of minutes, you should be able to open the interface through the button (green circle) in a new window (refresh the window if needed).

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Screenshot of dashboard running app

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Dashboard jobs: running the app
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This page will remain open while you work (or you can return to it via ‘Runs’ in the left panel). You can end your session early by pressing and holding ‘Stop application’ (pink circle), you can see how much time you have left (red circle) and you can add hours to your session as you go (buttons in blue square).

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Step 6

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If you are testing the genomic app, your interface should look like in the image below. Different apps might use other development environments. In this case, you will be working from JupyterLab. You can open Jupyter Notebooks (yellow square), R studio (blue square) or a terminal (black square) among others. In this case, #1 and #2 have all the software and packages that you will need pre-installed (this is not the case with Python 3 to the left).

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Screenshot of JupyterLab interface

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JupyterLab interface: running the app
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You can navigate through the different folders and start running the Python notebooks (pink arrow).

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Screenshot of Jupyter Notebook

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JupyterLab interface: openning notebook
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If you are an advanced user, you can also create your own Python files and select the kernel NGS (python) to use the pre-installed software. Learn how to manage (upload and download new data) and share files that you have created/developed with collaborators here.

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Create your own directories to save the output of your jobs. You will be able to access them later in your project folders under the resources you are using

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If you haven’t created any directories, look for the generated files under a folder with the same name as the job name you used.

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You are ready to start using Ucloud and the sandbox tools!

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HPC access

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The Sandbox is collaborating with the two major academic high performance computing platforms in Denmark. Computerome is located at the Technical University of Denmark (and co-owned by the University of Copenhagen) while UCloud is owned by the University of Southern Denmark. These HPC platforms each have their own strengths which we leverage in the Sandbox in different ways.

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UCloud

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UCloud is a relatively new HPC platform that can be accessed by students at Danish universities (via a WAYF university login). It has a user friendly graphical user interface that supports straightforward project, user, and resource management. UCloud provides access to many tools via selectable Apps matched with a range of flexible compute resources, and the Sandbox is deploying training modules in this form such that any UCloud user can easily access Sandbox materials independently. The Sandbox is also hosting workshops and training events on UCloud in conjunction with in-person training.

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Find detailed instructions on accessing Sandbox apps here via UCloud. Check out UCloud’s extensive user docs here.

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Computerome

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Computerome is the home of many sensitive health datasets via collaborations between DTU, KU, Rigshospitalet, and other major health sector players in the Capital Region of Denmark. Computerome has recently launched their secure cloud platform, DELPHI, and in collaboration with the Sandbox has built a Course Platform on the same backbone such that courses and training can be conducted in the same environment as real research would be performed in the secure cloud. The Sandbox is supporting courses in the Course Platform, but it is also available for independent use by educators at Danish universities. Please see their website for more information on independent use and pricing, and contact us if you’d like to collaborate on hosting a course on Computerome. We can help with tool installation, environment testing, and user support (ranging from using the environment to course content if we have Sandbox staff with matching expertise).

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Participants in courses co-hosted by the Sandbox can check here for access instructions.

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GenomeDK

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In development.

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Any other computing cluster

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In development.

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Your local PC

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In development.

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#statediagram-barbEnd{stroke:var(--md-mermaid-edge-color)}.entityBox{fill:var(--md-mermaid-label-bg-color);stroke:var(--md-mermaid-node-fg-color)}.entityLabel{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}.relationshipLabelBox{fill:var(--md-mermaid-label-bg-color);fill-opacity:1;background-color:var(--md-mermaid-label-bg-color);opacity:1}.relationshipLabel{fill:var(--md-mermaid-label-fg-color)}.relationshipLine{stroke:var(--md-mermaid-edge-color)}defs #ONE_OR_MORE_END *,defs #ONE_OR_MORE_START *,defs #ONLY_ONE_END *,defs #ONLY_ONE_START *,defs #ZERO_OR_MORE_END *,defs #ZERO_OR_MORE_START *,defs #ZERO_OR_ONE_END *,defs #ZERO_OR_ONE_START *{stroke:var(--md-mermaid-edge-color)!important}.actor,defs #ZERO_OR_MORE_END circle,defs #ZERO_OR_MORE_START circle{fill:var(--md-mermaid-label-bg-color)}.actor{stroke:var(--md-mermaid-node-fg-color)}text.actor>tspan{fill:var(--md-mermaid-label-fg-color);font-family:var(--md-mermaid-font-family)}line{stroke:var(--md-default-fg-color--lighter)}.messageLine0,.messageLine1{stroke:var(--md-mermaid-edge-color)}.loopText>tspan,.messageText{font-family:var(--md-mermaid-font-family)!important}#arrowhead path,.loopText>tspan,.messageText{fill:var(--md-mermaid-edge-color);stroke:none}.loopLine{stroke:var(--md-mermaid-node-fg-color)}.labelBox,.loopLine{fill:var(--md-mermaid-node-bg-color)}.labelBox{stroke:none}.labelText,.labelText>span{fill:var(--md-mermaid-node-fg-color);font-family:var(--md-mermaid-font-family)}";var Jr,ps=0;function ls(){return typeof mermaid=="undefined"||mermaid instanceof Element?Fo("https://unpkg.com/mermaid@9.0.1/dist/mermaid.min.js"):P(void 0)}function ii(e){return e.classList.remove("mermaid"),Jr||(Jr=ls().pipe(O(()=>mermaid.initialize({startOnLoad:!1,themeCSS:oi})),m(()=>{}),X(1))),Jr.subscribe(()=>{e.classList.add("mermaid");let t=`__mermaid_${ps++}`,r=L("div",{class:"mermaid"});mermaid.mermaidAPI.render(t,e.textContent,n=>{let o=r.attachShadow({mode:"closed"});o.innerHTML=n,e.replaceWith(r)})}),Jr.pipe(m(()=>({ref:e})))}function ms(e,{target$:t,print$:r}){let n=!0;return A(t.pipe(m(o=>o.closest("details:not([open])")),M(o=>e===o),m(()=>({action:"open",reveal:!0}))),r.pipe(M(o=>o||!n),O(()=>n=e.open),m(o=>({action:o?"open":"close"}))))}function ai(e,t){return j(()=>{let r=new _;return r.subscribe(({action:n,reveal:o})=>{n==="open"?e.setAttribute("open",""):e.removeAttribute("open"),o&&e.scrollIntoView()}),ms(e,t).pipe(O(n=>r.next(n)),C(()=>r.complete()),m(n=>U({ref:e},n)))})}var si=L("table");function ci(e){return e.replaceWith(si),si.replaceWith(Bo(e)),P({ref:e})}function ds(e){let t=B(":scope > input",e),r=t.find(n=>n.checked)||t[0];return A(...t.map(n=>g(n,"change").pipe(m(()=>Q(`label[for="${n.id}"]`))))).pipe(q(Q(`label[for="${r.id}"]`)),m(n=>({active:n})))}function fi(e){let t=Gr("prev");e.append(t);let r=Gr("next");e.append(r);let n=Q(".tabbed-labels",e);return j(()=>{let o=new _,i=o.pipe(fe(1));return Y([o,de(e)]).pipe($e(1,Te),Z(i)).subscribe({next([{active:a},s]){let c=ze(a),{width:f}=Ae(a);e.style.setProperty("--md-indicator-x",`${c.x}px`),e.style.setProperty("--md-indicator-width",`${f}px`);let u=or(n);(c.xu.x+s.width)&&n.scrollTo({left:Math.max(0,c.x-16),behavior:"smooth"})},complete(){e.style.removeProperty("--md-indicator-x"),e.style.removeProperty("--md-indicator-width")}}),Y([pt(n),de(n)]).pipe(Z(i)).subscribe(([a,s])=>{let c=mt(n);t.hidden=a.x<16,r.hidden=a.x>c.width-s.width-16}),A(g(t,"click").pipe(m(()=>-1)),g(r,"click").pipe(m(()=>1))).pipe(Z(i)).subscribe(a=>{let{width:s}=Ae(n);n.scrollBy({left:s*a,behavior:"smooth"})}),oe("content.tabs.link")&&o.pipe(Le(1)).subscribe(({active:a})=>{let s=a.innerText.trim();for(let f of B("[data-tabs]"))for(let u of B(":scope > input",f))if(Q(`label[for="${u.id}"]`).innerText.trim()===s){u.click();break}let c=__md_get("__tabs")||[];__md_set("__tabs",[...new Set([s,...c])])}),ds(e).pipe(O(a=>o.next(a)),C(()=>o.complete()),m(a=>U({ref:e},a)))}).pipe(Be(ue))}function ui(e,{target$:t,print$:r}){return A(...B("pre:not(.mermaid) > code",e).map(n=>ni(n,{print$:r})),...B("pre.mermaid",e).map(n=>ii(n)),...B("table:not([class])",e).map(n=>ci(n)),...B("details",e).map(n=>ai(n,{target$:t,print$:r})),...B("[data-tabs]",e).map(n=>fi(n)))}function hs(e,{alert$:t}){return t.pipe(x(r=>A(P(!0),P(!1).pipe(Fe(2e3))).pipe(m(n=>({message:r,active:n})))))}function pi(e,t){let r=Q(".md-typeset",e);return j(()=>{let n=new _;return n.subscribe(({message:o,active:i})=>{e.classList.toggle("md-dialog--active",i),r.textContent=o}),hs(e,t).pipe(O(o=>n.next(o)),C(()=>n.complete()),m(o=>U({ref:e},o)))})}function bs({viewport$:e}){if(!oe("header.autohide"))return P(!1);let t=e.pipe(m(({offset:{y:o}})=>o),Me(2,1),m(([o,i])=>[oMath.abs(i-o.y)>100),m(([,[o]])=>o),K()),n=dt("search");return Y([e,n]).pipe(m(([{offset:o},i])=>o.y>400&&!i),K(),x(o=>o?r:P(!1)),q(!1))}function li(e,t){return j(()=>Y([de(e),bs(t)])).pipe(m(([{height:r},n])=>({height:r,hidden:n})),K((r,n)=>r.height===n.height&&r.hidden===n.hidden),X(1))}function mi(e,{header$:t,main$:r}){return j(()=>{let n=new _,o=n.pipe(fe(1));return n.pipe(J("active"),Je(t)).subscribe(([{active:i},{hidden:a}])=>{e.classList.toggle("md-header--shadow",i&&!a),e.hidden=a}),r.subscribe(n),t.pipe(Z(o),m(i=>U({ref:e},i)))})}function vs(e,{viewport$:t,header$:r}){return mr(e,{viewport$:t,header$:r}).pipe(m(({offset:{y:n}})=>{let{height:o}=Ae(e);return{active:n>=o}}),J("active"))}function di(e,t){return j(()=>{let r=new _;r.subscribe(({active:o})=>{e.classList.toggle("md-header__title--active",o)});let n=pe("article h1");return typeof n=="undefined"?k:vs(n,t).pipe(O(o=>r.next(o)),C(()=>r.complete()),m(o=>U({ref:e},o)))})}function hi(e,{viewport$:t,header$:r}){let n=r.pipe(m(({height:i})=>i),K()),o=n.pipe(x(()=>de(e).pipe(m(({height:i})=>({top:e.offsetTop,bottom:e.offsetTop+i})),J("bottom"))));return Y([n,o,t]).pipe(m(([i,{top:a,bottom:s},{offset:{y:c},size:{height:f}}])=>(f=Math.max(0,f-Math.max(0,a-c,i)-Math.max(0,f+c-s)),{offset:a-i,height:f,active:a-i<=c})),K((i,a)=>i.offset===a.offset&&i.height===a.height&&i.active===a.active))}function gs(e){let t=__md_get("__palette")||{index:e.findIndex(r=>matchMedia(r.getAttribute("data-md-color-media")).matches)};return P(...e).pipe(se(r=>g(r,"change").pipe(m(()=>r))),q(e[Math.max(0,t.index)]),m(r=>({index:e.indexOf(r),color:{scheme:r.getAttribute("data-md-color-scheme"),primary:r.getAttribute("data-md-color-primary"),accent:r.getAttribute("data-md-color-accent")}})),X(1))}function bi(e){return j(()=>{let t=new 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e.map(o=>o.replace(t.slice(0,n),""))}function dr(e){let t=__md_get("__sitemap",sessionStorage,e);if(t)return P(t);{let r=he();return jo(new URL("sitemap.xml",e||r.base)).pipe(m(n=>xs(B("loc",n).map(o=>o.textContent))),ce(()=>k),je([]),O(n=>__md_set("__sitemap",n,sessionStorage,e)))}}function gi({document$:e,location$:t,viewport$:r}){let n=he();if(location.protocol==="file:")return;"scrollRestoration"in history&&(history.scrollRestoration="manual",g(window,"beforeunload").subscribe(()=>{history.scrollRestoration="auto"}));let o=pe("link[rel=icon]");typeof o!="undefined"&&(o.href=o.href);let i=dr().pipe(m(f=>f.map(u=>`${new URL(u,n.base)}`)),x(f=>g(document.body,"click").pipe(M(u=>!u.metaKey&&!u.ctrlKey),x(u=>{if(u.target instanceof Element){let p=u.target.closest("a");if(p&&!p.target){let l=new URL(p.href);if(l.search="",l.hash="",l.pathname!==location.pathname&&f.includes(l.toString()))return u.preventDefault(),P({url:new URL(p.href)})}}return xe}))),ne()),a=g(window,"popstate").pipe(M(f=>f.state!==null),m(f=>({url:new URL(location.href),offset:f.state})),ne());A(i,a).pipe(K((f,u)=>f.url.href===u.url.href),m(({url:f})=>f)).subscribe(t);let s=t.pipe(J("pathname"),x(f=>lr(f.href).pipe(ce(()=>(ur(f),xe)))),ne());i.pipe(ut(s)).subscribe(({url:f})=>{history.pushState({},"",`${f}`)});let c=new DOMParser;s.pipe(x(f=>f.text()),m(f=>c.parseFromString(f,"text/html"))).subscribe(e),e.pipe(Le(1)).subscribe(f=>{for(let u of["title","link[rel=canonical]","meta[name=author]","meta[name=description]","[data-md-component=announce]","[data-md-component=container]","[data-md-component=header-topic]","[data-md-component=outdated]","[data-md-component=logo]","[data-md-component=skip]",...oe("navigation.tabs.sticky")?["[data-md-component=tabs]"]:[]]){let p=pe(u),l=pe(u,f);typeof p!="undefined"&&typeof l!="undefined"&&p.replaceWith(l)}}),e.pipe(Le(1),m(()=>we("container")),x(f=>B("script",f)),Ir(f=>{let u=L("script");if(f.src){for(let p of f.getAttributeNames())u.setAttribute(p,f.getAttribute(p));return f.replaceWith(u),new $(p=>{u.onload=()=>p.complete()})}else return u.textContent=f.textContent,f.replaceWith(u),k})).subscribe(),A(i,a).pipe(ut(e)).subscribe(({url:f,offset:u})=>{f.hash&&!u?Po(f.hash):window.scrollTo(0,(u==null?void 0:u.y)||0)}),r.pipe(Tt(i),Xe(250),J("offset")).subscribe(({offset:f})=>{history.replaceState(f,"")}),A(i,a).pipe(Me(2,1),M(([f,u])=>f.url.pathname===u.url.pathname),m(([,f])=>f)).subscribe(({offset:f})=>{window.scrollTo(0,(f==null?void 0:f.y)||0)})}var Es=Ye(Zr());var xi=Ye(Zr());function en(e,t){let r=new RegExp(e.separator,"img"),n=(o,i,a)=>`${i}${a}`;return o=>{o=o.replace(/[\s*+\-:~^]+/g," ").trim();let i=new RegExp(`(^|${e.separator})(${o.replace(/[|\\{}()[\]^$+*?.-]/g,"\\$&").replace(r,"|")})`,"img");return a=>(t?(0,xi.default)(a):a).replace(i,n).replace(/<\/mark>(\s+)]*>/img,"$1")}}function Si(e){return e.split(/"([^"]+)"/g).map((t,r)=>r&1?t.replace(/^\b|^(?![^\x00-\x7F]|$)|\s+/g," 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Map(o.map(i=>[`${new URL(`../${i.version}/`,t.base)}`,i]))),x(o=>g(document.body,"click").pipe(M(i=>!i.metaKey&&!i.ctrlKey),ge(n),x(([i,a])=>{if(i.target instanceof Element){let s=i.target.closest("a");if(s&&!s.target&&o.has(s.href)){let c=s.href;return!i.target.closest(".md-version")&&o.get(c)===a?k:(i.preventDefault(),P(c))}}return k}),x(i=>{let{version:a}=o.get(i);return dr(new URL(i)).pipe(m(s=>{let f=Se().href.replace(t.base,"");return s.includes(f)?new URL(`../${a}/${f}`,t.base):new URL(i)}))})))).subscribe(o=>ur(o)),Y([r,n]).subscribe(([o,i])=>{Q(".md-header__topic").appendChild(Go(o,i))}),e.pipe(x(()=>n)).subscribe(o=>{var a;let i=__md_get("__outdated",sessionStorage);if(i===null){let s=((a=t.version)==null?void 0:a.default)||"latest";i=!o.aliases.includes(s),__md_set("__outdated",i,sessionStorage)}if(i)for(let s of ae("outdated"))s.hidden=!1})}function Ts(e,{rx$:t}){let r=(__search==null?void 0:__search.transform)||Si,{searchParams:n}=Se();n.has("q")&&qe("search",!0);let o=t.pipe(M(bt),re(1),m(()=>n.get("q")||""));dt("search").pipe(M(s=>!s),re(1)).subscribe(()=>{let s=new URL(location.href);s.searchParams.delete("q"),history.replaceState({},"",`${s}`)}),o.subscribe(s=>{s&&(e.value=s,e.focus())});let i=nr(e),a=A(g(e,"keyup"),g(e,"focus").pipe(Fe(1)),o).pipe(m(()=>r(e.value)),q(""),K());return Y([a,i]).pipe(m(([s,c])=>({value:s,focus:c})),X(1))}function _i(e,{tx$:t,rx$:r}){let n=new _,o=n.pipe(fe(1));return n.pipe(J("value"),m(({value:i})=>({type:2,data:i}))).subscribe(t.next.bind(t)),n.pipe(J("focus")).subscribe(({focus:i})=>{i?(qe("search",i),e.placeholder=""):e.placeholder=ee("search.placeholder")}),g(e.form,"reset").pipe(Z(o)).subscribe(()=>e.focus()),Ts(e,{tx$:t,rx$:r}).pipe(O(i=>n.next(i)),C(()=>n.complete()),m(i=>U({ref:e},i)),ne())}function Ti(e,{rx$:t},{query$:r}){let n=new _,o=Mo(e.parentElement).pipe(M(Boolean)),i=Q(":scope > :first-child",e),a=Q(":scope > :last-child",e),s=t.pipe(M(bt),re(1));return n.pipe(ge(r),Tt(s)).subscribe(([{items:f},{value:u}])=>{if(u)switch(f.length){case 0:i.textContent=ee("search.result.none");break;case 1:i.textContent=ee("search.result.one");break;default:i.textContent=ee("search.result.other",pr(f.length))}else i.textContent=ee("search.result.placeholder")}),n.pipe(O(()=>a.innerHTML=""),x(({items:f})=>A(P(...f.slice(0,10)),P(...f.slice(10)).pipe(Me(4),Nr(o),x(([u])=>u))))).subscribe(f=>a.appendChild(Yo(f))),t.pipe(M(vt),m(({data:f})=>f)).pipe(O(f=>n.next(f)),C(()=>n.complete()),m(f=>U({ref:e},f)))}function Ms(e,{query$:t}){return t.pipe(m(({value:r})=>{let n=Se();return n.hash="",n.searchParams.delete("h"),n.searchParams.set("q",r),{url:n}}))}function Mi(e,t){let r=new _;return r.subscribe(({url:n})=>{e.setAttribute("data-clipboard-text",e.href),e.href=`${n}`}),g(e,"click").subscribe(n=>n.preventDefault()),Ms(e,t).pipe(O(n=>r.next(n)),C(()=>r.complete()),m(n=>U({ref:e},n)))}function Li(e,{rx$:t},{keyboard$:r}){let n=new 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define(factory) :\n (factory());\n}(this, (function () { 'use strict';\n\n /**\n * Applies the :focus-visible polyfill at the given scope.\n * A scope in this case is either the top-level Document or a Shadow Root.\n *\n * @param {(Document|ShadowRoot)} scope\n * @see https://github.com/WICG/focus-visible\n */\n function applyFocusVisiblePolyfill(scope) {\n var hadKeyboardEvent = true;\n var hadFocusVisibleRecently = false;\n var hadFocusVisibleRecentlyTimeout = null;\n\n var inputTypesAllowlist = {\n text: true,\n search: true,\n url: true,\n tel: true,\n email: true,\n password: true,\n number: true,\n date: true,\n month: true,\n week: true,\n time: true,\n datetime: true,\n 'datetime-local': true\n };\n\n /**\n * Helper function for legacy browsers and iframes which sometimes focus\n * elements like document, body, and non-interactive SVG.\n * @param {Element} el\n */\n function isValidFocusTarget(el) {\n if (\n el &&\n el !== document &&\n el.nodeName !== 'HTML' &&\n el.nodeName !== 'BODY' &&\n 'classList' in el &&\n 'contains' in el.classList\n ) {\n return true;\n }\n return false;\n }\n\n /**\n * Computes whether the given element should automatically trigger the\n * `focus-visible` class being added, i.e. whether it should always match\n * `:focus-visible` when focused.\n * @param {Element} el\n * @return {boolean}\n */\n function focusTriggersKeyboardModality(el) {\n var type = el.type;\n var tagName = el.tagName;\n\n if (tagName === 'INPUT' && inputTypesAllowlist[type] && !el.readOnly) {\n return true;\n }\n\n if (tagName === 'TEXTAREA' && !el.readOnly) {\n return true;\n }\n\n if (el.isContentEditable) {\n return true;\n }\n\n return false;\n }\n\n /**\n * Add the `focus-visible` class to the given element if it was not added by\n * the author.\n * @param {Element} el\n */\n function addFocusVisibleClass(el) {\n if (el.classList.contains('focus-visible')) {\n return;\n }\n el.classList.add('focus-visible');\n el.setAttribute('data-focus-visible-added', '');\n }\n\n /**\n * Remove the `focus-visible` class from the given element if it was not\n * originally added by the author.\n * @param {Element} el\n */\n function removeFocusVisibleClass(el) {\n if (!el.hasAttribute('data-focus-visible-added')) {\n return;\n }\n el.classList.remove('focus-visible');\n el.removeAttribute('data-focus-visible-added');\n }\n\n /**\n * If the most recent user interaction was via the keyboard;\n * and the key press did not include a meta, alt/option, or control key;\n * then the modality is keyboard. Otherwise, the modality is not keyboard.\n * Apply `focus-visible` to any current active element and keep track\n * of our keyboard modality state with `hadKeyboardEvent`.\n * @param {KeyboardEvent} e\n */\n function onKeyDown(e) {\n if (e.metaKey || e.altKey || e.ctrlKey) {\n return;\n }\n\n if (isValidFocusTarget(scope.activeElement)) {\n addFocusVisibleClass(scope.activeElement);\n }\n\n hadKeyboardEvent = true;\n }\n\n /**\n * If at any point a user clicks with a pointing device, ensure that we change\n * the modality away from keyboard.\n * This avoids the situation where a user presses a key on an already focused\n * element, and then clicks on a different element, focusing it with a\n * pointing device, while we still think we're in keyboard modality.\n * @param {Event} e\n */\n function onPointerDown(e) {\n hadKeyboardEvent = false;\n }\n\n /**\n * On `focus`, add the `focus-visible` class to the target if:\n * - the target received focus as a result of keyboard navigation, or\n * - the event target is an element that will likely require interaction\n * via the keyboard (e.g. a text box)\n * @param {Event} e\n */\n function onFocus(e) {\n // Prevent IE from focusing the document or HTML element.\n if (!isValidFocusTarget(e.target)) {\n return;\n }\n\n if (hadKeyboardEvent || focusTriggersKeyboardModality(e.target)) {\n addFocusVisibleClass(e.target);\n }\n }\n\n /**\n * On `blur`, remove the `focus-visible` class from the target.\n * @param {Event} e\n */\n function onBlur(e) {\n if (!isValidFocusTarget(e.target)) {\n return;\n }\n\n if (\n e.target.classList.contains('focus-visible') ||\n e.target.hasAttribute('data-focus-visible-added')\n ) {\n // To detect a tab/window switch, we look for a blur event followed\n // rapidly by a visibility change.\n // If we don't see a visibility change within 100ms, it's probably a\n // regular focus change.\n hadFocusVisibleRecently = true;\n window.clearTimeout(hadFocusVisibleRecentlyTimeout);\n hadFocusVisibleRecentlyTimeout = window.setTimeout(function() {\n hadFocusVisibleRecently = false;\n }, 100);\n removeFocusVisibleClass(e.target);\n }\n }\n\n /**\n * If the user changes tabs, keep track of whether or not the previously\n * focused element had .focus-visible.\n * @param {Event} e\n */\n function onVisibilityChange(e) {\n if (document.visibilityState === 'hidden') {\n // If the tab becomes active again, the browser will handle calling focus\n // on the element (Safari actually calls it twice).\n // If this tab change caused a blur on an element with focus-visible,\n // re-apply the class when the user switches back to the tab.\n if (hadFocusVisibleRecently) {\n hadKeyboardEvent = true;\n }\n addInitialPointerMoveListeners();\n }\n }\n\n /**\n * Add a group of listeners to detect usage of any pointing devices.\n * These listeners will be added when the polyfill first loads, and anytime\n * the window is blurred, so that they are active when the window regains\n * focus.\n */\n function addInitialPointerMoveListeners() {\n document.addEventListener('mousemove', onInitialPointerMove);\n document.addEventListener('mousedown', onInitialPointerMove);\n document.addEventListener('mouseup', onInitialPointerMove);\n document.addEventListener('pointermove', onInitialPointerMove);\n document.addEventListener('pointerdown', onInitialPointerMove);\n document.addEventListener('pointerup', onInitialPointerMove);\n document.addEventListener('touchmove', onInitialPointerMove);\n document.addEventListener('touchstart', onInitialPointerMove);\n document.addEventListener('touchend', onInitialPointerMove);\n }\n\n function removeInitialPointerMoveListeners() {\n document.removeEventListener('mousemove', onInitialPointerMove);\n document.removeEventListener('mousedown', onInitialPointerMove);\n document.removeEventListener('mouseup', onInitialPointerMove);\n document.removeEventListener('pointermove', onInitialPointerMove);\n document.removeEventListener('pointerdown', onInitialPointerMove);\n document.removeEventListener('pointerup', onInitialPointerMove);\n document.removeEventListener('touchmove', onInitialPointerMove);\n document.removeEventListener('touchstart', onInitialPointerMove);\n document.removeEventListener('touchend', onInitialPointerMove);\n }\n\n /**\n * When the polfyill first loads, assume the user is in keyboard modality.\n * If any event is received from a pointing device (e.g. mouse, pointer,\n * touch), turn off keyboard modality.\n * This accounts for situations where focus enters the page from the URL bar.\n * @param {Event} e\n */\n function onInitialPointerMove(e) {\n // Work around a Safari quirk that fires a mousemove on whenever the\n // window blurs, even if you're tabbing out of the page. \u00AF\\_(\u30C4)_/\u00AF\n if (e.target.nodeName && e.target.nodeName.toLowerCase() === 'html') {\n return;\n }\n\n hadKeyboardEvent = false;\n removeInitialPointerMoveListeners();\n }\n\n // For some kinds of state, we are interested in changes at the global scope\n // only. For example, global pointer input, global key presses and global\n // visibility change should affect the state at every scope:\n document.addEventListener('keydown', onKeyDown, true);\n document.addEventListener('mousedown', onPointerDown, true);\n document.addEventListener('pointerdown', onPointerDown, true);\n document.addEventListener('touchstart', onPointerDown, true);\n document.addEventListener('visibilitychange', onVisibilityChange, true);\n\n addInitialPointerMoveListeners();\n\n // For focus and blur, we specifically care about state changes in the local\n // scope. This is because focus / blur events that originate from within a\n // shadow root are not re-dispatched from the host element if it was already\n // the active element in its own scope:\n scope.addEventListener('focus', onFocus, true);\n scope.addEventListener('blur', onBlur, true);\n\n // We detect that a node is a ShadowRoot by ensuring that it is a\n // DocumentFragment and also has a host property. This check covers native\n // implementation and polyfill implementation transparently. If we only cared\n // about the native implementation, we could just check if the scope was\n // an instance of a ShadowRoot.\n if (scope.nodeType === Node.DOCUMENT_FRAGMENT_NODE && scope.host) {\n // Since a ShadowRoot is a special kind of DocumentFragment, it does not\n // have a root element to add a class to. So, we add this attribute to the\n // host element instead:\n scope.host.setAttribute('data-js-focus-visible', '');\n } else if (scope.nodeType === Node.DOCUMENT_NODE) {\n document.documentElement.classList.add('js-focus-visible');\n document.documentElement.setAttribute('data-js-focus-visible', '');\n }\n }\n\n // It is important to wrap all references to global window and document in\n // these checks to support server-side rendering use cases\n // @see https://github.com/WICG/focus-visible/issues/199\n if (typeof window !== 'undefined' && typeof document !== 'undefined') {\n // Make the polyfill helper globally available. This can be used as a signal\n // to interested libraries that wish to coordinate with the polyfill for e.g.,\n // applying the polyfill to a shadow root:\n window.applyFocusVisiblePolyfill = applyFocusVisiblePolyfill;\n\n // Notify interested libraries of the polyfill's presence, in case the\n // polyfill was loaded lazily:\n var event;\n\n try {\n event = new CustomEvent('focus-visible-polyfill-ready');\n } catch (error) {\n // IE11 does not support using CustomEvent as a constructor directly:\n event = document.createEvent('CustomEvent');\n event.initCustomEvent('focus-visible-polyfill-ready', false, false, {});\n }\n\n window.dispatchEvent(event);\n }\n\n if (typeof document !== 'undefined') {\n // Apply the polyfill to the global document, so that no JavaScript\n // coordination is required to use the polyfill in the top-level document:\n applyFocusVisiblePolyfill(document);\n }\n\n})));\n", "(function(global) {\r\n /**\r\n * Polyfill URLSearchParams\r\n *\r\n * Inspired from : https://github.com/WebReflection/url-search-params/blob/master/src/url-search-params.js\r\n */\r\n\r\n var checkIfIteratorIsSupported = function() {\r\n try {\r\n return !!Symbol.iterator;\r\n } catch (error) {\r\n return false;\r\n }\r\n };\r\n\r\n\r\n var iteratorSupported = checkIfIteratorIsSupported();\r\n\r\n var createIterator = function(items) {\r\n var iterator = {\r\n next: function() {\r\n var value = items.shift();\r\n return { done: value === void 0, value: value };\r\n }\r\n };\r\n\r\n if (iteratorSupported) {\r\n iterator[Symbol.iterator] = function() {\r\n return iterator;\r\n };\r\n }\r\n\r\n return iterator;\r\n };\r\n\r\n /**\r\n * Search param name and values should be encoded according to https://url.spec.whatwg.org/#urlencoded-serializing\r\n * encodeURIComponent() produces the same result except encoding spaces as `%20` instead of `+`.\r\n */\r\n var serializeParam = function(value) {\r\n return encodeURIComponent(value).replace(/%20/g, '+');\r\n };\r\n\r\n var deserializeParam = function(value) {\r\n return decodeURIComponent(String(value).replace(/\\+/g, ' '));\r\n };\r\n\r\n var polyfillURLSearchParams = function() {\r\n\r\n var URLSearchParams = function(searchString) {\r\n Object.defineProperty(this, '_entries', { writable: true, value: {} });\r\n var typeofSearchString = typeof searchString;\r\n\r\n if (typeofSearchString === 'undefined') {\r\n // do nothing\r\n } else if (typeofSearchString === 'string') {\r\n if (searchString !== '') {\r\n this._fromString(searchString);\r\n }\r\n } else if (searchString instanceof URLSearchParams) {\r\n var _this = this;\r\n searchString.forEach(function(value, name) {\r\n _this.append(name, value);\r\n });\r\n } else if ((searchString !== null) && (typeofSearchString === 'object')) {\r\n if (Object.prototype.toString.call(searchString) === '[object Array]') {\r\n for (var i = 0; i < searchString.length; i++) {\r\n var entry = searchString[i];\r\n if ((Object.prototype.toString.call(entry) === '[object Array]') || (entry.length !== 2)) {\r\n this.append(entry[0], entry[1]);\r\n } else {\r\n throw new TypeError('Expected [string, any] as entry at index ' + i + ' of URLSearchParams\\'s input');\r\n }\r\n }\r\n } else {\r\n for (var key in searchString) {\r\n if (searchString.hasOwnProperty(key)) {\r\n this.append(key, searchString[key]);\r\n }\r\n }\r\n }\r\n } else {\r\n throw new TypeError('Unsupported input\\'s type for URLSearchParams');\r\n }\r\n };\r\n\r\n var proto = URLSearchParams.prototype;\r\n\r\n proto.append = function(name, value) {\r\n if (name in this._entries) {\r\n this._entries[name].push(String(value));\r\n } else {\r\n this._entries[name] = [String(value)];\r\n }\r\n };\r\n\r\n proto.delete = function(name) {\r\n delete this._entries[name];\r\n };\r\n\r\n proto.get = function(name) {\r\n return (name in this._entries) ? this._entries[name][0] : null;\r\n };\r\n\r\n proto.getAll = function(name) {\r\n return (name in this._entries) ? this._entries[name].slice(0) : [];\r\n };\r\n\r\n proto.has = function(name) {\r\n return (name in this._entries);\r\n };\r\n\r\n proto.set = function(name, value) {\r\n this._entries[name] = [String(value)];\r\n };\r\n\r\n proto.forEach = function(callback, thisArg) {\r\n var entries;\r\n for (var name in this._entries) {\r\n if (this._entries.hasOwnProperty(name)) {\r\n entries = this._entries[name];\r\n for (var i = 0; i < entries.length; i++) {\r\n callback.call(thisArg, entries[i], name, this);\r\n }\r\n }\r\n }\r\n };\r\n\r\n proto.keys = function() {\r\n var items = [];\r\n this.forEach(function(value, name) {\r\n items.push(name);\r\n });\r\n return createIterator(items);\r\n };\r\n\r\n proto.values = function() {\r\n var items = [];\r\n this.forEach(function(value) {\r\n items.push(value);\r\n });\r\n return createIterator(items);\r\n };\r\n\r\n proto.entries = function() {\r\n var items = [];\r\n this.forEach(function(value, name) {\r\n items.push([name, value]);\r\n });\r\n return createIterator(items);\r\n };\r\n\r\n if (iteratorSupported) {\r\n proto[Symbol.iterator] = proto.entries;\r\n }\r\n\r\n proto.toString = function() {\r\n var searchArray = [];\r\n this.forEach(function(value, name) {\r\n searchArray.push(serializeParam(name) + '=' + serializeParam(value));\r\n });\r\n return searchArray.join('&');\r\n };\r\n\r\n\r\n global.URLSearchParams = URLSearchParams;\r\n };\r\n\r\n var checkIfURLSearchParamsSupported = function() {\r\n try {\r\n var URLSearchParams = global.URLSearchParams;\r\n\r\n return (\r\n (new URLSearchParams('?a=1').toString() === 'a=1') &&\r\n (typeof URLSearchParams.prototype.set === 'function') &&\r\n (typeof URLSearchParams.prototype.entries === 'function')\r\n );\r\n } catch (e) {\r\n return false;\r\n }\r\n };\r\n\r\n if (!checkIfURLSearchParamsSupported()) {\r\n polyfillURLSearchParams();\r\n }\r\n\r\n var proto = global.URLSearchParams.prototype;\r\n\r\n if (typeof proto.sort !== 'function') {\r\n proto.sort = function() {\r\n var _this = this;\r\n var items = [];\r\n this.forEach(function(value, name) {\r\n items.push([name, value]);\r\n if (!_this._entries) {\r\n _this.delete(name);\r\n }\r\n });\r\n items.sort(function(a, b) {\r\n if (a[0] < b[0]) {\r\n return -1;\r\n } else if (a[0] > b[0]) {\r\n return +1;\r\n } else {\r\n return 0;\r\n }\r\n });\r\n if (_this._entries) { // force reset because IE keeps keys index\r\n _this._entries = {};\r\n }\r\n for (var i = 0; i < items.length; i++) {\r\n this.append(items[i][0], items[i][1]);\r\n }\r\n };\r\n }\r\n\r\n if (typeof proto._fromString !== 'function') {\r\n Object.defineProperty(proto, '_fromString', {\r\n enumerable: false,\r\n configurable: false,\r\n writable: false,\r\n value: function(searchString) {\r\n if (this._entries) {\r\n this._entries = {};\r\n } else {\r\n var keys = [];\r\n this.forEach(function(value, name) {\r\n keys.push(name);\r\n });\r\n for (var i = 0; i < keys.length; i++) {\r\n this.delete(keys[i]);\r\n }\r\n }\r\n\r\n searchString = searchString.replace(/^\\?/, '');\r\n var attributes = searchString.split('&');\r\n var attribute;\r\n for (var i = 0; i < attributes.length; i++) {\r\n attribute = attributes[i].split('=');\r\n this.append(\r\n deserializeParam(attribute[0]),\r\n (attribute.length > 1) ? deserializeParam(attribute[1]) : ''\r\n );\r\n }\r\n }\r\n });\r\n }\r\n\r\n // HTMLAnchorElement\r\n\r\n})(\r\n (typeof global !== 'undefined') ? global\r\n : ((typeof window !== 'undefined') ? window\r\n : ((typeof self !== 'undefined') ? self : this))\r\n);\r\n\r\n(function(global) {\r\n /**\r\n * Polyfill URL\r\n *\r\n * Inspired from : https://github.com/arv/DOM-URL-Polyfill/blob/master/src/url.js\r\n */\r\n\r\n var checkIfURLIsSupported = function() {\r\n try {\r\n var u = new global.URL('b', 'http://a');\r\n u.pathname = 'c d';\r\n return (u.href === 'http://a/c%20d') && u.searchParams;\r\n } catch (e) {\r\n return false;\r\n }\r\n };\r\n\r\n\r\n var polyfillURL = function() {\r\n var _URL = global.URL;\r\n\r\n var URL = function(url, base) {\r\n if (typeof url !== 'string') url = String(url);\r\n if (base && typeof base !== 'string') base = String(base);\r\n\r\n // Only create another document if the base is different from current location.\r\n var doc = document, baseElement;\r\n if (base && (global.location === void 0 || base !== global.location.href)) {\r\n base = base.toLowerCase();\r\n doc = document.implementation.createHTMLDocument('');\r\n baseElement = doc.createElement('base');\r\n baseElement.href = base;\r\n doc.head.appendChild(baseElement);\r\n try {\r\n if (baseElement.href.indexOf(base) !== 0) throw new Error(baseElement.href);\r\n } catch (err) {\r\n throw new Error('URL unable to set base ' + base + ' due to ' + err);\r\n }\r\n }\r\n\r\n var anchorElement = doc.createElement('a');\r\n anchorElement.href = url;\r\n if (baseElement) {\r\n doc.body.appendChild(anchorElement);\r\n anchorElement.href = anchorElement.href; // force href to refresh\r\n }\r\n\r\n var inputElement = doc.createElement('input');\r\n inputElement.type = 'url';\r\n inputElement.value = url;\r\n\r\n if (anchorElement.protocol === ':' || !/:/.test(anchorElement.href) || (!inputElement.checkValidity() && !base)) {\r\n throw new TypeError('Invalid URL');\r\n }\r\n\r\n Object.defineProperty(this, '_anchorElement', {\r\n value: anchorElement\r\n });\r\n\r\n\r\n // create a linked searchParams which reflect its changes on URL\r\n var searchParams = new global.URLSearchParams(this.search);\r\n var enableSearchUpdate = true;\r\n var enableSearchParamsUpdate = true;\r\n var _this = this;\r\n ['append', 'delete', 'set'].forEach(function(methodName) {\r\n var method = searchParams[methodName];\r\n searchParams[methodName] = function() {\r\n method.apply(searchParams, arguments);\r\n if (enableSearchUpdate) {\r\n enableSearchParamsUpdate = false;\r\n _this.search = searchParams.toString();\r\n enableSearchParamsUpdate = true;\r\n }\r\n };\r\n });\r\n\r\n Object.defineProperty(this, 'searchParams', {\r\n value: searchParams,\r\n enumerable: true\r\n });\r\n\r\n var search = void 0;\r\n Object.defineProperty(this, '_updateSearchParams', {\r\n enumerable: false,\r\n configurable: false,\r\n writable: false,\r\n value: function() {\r\n if (this.search !== search) {\r\n search = this.search;\r\n if (enableSearchParamsUpdate) {\r\n enableSearchUpdate = false;\r\n this.searchParams._fromString(this.search);\r\n enableSearchUpdate = true;\r\n }\r\n }\r\n }\r\n });\r\n };\r\n\r\n var proto = URL.prototype;\r\n\r\n var linkURLWithAnchorAttribute = function(attributeName) {\r\n Object.defineProperty(proto, attributeName, {\r\n get: function() {\r\n return this._anchorElement[attributeName];\r\n },\r\n set: function(value) {\r\n this._anchorElement[attributeName] = value;\r\n },\r\n enumerable: true\r\n });\r\n };\r\n\r\n ['hash', 'host', 'hostname', 'port', 'protocol']\r\n .forEach(function(attributeName) {\r\n linkURLWithAnchorAttribute(attributeName);\r\n });\r\n\r\n Object.defineProperty(proto, 'search', {\r\n get: function() {\r\n return this._anchorElement['search'];\r\n },\r\n set: function(value) {\r\n this._anchorElement['search'] = value;\r\n this._updateSearchParams();\r\n },\r\n enumerable: true\r\n });\r\n\r\n Object.defineProperties(proto, {\r\n\r\n 'toString': {\r\n get: function() {\r\n var _this = this;\r\n return function() {\r\n return _this.href;\r\n };\r\n }\r\n },\r\n\r\n 'href': {\r\n get: function() {\r\n return this._anchorElement.href.replace(/\\?$/, '');\r\n },\r\n set: function(value) {\r\n this._anchorElement.href = value;\r\n this._updateSearchParams();\r\n },\r\n enumerable: true\r\n },\r\n\r\n 'pathname': {\r\n get: function() {\r\n return this._anchorElement.pathname.replace(/(^\\/?)/, '/');\r\n },\r\n set: function(value) {\r\n this._anchorElement.pathname = value;\r\n },\r\n enumerable: true\r\n },\r\n\r\n 'origin': {\r\n get: function() {\r\n // get expected port from protocol\r\n var expectedPort = { 'http:': 80, 'https:': 443, 'ftp:': 21 }[this._anchorElement.protocol];\r\n // add port to origin if, expected port is different than actual port\r\n // and it is not empty f.e http://foo:8080\r\n // 8080 != 80 && 8080 != ''\r\n var addPortToOrigin = this._anchorElement.port != expectedPort &&\r\n this._anchorElement.port !== '';\r\n\r\n return this._anchorElement.protocol +\r\n '//' +\r\n this._anchorElement.hostname +\r\n (addPortToOrigin ? (':' + this._anchorElement.port) : '');\r\n },\r\n enumerable: true\r\n },\r\n\r\n 'password': { // TODO\r\n get: function() {\r\n return '';\r\n },\r\n set: function(value) {\r\n },\r\n enumerable: true\r\n },\r\n\r\n 'username': { // TODO\r\n get: function() {\r\n return '';\r\n },\r\n set: function(value) {\r\n },\r\n enumerable: true\r\n },\r\n });\r\n\r\n URL.createObjectURL = function(blob) {\r\n return _URL.createObjectURL.apply(_URL, arguments);\r\n };\r\n\r\n URL.revokeObjectURL = function(url) {\r\n return _URL.revokeObjectURL.apply(_URL, arguments);\r\n };\r\n\r\n global.URL = URL;\r\n\r\n };\r\n\r\n if (!checkIfURLIsSupported()) {\r\n polyfillURL();\r\n }\r\n\r\n if ((global.location !== void 0) && !('origin' in global.location)) {\r\n var getOrigin = function() {\r\n return global.location.protocol + '//' + global.location.hostname + (global.location.port ? 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IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,\r\nINDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM\r\nLOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR\r\nOTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR\r\nPERFORMANCE OF THIS SOFTWARE.\r\n***************************************************************************** */\r\n/* global global, define, System, Reflect, Promise */\r\nvar __extends;\r\nvar __assign;\r\nvar __rest;\r\nvar __decorate;\r\nvar __param;\r\nvar __metadata;\r\nvar __awaiter;\r\nvar __generator;\r\nvar __exportStar;\r\nvar __values;\r\nvar __read;\r\nvar __spread;\r\nvar __spreadArrays;\r\nvar __spreadArray;\r\nvar __await;\r\nvar __asyncGenerator;\r\nvar __asyncDelegator;\r\nvar __asyncValues;\r\nvar __makeTemplateObject;\r\nvar __importStar;\r\nvar __importDefault;\r\nvar __classPrivateFieldGet;\r\nvar __classPrivateFieldSet;\r\nvar __createBinding;\r\n(function (factory) {\r\n var root = typeof global === \"object\" ? global : typeof self === \"object\" ? self : typeof this === \"object\" ? this : {};\r\n if (typeof define === \"function\" && define.amd) {\r\n define(\"tslib\", [\"exports\"], function (exports) { factory(createExporter(root, createExporter(exports))); });\r\n }\r\n else if (typeof module === \"object\" && typeof module.exports === \"object\") {\r\n factory(createExporter(root, createExporter(module.exports)));\r\n }\r\n else {\r\n factory(createExporter(root));\r\n }\r\n function createExporter(exports, previous) {\r\n if (exports !== root) {\r\n if (typeof Object.create === \"function\") {\r\n Object.defineProperty(exports, \"__esModule\", { value: true });\r\n }\r\n else {\r\n exports.__esModule = true;\r\n }\r\n }\r\n return function (id, v) { return exports[id] = previous ? previous(id, v) : v; };\r\n }\r\n})\r\n(function (exporter) {\r\n var extendStatics = Object.setPrototypeOf ||\r\n ({ __proto__: [] } instanceof Array && function (d, b) { d.__proto__ = b; }) ||\r\n function (d, b) { for (var p in b) if (Object.prototype.hasOwnProperty.call(b, p)) d[p] = b[p]; };\r\n\r\n __extends = function (d, b) {\r\n if (typeof b !== \"function\" && b !== null)\r\n throw new TypeError(\"Class extends value \" + String(b) + \" is not a constructor or null\");\r\n extendStatics(d, b);\r\n function __() { this.constructor = d; }\r\n d.prototype = b === null ? 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'right' : 'left'] = '-9999px'; // Move element to the same position vertically\n\n var yPosition = window.pageYOffset || document.documentElement.scrollTop;\n fakeElement.style.top = \"\".concat(yPosition, \"px\");\n fakeElement.setAttribute('readonly', '');\n fakeElement.value = value;\n return fakeElement;\n}\n;// CONCATENATED MODULE: ./src/actions/copy.js\n\n\n\n/**\n * Create fake copy action wrapper using a fake element.\n * @param {String} target\n * @param {Object} options\n * @return {String}\n */\n\nvar fakeCopyAction = function fakeCopyAction(value, options) {\n var fakeElement = createFakeElement(value);\n options.container.appendChild(fakeElement);\n var selectedText = select_default()(fakeElement);\n command('copy');\n fakeElement.remove();\n return selectedText;\n};\n/**\n * Copy action wrapper.\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @return {String}\n */\n\n\nvar ClipboardActionCopy = function ClipboardActionCopy(target) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n container: document.body\n };\n var selectedText = '';\n\n if (typeof target === 'string') {\n selectedText = fakeCopyAction(target, options);\n } else if (target instanceof HTMLInputElement && !['text', 'search', 'url', 'tel', 'password'].includes(target === null || target === void 0 ? void 0 : target.type)) {\n // If input type doesn't support `setSelectionRange`. Simulate it. https://developer.mozilla.org/en-US/docs/Web/API/HTMLInputElement/setSelectionRange\n selectedText = fakeCopyAction(target.value, options);\n } else {\n selectedText = select_default()(target);\n command('copy');\n }\n\n return selectedText;\n};\n\n/* harmony default export */ var actions_copy = (ClipboardActionCopy);\n;// CONCATENATED MODULE: ./src/actions/default.js\nfunction _typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { _typeof = function _typeof(obj) { return typeof obj; }; } else { _typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return _typeof(obj); }\n\n\n\n/**\n * Inner function which performs selection from either `text` or `target`\n * properties and then executes copy or cut operations.\n * @param {Object} options\n */\n\nvar ClipboardActionDefault = function ClipboardActionDefault() {\n var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n // Defines base properties passed from constructor.\n var _options$action = options.action,\n action = _options$action === void 0 ? 'copy' : _options$action,\n container = options.container,\n target = options.target,\n text = options.text; // Sets the `action` to be performed which can be either 'copy' or 'cut'.\n\n if (action !== 'copy' && action !== 'cut') {\n throw new Error('Invalid \"action\" value, use either \"copy\" or \"cut\"');\n } // Sets the `target` property using an element that will be have its content copied.\n\n\n if (target !== undefined) {\n if (target && _typeof(target) === 'object' && target.nodeType === 1) {\n if (action === 'copy' && target.hasAttribute('disabled')) {\n throw new Error('Invalid \"target\" attribute. Please use \"readonly\" instead of \"disabled\" attribute');\n }\n\n if (action === 'cut' && (target.hasAttribute('readonly') || target.hasAttribute('disabled'))) {\n throw new Error('Invalid \"target\" attribute. You can\\'t cut text from elements with \"readonly\" or \"disabled\" attributes');\n }\n } else {\n throw new Error('Invalid \"target\" value, use a valid Element');\n }\n } // Define selection strategy based on `text` property.\n\n\n if (text) {\n return actions_copy(text, {\n container: container\n });\n } // Defines which selection strategy based on `target` property.\n\n\n if (target) {\n return action === 'cut' ? actions_cut(target) : actions_copy(target, {\n container: container\n });\n }\n};\n\n/* harmony default export */ var actions_default = (ClipboardActionDefault);\n;// CONCATENATED MODULE: ./src/clipboard.js\nfunction clipboard_typeof(obj) { \"@babel/helpers - typeof\"; if (typeof Symbol === \"function\" && typeof Symbol.iterator === \"symbol\") { clipboard_typeof = function _typeof(obj) { return typeof obj; }; } else { clipboard_typeof = function _typeof(obj) { return obj && typeof Symbol === \"function\" && obj.constructor === Symbol && obj !== Symbol.prototype ? \"symbol\" : typeof obj; }; } return clipboard_typeof(obj); }\n\nfunction _classCallCheck(instance, Constructor) { if (!(instance instanceof Constructor)) { throw new TypeError(\"Cannot call a class as a function\"); } }\n\nfunction _defineProperties(target, props) { for (var i = 0; i < props.length; i++) { var descriptor = props[i]; descriptor.enumerable = descriptor.enumerable || false; descriptor.configurable = true; if (\"value\" in descriptor) descriptor.writable = true; Object.defineProperty(target, descriptor.key, descriptor); } }\n\nfunction _createClass(Constructor, protoProps, staticProps) { if (protoProps) _defineProperties(Constructor.prototype, protoProps); if (staticProps) _defineProperties(Constructor, staticProps); return Constructor; }\n\nfunction _inherits(subClass, superClass) { if (typeof superClass !== \"function\" && superClass !== null) { throw new TypeError(\"Super expression must either be null or a function\"); } subClass.prototype = Object.create(superClass && superClass.prototype, { constructor: { value: subClass, writable: true, configurable: true } }); if (superClass) _setPrototypeOf(subClass, superClass); }\n\nfunction _setPrototypeOf(o, p) { _setPrototypeOf = Object.setPrototypeOf || function _setPrototypeOf(o, p) { o.__proto__ = p; return o; }; return _setPrototypeOf(o, p); }\n\nfunction _createSuper(Derived) { var hasNativeReflectConstruct = _isNativeReflectConstruct(); return function _createSuperInternal() { var Super = _getPrototypeOf(Derived), result; if (hasNativeReflectConstruct) { var NewTarget = _getPrototypeOf(this).constructor; result = Reflect.construct(Super, arguments, NewTarget); } else { result = Super.apply(this, arguments); } return _possibleConstructorReturn(this, result); }; }\n\nfunction _possibleConstructorReturn(self, call) { if (call && (clipboard_typeof(call) === \"object\" || typeof call === \"function\")) { return call; } return _assertThisInitialized(self); }\n\nfunction _assertThisInitialized(self) { if (self === void 0) { throw new ReferenceError(\"this hasn't been initialised - super() hasn't been called\"); } return self; }\n\nfunction _isNativeReflectConstruct() { if (typeof Reflect === \"undefined\" || !Reflect.construct) return false; if (Reflect.construct.sham) return false; if (typeof Proxy === \"function\") return true; try { Date.prototype.toString.call(Reflect.construct(Date, [], function () {})); return true; } catch (e) { return false; } }\n\nfunction _getPrototypeOf(o) { _getPrototypeOf = Object.setPrototypeOf ? Object.getPrototypeOf : function _getPrototypeOf(o) { return o.__proto__ || Object.getPrototypeOf(o); }; return _getPrototypeOf(o); }\n\n\n\n\n\n\n/**\n * Helper function to retrieve attribute value.\n * @param {String} suffix\n * @param {Element} element\n */\n\nfunction getAttributeValue(suffix, element) {\n var attribute = \"data-clipboard-\".concat(suffix);\n\n if (!element.hasAttribute(attribute)) {\n return;\n }\n\n return element.getAttribute(attribute);\n}\n/**\n * Base class which takes one or more elements, adds event listeners to them,\n * and instantiates a new `ClipboardAction` on each click.\n */\n\n\nvar Clipboard = /*#__PURE__*/function (_Emitter) {\n _inherits(Clipboard, _Emitter);\n\n var _super = _createSuper(Clipboard);\n\n /**\n * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n * @param {Object} options\n */\n function Clipboard(trigger, options) {\n var _this;\n\n _classCallCheck(this, Clipboard);\n\n _this = _super.call(this);\n\n _this.resolveOptions(options);\n\n _this.listenClick(trigger);\n\n return _this;\n }\n /**\n * Defines if attributes would be resolved using internal setter functions\n * or custom functions that were passed in the constructor.\n * @param {Object} options\n */\n\n\n _createClass(Clipboard, [{\n key: \"resolveOptions\",\n value: function resolveOptions() {\n var options = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : {};\n this.action = typeof options.action === 'function' ? options.action : this.defaultAction;\n this.target = typeof options.target === 'function' ? options.target : this.defaultTarget;\n this.text = typeof options.text === 'function' ? options.text : this.defaultText;\n this.container = clipboard_typeof(options.container) === 'object' ? options.container : document.body;\n }\n /**\n * Adds a click event listener to the passed trigger.\n * @param {String|HTMLElement|HTMLCollection|NodeList} trigger\n */\n\n }, {\n key: \"listenClick\",\n value: function listenClick(trigger) {\n var _this2 = this;\n\n this.listener = listen_default()(trigger, 'click', function (e) {\n return _this2.onClick(e);\n });\n }\n /**\n * Defines a new `ClipboardAction` on each click event.\n * @param {Event} e\n */\n\n }, {\n key: \"onClick\",\n value: function onClick(e) {\n var trigger = e.delegateTarget || e.currentTarget;\n var action = this.action(trigger) || 'copy';\n var text = actions_default({\n action: action,\n container: this.container,\n target: this.target(trigger),\n text: this.text(trigger)\n }); // Fires an event based on the copy operation result.\n\n this.emit(text ? 'success' : 'error', {\n action: action,\n text: text,\n trigger: trigger,\n clearSelection: function clearSelection() {\n if (trigger) {\n trigger.focus();\n }\n\n window.getSelection().removeAllRanges();\n }\n });\n }\n /**\n * Default `action` lookup function.\n * @param {Element} trigger\n */\n\n }, {\n key: \"defaultAction\",\n value: function defaultAction(trigger) {\n return getAttributeValue('action', trigger);\n }\n /**\n * Default `target` lookup function.\n * @param {Element} trigger\n */\n\n }, {\n key: \"defaultTarget\",\n value: function defaultTarget(trigger) {\n var selector = getAttributeValue('target', trigger);\n\n if (selector) {\n return document.querySelector(selector);\n }\n }\n /**\n * Allow fire programmatically a copy action\n * @param {String|HTMLElement} target\n * @param {Object} options\n * @returns Text copied.\n */\n\n }, {\n key: \"defaultText\",\n\n /**\n * Default `text` lookup function.\n * @param {Element} trigger\n */\n value: function defaultText(trigger) {\n return getAttributeValue('text', trigger);\n }\n /**\n * Destroy lifecycle.\n */\n\n }, {\n key: \"destroy\",\n value: function destroy() {\n this.listener.destroy();\n }\n }], [{\n key: \"copy\",\n value: function copy(target) {\n var options = arguments.length > 1 && arguments[1] !== undefined ? arguments[1] : {\n container: document.body\n };\n return actions_copy(target, options);\n }\n /**\n * Allow fire programmatically a cut action\n * @param {String|HTMLElement} target\n * @returns Text cutted.\n */\n\n }, {\n key: \"cut\",\n value: function cut(target) {\n return actions_cut(target);\n }\n /**\n * Returns the support of the given action, or all actions if no action is\n * given.\n * @param {String} [action]\n */\n\n }, {\n key: \"isSupported\",\n value: function isSupported() {\n var action = arguments.length > 0 && arguments[0] !== undefined ? arguments[0] : ['copy', 'cut'];\n var actions = typeof action === 'string' ? [action] : action;\n var support = !!document.queryCommandSupported;\n actions.forEach(function (action) {\n support = support && !!document.queryCommandSupported(action);\n });\n return support;\n }\n }]);\n\n return Clipboard;\n}((tiny_emitter_default()));\n\n/* harmony default export */ var clipboard = (Clipboard);\n\n/***/ }),\n\n/***/ 828:\n/***/ (function(module) {\n\nvar DOCUMENT_NODE_TYPE = 9;\n\n/**\n * A polyfill for Element.matches()\n */\nif (typeof Element !== 'undefined' && !Element.prototype.matches) {\n var proto = Element.prototype;\n\n proto.matches = proto.matchesSelector ||\n proto.mozMatchesSelector ||\n proto.msMatchesSelector ||\n proto.oMatchesSelector ||\n proto.webkitMatchesSelector;\n}\n\n/**\n * Finds the closest parent that matches a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @return {Function}\n */\nfunction closest (element, selector) {\n while (element && element.nodeType !== DOCUMENT_NODE_TYPE) {\n if (typeof element.matches === 'function' &&\n element.matches(selector)) {\n return element;\n }\n element = element.parentNode;\n }\n}\n\nmodule.exports = closest;\n\n\n/***/ }),\n\n/***/ 438:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar closest = __webpack_require__(828);\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction _delegate(element, selector, type, callback, useCapture) {\n var listenerFn = listener.apply(this, arguments);\n\n element.addEventListener(type, listenerFn, useCapture);\n\n return {\n destroy: function() {\n element.removeEventListener(type, listenerFn, useCapture);\n }\n }\n}\n\n/**\n * Delegates event to a selector.\n *\n * @param {Element|String|Array} [elements]\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @param {Boolean} useCapture\n * @return {Object}\n */\nfunction delegate(elements, selector, type, callback, useCapture) {\n // Handle the regular Element usage\n if (typeof elements.addEventListener === 'function') {\n return _delegate.apply(null, arguments);\n }\n\n // Handle Element-less usage, it defaults to global delegation\n if (typeof type === 'function') {\n // Use `document` as the first parameter, then apply arguments\n // This is a short way to .unshift `arguments` without running into deoptimizations\n return _delegate.bind(null, document).apply(null, arguments);\n }\n\n // Handle Selector-based usage\n if (typeof elements === 'string') {\n elements = document.querySelectorAll(elements);\n }\n\n // Handle Array-like based usage\n return Array.prototype.map.call(elements, function (element) {\n return _delegate(element, selector, type, callback, useCapture);\n });\n}\n\n/**\n * Finds closest match and invokes callback.\n *\n * @param {Element} element\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Function}\n */\nfunction listener(element, selector, type, callback) {\n return function(e) {\n e.delegateTarget = closest(e.target, selector);\n\n if (e.delegateTarget) {\n callback.call(element, e);\n }\n }\n}\n\nmodule.exports = delegate;\n\n\n/***/ }),\n\n/***/ 879:\n/***/ (function(__unused_webpack_module, exports) {\n\n/**\n * Check if argument is a HTML element.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.node = function(value) {\n return value !== undefined\n && value instanceof HTMLElement\n && value.nodeType === 1;\n};\n\n/**\n * Check if argument is a list of HTML elements.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.nodeList = function(value) {\n var type = Object.prototype.toString.call(value);\n\n return value !== undefined\n && (type === '[object NodeList]' || type === '[object HTMLCollection]')\n && ('length' in value)\n && (value.length === 0 || exports.node(value[0]));\n};\n\n/**\n * Check if argument is a string.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.string = function(value) {\n return typeof value === 'string'\n || value instanceof String;\n};\n\n/**\n * Check if argument is a function.\n *\n * @param {Object} value\n * @return {Boolean}\n */\nexports.fn = function(value) {\n var type = Object.prototype.toString.call(value);\n\n return type === '[object Function]';\n};\n\n\n/***/ }),\n\n/***/ 370:\n/***/ (function(module, __unused_webpack_exports, __webpack_require__) {\n\nvar is = __webpack_require__(879);\nvar delegate = __webpack_require__(438);\n\n/**\n * Validates all params and calls the right\n * listener function based on its target type.\n *\n * @param {String|HTMLElement|HTMLCollection|NodeList} target\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listen(target, type, callback) {\n if (!target && !type && !callback) {\n throw new Error('Missing required arguments');\n }\n\n if (!is.string(type)) {\n throw new TypeError('Second argument must be a String');\n }\n\n if (!is.fn(callback)) {\n throw new TypeError('Third argument must be a Function');\n }\n\n if (is.node(target)) {\n return listenNode(target, type, callback);\n }\n else if (is.nodeList(target)) {\n return listenNodeList(target, type, callback);\n }\n else if (is.string(target)) {\n return listenSelector(target, type, callback);\n }\n else {\n throw new TypeError('First argument must be a String, HTMLElement, HTMLCollection, or NodeList');\n }\n}\n\n/**\n * Adds an event listener to a HTML element\n * and returns a remove listener function.\n *\n * @param {HTMLElement} node\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNode(node, type, callback) {\n node.addEventListener(type, callback);\n\n return {\n destroy: function() {\n node.removeEventListener(type, callback);\n }\n }\n}\n\n/**\n * Add an event listener to a list of HTML elements\n * and returns a remove listener function.\n *\n * @param {NodeList|HTMLCollection} nodeList\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenNodeList(nodeList, type, callback) {\n Array.prototype.forEach.call(nodeList, function(node) {\n node.addEventListener(type, callback);\n });\n\n return {\n destroy: function() {\n Array.prototype.forEach.call(nodeList, function(node) {\n node.removeEventListener(type, callback);\n });\n }\n }\n}\n\n/**\n * Add an event listener to a selector\n * and returns a remove listener function.\n *\n * @param {String} selector\n * @param {String} type\n * @param {Function} callback\n * @return {Object}\n */\nfunction listenSelector(selector, type, callback) {\n return delegate(document.body, selector, type, callback);\n}\n\nmodule.exports = listen;\n\n\n/***/ }),\n\n/***/ 817:\n/***/ (function(module) {\n\nfunction select(element) {\n var selectedText;\n\n if (element.nodeName === 'SELECT') {\n element.focus();\n\n selectedText = element.value;\n }\n else if (element.nodeName === 'INPUT' || element.nodeName === 'TEXTAREA') {\n var isReadOnly = element.hasAttribute('readonly');\n\n if (!isReadOnly) {\n element.setAttribute('readonly', '');\n }\n\n element.select();\n element.setSelectionRange(0, element.value.length);\n\n if (!isReadOnly) {\n element.removeAttribute('readonly');\n }\n\n selectedText = element.value;\n }\n else {\n if (element.hasAttribute('contenteditable')) {\n element.focus();\n }\n\n var selection = window.getSelection();\n var range = document.createRange();\n\n range.selectNodeContents(element);\n selection.removeAllRanges();\n selection.addRange(range);\n\n selectedText = selection.toString();\n }\n\n return selectedText;\n}\n\nmodule.exports = select;\n\n\n/***/ }),\n\n/***/ 279:\n/***/ (function(module) {\n\nfunction E () {\n // Keep this empty so it's easier to inherit from\n // (via https://github.com/lipsmack from https://github.com/scottcorgan/tiny-emitter/issues/3)\n}\n\nE.prototype = {\n on: function (name, callback, ctx) {\n var e = this.e || (this.e = {});\n\n (e[name] || (e[name] = [])).push({\n fn: callback,\n ctx: ctx\n });\n\n return this;\n },\n\n once: function (name, callback, ctx) {\n var self = this;\n function listener () {\n self.off(name, listener);\n callback.apply(ctx, arguments);\n };\n\n listener._ = callback\n return this.on(name, listener, ctx);\n },\n\n emit: function (name) {\n var data = [].slice.call(arguments, 1);\n var evtArr = ((this.e || (this.e = {}))[name] || []).slice();\n var i = 0;\n var len = evtArr.length;\n\n for (i; i < len; i++) {\n evtArr[i].fn.apply(evtArr[i].ctx, data);\n }\n\n return this;\n },\n\n off: function (name, callback) {\n var e = this.e || (this.e = {});\n var evts = e[name];\n var liveEvents = [];\n\n if (evts && callback) {\n for (var i = 0, len = evts.length; i < len; i++) {\n if (evts[i].fn !== callback && evts[i].fn._ !== callback)\n liveEvents.push(evts[i]);\n }\n }\n\n // Remove event from queue to prevent memory leak\n // Suggested by https://github.com/lazd\n // Ref: https://github.com/scottcorgan/tiny-emitter/commit/c6ebfaa9bc973b33d110a84a307742b7cf94c953#commitcomment-5024910\n\n (liveEvents.length)\n ? e[name] = liveEvents\n : delete e[name];\n\n return this;\n }\n};\n\nmodule.exports = E;\nmodule.exports.TinyEmitter = E;\n\n\n/***/ })\n\n/******/ \t});\n/************************************************************************/\n/******/ \t// The module cache\n/******/ \tvar __webpack_module_cache__ = {};\n/******/ \t\n/******/ \t// The require function\n/******/ \tfunction __webpack_require__(moduleId) {\n/******/ \t\t// Check if module is in cache\n/******/ \t\tif(__webpack_module_cache__[moduleId]) {\n/******/ \t\t\treturn __webpack_module_cache__[moduleId].exports;\n/******/ \t\t}\n/******/ \t\t// Create a new module (and put it into the cache)\n/******/ \t\tvar module = __webpack_module_cache__[moduleId] = {\n/******/ \t\t\t// no module.id needed\n/******/ \t\t\t// no module.loaded needed\n/******/ \t\t\texports: {}\n/******/ \t\t};\n/******/ \t\n/******/ \t\t// Execute the module function\n/******/ \t\t__webpack_modules__[moduleId](module, module.exports, __webpack_require__);\n/******/ \t\n/******/ \t\t// Return the exports of the module\n/******/ \t\treturn module.exports;\n/******/ \t}\n/******/ \t\n/************************************************************************/\n/******/ \t/* webpack/runtime/compat get default export */\n/******/ \t!function() {\n/******/ \t\t// getDefaultExport function for compatibility with non-harmony modules\n/******/ \t\t__webpack_require__.n = function(module) {\n/******/ \t\t\tvar getter = module && module.__esModule ?\n/******/ \t\t\t\tfunction() { return module['default']; } :\n/******/ \t\t\t\tfunction() { return module; };\n/******/ \t\t\t__webpack_require__.d(getter, { a: getter });\n/******/ \t\t\treturn getter;\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/define property getters */\n/******/ \t!function() {\n/******/ \t\t// define getter functions for harmony exports\n/******/ \t\t__webpack_require__.d = function(exports, definition) {\n/******/ \t\t\tfor(var key in definition) {\n/******/ \t\t\t\tif(__webpack_require__.o(definition, key) && !__webpack_require__.o(exports, key)) {\n/******/ \t\t\t\t\tObject.defineProperty(exports, key, { enumerable: true, get: definition[key] });\n/******/ \t\t\t\t}\n/******/ \t\t\t}\n/******/ \t\t};\n/******/ \t}();\n/******/ \t\n/******/ \t/* webpack/runtime/hasOwnProperty shorthand */\n/******/ \t!function() {\n/******/ \t\t__webpack_require__.o = function(obj, prop) { return Object.prototype.hasOwnProperty.call(obj, prop); }\n/******/ \t}();\n/******/ \t\n/************************************************************************/\n/******/ \t// module exports must be returned from runtime so entry inlining is disabled\n/******/ \t// startup\n/******/ \t// Load entry module and return exports\n/******/ \treturn __webpack_require__(686);\n/******/ })()\n.default;\n});", "/*!\n * escape-html\n * Copyright(c) 2012-2013 TJ Holowaychuk\n * Copyright(c) 2015 Andreas Lubbe\n * Copyright(c) 2015 Tiancheng \"Timothy\" Gu\n * MIT Licensed\n */\n\n'use strict';\n\n/**\n * Module variables.\n * @private\n */\n\nvar matchHtmlRegExp = /[\"'&<>]/;\n\n/**\n * Module exports.\n * @public\n */\n\nmodule.exports = escapeHtml;\n\n/**\n * Escape special characters in the given string of html.\n *\n * @param {string} string The string to escape for inserting into HTML\n * @return {string}\n * @public\n */\n\nfunction escapeHtml(string) {\n var str = '' + string;\n var match = matchHtmlRegExp.exec(str);\n\n if (!match) {\n return str;\n }\n\n var escape;\n var html = '';\n var index = 0;\n var lastIndex = 0;\n\n for (index = match.index; index < str.length; index++) {\n switch (str.charCodeAt(index)) {\n case 34: // \"\n escape = '"';\n break;\n case 38: // &\n escape = '&';\n break;\n case 39: // '\n escape = ''';\n break;\n case 60: // <\n escape = '<';\n break;\n case 62: // >\n escape = '>';\n break;\n default:\n continue;\n }\n\n if (lastIndex !== index) {\n html += str.substring(lastIndex, index);\n }\n\n lastIndex = index + 1;\n html += escape;\n }\n\n return lastIndex !== index\n ? html + str.substring(lastIndex, index)\n : html;\n}\n", "Array.prototype.flat||Object.defineProperty(Array.prototype,\"flat\",{configurable:!0,value:function r(){var t=isNaN(arguments[0])?1:Number(arguments[0]);return t?Array.prototype.reduce.call(this,function(a,e){return Array.isArray(e)?a.push.apply(a,r.call(e,t-1)):a.push(e),a},[]):Array.prototype.slice.call(this)},writable:!0}),Array.prototype.flatMap||Object.defineProperty(Array.prototype,\"flatMap\",{configurable:!0,value:function(r){return Array.prototype.map.apply(this,arguments).flat()},writable:!0})\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport \"array-flat-polyfill\"\nimport \"focus-visible\"\nimport \"unfetch/polyfill\"\nimport \"url-polyfill\"\n\nimport {\n EMPTY,\n NEVER,\n Subject,\n defer,\n delay,\n filter,\n map,\n merge,\n mergeWith,\n shareReplay,\n switchMap\n} from \"rxjs\"\n\nimport { configuration, feature } from \"./_\"\nimport {\n at,\n getOptionalElement,\n requestJSON,\n setToggle,\n watchDocument,\n watchKeyboard,\n watchLocation,\n watchLocationTarget,\n watchMedia,\n watchPrint,\n watchViewport\n} from \"./browser\"\nimport {\n getComponentElement,\n getComponentElements,\n mountBackToTop,\n mountContent,\n mountDialog,\n mountHeader,\n mountHeaderTitle,\n mountPalette,\n mountSearch,\n mountSearchHiglight,\n mountSidebar,\n mountSource,\n mountTableOfContents,\n mountTabs,\n watchHeader,\n watchMain\n} from \"./components\"\nimport {\n SearchIndex,\n setupClipboardJS,\n setupInstantLoading,\n setupVersionSelector\n} from \"./integrations\"\nimport {\n patchIndeterminate,\n patchScrollfix,\n patchScrolllock\n} from \"./patches\"\nimport \"./polyfills\"\n\n/* ----------------------------------------------------------------------------\n * Application\n * ------------------------------------------------------------------------- */\n\n/* Yay, JavaScript is available */\ndocument.documentElement.classList.remove(\"no-js\")\ndocument.documentElement.classList.add(\"js\")\n\n/* Set up navigation observables and subjects */\nconst document$ = watchDocument()\nconst location$ = watchLocation()\nconst target$ = watchLocationTarget()\nconst keyboard$ = watchKeyboard()\n\n/* Set up media observables */\nconst viewport$ = watchViewport()\nconst tablet$ = watchMedia(\"(min-width: 960px)\")\nconst screen$ = watchMedia(\"(min-width: 1220px)\")\nconst print$ = watchPrint()\n\n/* Retrieve search index, if search is enabled */\nconst config = configuration()\nconst index$ = document.forms.namedItem(\"search\")\n ? __search?.index || requestJSON(\n new URL(\"search/search_index.json\", config.base)\n )\n : NEVER\n\n/* Set up Clipboard.js integration */\nconst alert$ = new Subject()\nsetupClipboardJS({ alert$ })\n\n/* Set up instant loading, if enabled */\nif (feature(\"navigation.instant\"))\n setupInstantLoading({ document$, location$, viewport$ })\n\n/* Set up version selector */\nif (config.version?.provider === \"mike\")\n setupVersionSelector({ document$ })\n\n/* Always close drawer and search on navigation */\nmerge(location$, target$)\n .pipe(\n delay(125)\n )\n .subscribe(() => {\n setToggle(\"drawer\", false)\n setToggle(\"search\", false)\n })\n\n/* Set up global keyboard handlers */\nkeyboard$\n .pipe(\n filter(({ mode }) => mode === \"global\")\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Go to previous page */\n case \"p\":\n case \",\":\n const prev = getOptionalElement(\"[href][rel=prev]\")\n if (typeof prev !== \"undefined\")\n prev.click()\n break\n\n /* Go to next page */\n case \"n\":\n case \".\":\n const next = getOptionalElement(\"[href][rel=next]\")\n if (typeof next !== \"undefined\")\n next.click()\n break\n }\n })\n\n/* Set up patches */\npatchIndeterminate({ document$, tablet$ })\npatchScrollfix({ document$ })\npatchScrolllock({ viewport$, tablet$ })\n\n/* Set up header and main area observable */\nconst header$ = watchHeader(getComponentElement(\"header\"), { viewport$ })\nconst main$ = document$\n .pipe(\n map(() => getComponentElement(\"main\")),\n switchMap(el => watchMain(el, { viewport$, header$ })),\n shareReplay(1)\n )\n\n/* Set up control component observables */\nconst control$ = merge(\n\n /* Dialog */\n ...getComponentElements(\"dialog\")\n .map(el => mountDialog(el, { alert$ })),\n\n /* Header */\n ...getComponentElements(\"header\")\n .map(el => mountHeader(el, { viewport$, header$, main$ })),\n\n /* Color palette */\n ...getComponentElements(\"palette\")\n .map(el => mountPalette(el)),\n\n /* Search */\n ...getComponentElements(\"search\")\n .map(el => mountSearch(el, { index$, keyboard$ })),\n\n /* Repository information */\n ...getComponentElements(\"source\")\n .map(el => mountSource(el))\n)\n\n/* Set up content component observables */\nconst content$ = defer(() => merge(\n\n /* Content */\n ...getComponentElements(\"content\")\n .map(el => mountContent(el, { target$, print$ })),\n\n /* Search highlighting */\n ...getComponentElements(\"content\")\n .map(el => feature(\"search.highlight\")\n ? mountSearchHiglight(el, { index$, location$ })\n : EMPTY\n ),\n\n /* Header title */\n ...getComponentElements(\"header-title\")\n .map(el => mountHeaderTitle(el, { viewport$, header$ })),\n\n /* Sidebar */\n ...getComponentElements(\"sidebar\")\n .map(el => el.getAttribute(\"data-md-type\") === \"navigation\"\n ? at(screen$, () => mountSidebar(el, { viewport$, header$, main$ }))\n : at(tablet$, () => mountSidebar(el, { viewport$, header$, main$ }))\n ),\n\n /* Navigation tabs */\n ...getComponentElements(\"tabs\")\n .map(el => mountTabs(el, { viewport$, header$ })),\n\n /* Table of contents */\n ...getComponentElements(\"toc\")\n .map(el => mountTableOfContents(el, { viewport$, header$, target$ })),\n\n /* Back-to-top button */\n ...getComponentElements(\"top\")\n .map(el => mountBackToTop(el, { viewport$, header$, main$, target$ }))\n))\n\n/* Set up component observables */\nconst component$ = document$\n .pipe(\n switchMap(() => content$),\n mergeWith(control$),\n shareReplay(1)\n )\n\n/* Subscribe to all components */\ncomponent$.subscribe()\n\n/* ----------------------------------------------------------------------------\n * Exports\n * ------------------------------------------------------------------------- */\n\nwindow.document$ = document$ /* Document observable */\nwindow.location$ = location$ /* Location subject */\nwindow.target$ = target$ /* Location target observable */\nwindow.keyboard$ = keyboard$ /* Keyboard observable */\nwindow.viewport$ = viewport$ /* Viewport observable */\nwindow.tablet$ = tablet$ /* Media tablet observable */\nwindow.screen$ = screen$ /* Media screen observable */\nwindow.print$ = print$ /* Media print observable */\nwindow.alert$ = alert$ /* Alert subject */\nwindow.component$ = component$ /* Component observable */\n", "self.fetch||(self.fetch=function(e,n){return n=n||{},new Promise(function(t,s){var r=new XMLHttpRequest,o=[],u=[],i={},a=function(){return{ok:2==(r.status/100|0),statusText:r.statusText,status:r.status,url:r.responseURL,text:function(){return Promise.resolve(r.responseText)},json:function(){return Promise.resolve(r.responseText).then(JSON.parse)},blob:function(){return Promise.resolve(new Blob([r.response]))},clone:a,headers:{keys:function(){return o},entries:function(){return u},get:function(e){return i[e.toLowerCase()]},has:function(e){return e.toLowerCase()in i}}}};for(var c in r.open(n.method||\"get\",e,!0),r.onload=function(){r.getAllResponseHeaders().replace(/^(.*?):[^\\S\\n]*([\\s\\S]*?)$/gm,function(e,n,t){o.push(n=n.toLowerCase()),u.push([n,t]),i[n]=i[n]?i[n]+\",\"+t:t}),t(a())},r.onerror=s,r.withCredentials=\"include\"==n.credentials,n.headers)r.setRequestHeader(c,n.headers[c]);r.send(n.body||null)})});\n", "import tslib from '../tslib.js';\r\nconst {\r\n __extends,\r\n __assign,\r\n __rest,\r\n __decorate,\r\n __param,\r\n __metadata,\r\n __awaiter,\r\n __generator,\r\n __exportStar,\r\n __createBinding,\r\n __values,\r\n __read,\r\n __spread,\r\n __spreadArrays,\r\n __spreadArray,\r\n __await,\r\n __asyncGenerator,\r\n __asyncDelegator,\r\n __asyncValues,\r\n __makeTemplateObject,\r\n __importStar,\r\n __importDefault,\r\n __classPrivateFieldGet,\r\n __classPrivateFieldSet,\r\n} = tslib;\r\nexport {\r\n __extends,\r\n __assign,\r\n __rest,\r\n __decorate,\r\n __param,\r\n __metadata,\r\n __awaiter,\r\n __generator,\r\n __exportStar,\r\n __createBinding,\r\n __values,\r\n __read,\r\n __spread,\r\n __spreadArrays,\r\n __spreadArray,\r\n __await,\r\n __asyncGenerator,\r\n __asyncDelegator,\r\n __asyncValues,\r\n __makeTemplateObject,\r\n __importStar,\r\n __importDefault,\r\n __classPrivateFieldGet,\r\n __classPrivateFieldSet,\r\n};\r\n", null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, null, "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n ReplaySubject,\n Subject,\n fromEvent\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch document\n *\n * Documents are implemented as subjects, so all downstream observables are\n * automatically updated when a new document is emitted.\n *\n * @returns Document subject\n */\nexport function watchDocument(): Subject {\n const document$ = new ReplaySubject(1)\n fromEvent(document, \"DOMContentLoaded\", { once: true })\n .subscribe(() => document$.next(document))\n\n /* Return document */\n return document$\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve all elements matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Elements\n */\nexport function getElements(\n selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T][]\n\nexport function getElements(\n selector: string, node?: ParentNode\n): T[]\n\nexport function getElements(\n selector: string, node: ParentNode = document\n): T[] {\n return Array.from(node.querySelectorAll(selector))\n}\n\n/**\n * Retrieve an element matching a query selector or throw a reference error\n *\n * Note that this function assumes that the element is present. If unsure if an\n * element is existent, use the `getOptionalElement` function instead.\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element\n */\nexport function getElement(\n selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T]\n\nexport function getElement(\n selector: string, node?: ParentNode\n): T\n\nexport function getElement(\n selector: string, node: ParentNode = document\n): T {\n const el = getOptionalElement(selector, node)\n if (typeof el === \"undefined\")\n throw new ReferenceError(\n `Missing element: expected \"${selector}\" to be present`\n )\n\n /* Return element */\n return el\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Retrieve an optional element matching the query selector\n *\n * @template T - Element type\n *\n * @param selector - Query selector\n * @param node - Node of reference\n *\n * @returns Element or nothing\n */\nexport function getOptionalElement(\n selector: T, node?: ParentNode\n): HTMLElementTagNameMap[T] | undefined\n\nexport function getOptionalElement(\n selector: string, node?: ParentNode\n): T | undefined\n\nexport function getOptionalElement(\n selector: string, node: ParentNode = document\n): T | undefined {\n return node.querySelector(selector) || undefined\n}\n\n/**\n * Retrieve the currently active element\n *\n * @returns Element or nothing\n */\nexport function getActiveElement(): HTMLElement | undefined {\n return document.activeElement instanceof HTMLElement\n ? document.activeElement || undefined\n : undefined\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n debounceTime,\n distinctUntilChanged,\n fromEvent,\n map,\n merge,\n startWith\n} from \"rxjs\"\n\nimport { getActiveElement } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch element focus\n *\n * Previously, this function used `focus` and `blur` events to determine whether\n * an element is focused, but this doesn't work if there are focusable elements\n * within the elements itself. A better solutions are `focusin` and `focusout`\n * events, which bubble up the tree and allow for more fine-grained control.\n *\n * `debounceTime` is necessary, because when a focus change happens inside an\n * element, the observable would first emit `false` and then `true` again.\n *\n * @param el - Element\n *\n * @returns Element focus observable\n */\nexport function watchElementFocus(\n el: HTMLElement\n): Observable {\n return merge(\n fromEvent(document.body, \"focusin\"),\n fromEvent(document.body, \"focusout\")\n )\n .pipe(\n debounceTime(1),\n map(() => {\n const active = getActiveElement()\n return typeof active !== \"undefined\"\n ? el.contains(active)\n : false\n }),\n startWith(el === getActiveElement()),\n distinctUntilChanged()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n animationFrameScheduler,\n auditTime,\n fromEvent,\n map,\n merge,\n startWith\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Element offset\n */\nexport interface ElementOffset {\n x: number /* Horizontal offset */\n y: number /* Vertical offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element offset\n *\n * @param el - Element\n *\n * @returns Element offset\n */\nexport function getElementOffset(\n el: HTMLElement\n): ElementOffset {\n return {\n x: el.offsetLeft,\n y: el.offsetTop\n }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element offset\n *\n * @param el - Element\n *\n * @returns Element offset observable\n */\nexport function watchElementOffset(\n el: HTMLElement\n): Observable {\n return merge(\n fromEvent(window, \"load\"),\n fromEvent(window, \"resize\")\n )\n .pipe(\n auditTime(0, animationFrameScheduler),\n map(() => getElementOffset(el)),\n startWith(getElementOffset(el))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n animationFrameScheduler,\n auditTime,\n fromEvent,\n map,\n merge,\n startWith\n} from \"rxjs\"\n\nimport { ElementOffset } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element content offset (= scroll offset)\n *\n * @param el - Element\n *\n * @returns Element content offset\n */\nexport function getElementContentOffset(\n el: HTMLElement\n): ElementOffset {\n return {\n x: el.scrollLeft,\n y: el.scrollTop\n }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element content offset\n *\n * @param el - Element\n *\n * @returns Element content offset observable\n */\nexport function watchElementContentOffset(\n el: HTMLElement\n): Observable {\n return merge(\n fromEvent(el, \"scroll\"),\n fromEvent(window, \"resize\")\n )\n .pipe(\n auditTime(0, animationFrameScheduler),\n map(() => getElementContentOffset(el)),\n startWith(getElementContentOffset(el))\n )\n}\n", "/**\r\n * A collection of shims that provide minimal functionality of the ES6 collections.\r\n *\r\n * These implementations are not meant to be used outside of the ResizeObserver\r\n * modules as they cover only a limited range of use cases.\r\n */\r\n/* eslint-disable require-jsdoc, valid-jsdoc */\r\nvar MapShim = (function () {\r\n if (typeof Map !== 'undefined') {\r\n return Map;\r\n }\r\n /**\r\n * Returns index in provided array that matches the specified key.\r\n *\r\n * @param {Array} arr\r\n * @param {*} key\r\n * @returns {number}\r\n */\r\n function getIndex(arr, key) {\r\n var result = -1;\r\n arr.some(function (entry, index) {\r\n if (entry[0] === key) {\r\n result = index;\r\n return true;\r\n }\r\n return false;\r\n });\r\n return result;\r\n }\r\n return /** @class */ (function () {\r\n function class_1() {\r\n this.__entries__ = [];\r\n }\r\n Object.defineProperty(class_1.prototype, \"size\", {\r\n /**\r\n * @returns {boolean}\r\n */\r\n get: function () {\r\n return this.__entries__.length;\r\n },\r\n enumerable: true,\r\n configurable: true\r\n });\r\n /**\r\n * @param {*} key\r\n * @returns {*}\r\n */\r\n class_1.prototype.get = function (key) {\r\n var index = getIndex(this.__entries__, key);\r\n var entry = this.__entries__[index];\r\n return entry && entry[1];\r\n };\r\n /**\r\n * @param {*} key\r\n * @param {*} value\r\n * @returns {void}\r\n */\r\n class_1.prototype.set = function (key, value) {\r\n var index = getIndex(this.__entries__, key);\r\n if (~index) {\r\n this.__entries__[index][1] = value;\r\n }\r\n else {\r\n this.__entries__.push([key, value]);\r\n }\r\n };\r\n /**\r\n * @param {*} key\r\n * @returns {void}\r\n */\r\n class_1.prototype.delete = function (key) {\r\n var entries = this.__entries__;\r\n var index = getIndex(entries, key);\r\n if (~index) {\r\n entries.splice(index, 1);\r\n }\r\n };\r\n /**\r\n * @param {*} key\r\n * @returns {void}\r\n */\r\n class_1.prototype.has = function (key) {\r\n return !!~getIndex(this.__entries__, key);\r\n };\r\n /**\r\n * @returns {void}\r\n */\r\n class_1.prototype.clear = function () {\r\n this.__entries__.splice(0);\r\n };\r\n /**\r\n * @param {Function} callback\r\n * @param {*} [ctx=null]\r\n * @returns {void}\r\n */\r\n class_1.prototype.forEach = function (callback, ctx) {\r\n if (ctx === void 0) { ctx = null; }\r\n for (var _i = 0, _a = this.__entries__; _i < _a.length; _i++) {\r\n var entry = _a[_i];\r\n callback.call(ctx, entry[1], entry[0]);\r\n }\r\n };\r\n return class_1;\r\n }());\r\n})();\n\n/**\r\n * Detects whether window and document objects are available in current environment.\r\n */\r\nvar isBrowser = typeof window !== 'undefined' && typeof document !== 'undefined' && window.document === document;\n\n// Returns global object of a current environment.\r\nvar global$1 = (function () {\r\n if (typeof global !== 'undefined' && global.Math === Math) {\r\n return global;\r\n }\r\n if (typeof self !== 'undefined' && self.Math === Math) {\r\n return self;\r\n }\r\n if (typeof window !== 'undefined' && window.Math === Math) {\r\n return window;\r\n }\r\n // eslint-disable-next-line no-new-func\r\n return Function('return this')();\r\n})();\n\n/**\r\n * A shim for the requestAnimationFrame which falls back to the setTimeout if\r\n * first one is not supported.\r\n *\r\n * @returns {number} Requests' identifier.\r\n */\r\nvar requestAnimationFrame$1 = (function () {\r\n if (typeof requestAnimationFrame === 'function') {\r\n // It's required to use a bounded function because IE sometimes throws\r\n // an \"Invalid calling object\" error if rAF is invoked without the global\r\n // object on the left hand side.\r\n return requestAnimationFrame.bind(global$1);\r\n }\r\n return function (callback) { return setTimeout(function () { return callback(Date.now()); }, 1000 / 60); };\r\n})();\n\n// Defines minimum timeout before adding a trailing call.\r\nvar trailingTimeout = 2;\r\n/**\r\n * Creates a wrapper function which ensures that provided callback will be\r\n * invoked only once during the specified delay period.\r\n *\r\n * @param {Function} callback - Function to be invoked after the delay period.\r\n * @param {number} delay - Delay after which to invoke callback.\r\n * @returns {Function}\r\n */\r\nfunction throttle (callback, delay) {\r\n var leadingCall = false, trailingCall = false, lastCallTime = 0;\r\n /**\r\n * Invokes the original callback function and schedules new invocation if\r\n * the \"proxy\" was called during current request.\r\n *\r\n * @returns {void}\r\n */\r\n function resolvePending() {\r\n if (leadingCall) {\r\n leadingCall = false;\r\n callback();\r\n }\r\n if (trailingCall) {\r\n proxy();\r\n }\r\n }\r\n /**\r\n * Callback invoked after the specified delay. It will further postpone\r\n * invocation of the original function delegating it to the\r\n * requestAnimationFrame.\r\n *\r\n * @returns {void}\r\n */\r\n function timeoutCallback() {\r\n requestAnimationFrame$1(resolvePending);\r\n }\r\n /**\r\n * Schedules invocation of the original function.\r\n *\r\n * @returns {void}\r\n */\r\n function proxy() {\r\n var timeStamp = Date.now();\r\n if (leadingCall) {\r\n // Reject immediately following calls.\r\n if (timeStamp - lastCallTime < trailingTimeout) {\r\n return;\r\n }\r\n // Schedule new call to be in invoked when the pending one is resolved.\r\n // This is important for \"transitions\" which never actually start\r\n // immediately so there is a chance that we might miss one if change\r\n // happens amids the pending invocation.\r\n trailingCall = true;\r\n }\r\n else {\r\n leadingCall = true;\r\n trailingCall = false;\r\n setTimeout(timeoutCallback, delay);\r\n }\r\n lastCallTime = timeStamp;\r\n }\r\n return proxy;\r\n}\n\n// Minimum delay before invoking the update of observers.\r\nvar REFRESH_DELAY = 20;\r\n// A list of substrings of CSS properties used to find transition events that\r\n// might affect dimensions of observed elements.\r\nvar transitionKeys = ['top', 'right', 'bottom', 'left', 'width', 'height', 'size', 'weight'];\r\n// Check if MutationObserver is available.\r\nvar mutationObserverSupported = typeof MutationObserver !== 'undefined';\r\n/**\r\n * Singleton controller class which handles updates of ResizeObserver instances.\r\n */\r\nvar ResizeObserverController = /** @class */ (function () {\r\n /**\r\n * Creates a new instance of ResizeObserverController.\r\n *\r\n * @private\r\n */\r\n function ResizeObserverController() {\r\n /**\r\n * Indicates whether DOM listeners have been added.\r\n *\r\n * @private {boolean}\r\n */\r\n this.connected_ = false;\r\n /**\r\n * Tells that controller has subscribed for Mutation Events.\r\n *\r\n * @private {boolean}\r\n */\r\n this.mutationEventsAdded_ = false;\r\n /**\r\n * Keeps reference to the instance of MutationObserver.\r\n *\r\n * @private {MutationObserver}\r\n */\r\n this.mutationsObserver_ = null;\r\n /**\r\n * A list of connected observers.\r\n *\r\n * @private {Array}\r\n */\r\n this.observers_ = [];\r\n this.onTransitionEnd_ = this.onTransitionEnd_.bind(this);\r\n this.refresh = throttle(this.refresh.bind(this), REFRESH_DELAY);\r\n }\r\n /**\r\n * Adds observer to observers list.\r\n *\r\n * @param {ResizeObserverSPI} observer - Observer to be added.\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.addObserver = function (observer) {\r\n if (!~this.observers_.indexOf(observer)) {\r\n this.observers_.push(observer);\r\n }\r\n // Add listeners if they haven't been added yet.\r\n if (!this.connected_) {\r\n this.connect_();\r\n }\r\n };\r\n /**\r\n * Removes observer from observers list.\r\n *\r\n * @param {ResizeObserverSPI} observer - Observer to be removed.\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.removeObserver = function (observer) {\r\n var observers = this.observers_;\r\n var index = observers.indexOf(observer);\r\n // Remove observer if it's present in registry.\r\n if (~index) {\r\n observers.splice(index, 1);\r\n }\r\n // Remove listeners if controller has no connected observers.\r\n if (!observers.length && this.connected_) {\r\n this.disconnect_();\r\n }\r\n };\r\n /**\r\n * Invokes the update of observers. It will continue running updates insofar\r\n * it detects changes.\r\n *\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.refresh = function () {\r\n var changesDetected = this.updateObservers_();\r\n // Continue running updates if changes have been detected as there might\r\n // be future ones caused by CSS transitions.\r\n if (changesDetected) {\r\n this.refresh();\r\n }\r\n };\r\n /**\r\n * Updates every observer from observers list and notifies them of queued\r\n * entries.\r\n *\r\n * @private\r\n * @returns {boolean} Returns \"true\" if any observer has detected changes in\r\n * dimensions of it's elements.\r\n */\r\n ResizeObserverController.prototype.updateObservers_ = function () {\r\n // Collect observers that have active observations.\r\n var activeObservers = this.observers_.filter(function (observer) {\r\n return observer.gatherActive(), observer.hasActive();\r\n });\r\n // Deliver notifications in a separate cycle in order to avoid any\r\n // collisions between observers, e.g. when multiple instances of\r\n // ResizeObserver are tracking the same element and the callback of one\r\n // of them changes content dimensions of the observed target. Sometimes\r\n // this may result in notifications being blocked for the rest of observers.\r\n activeObservers.forEach(function (observer) { return observer.broadcastActive(); });\r\n return activeObservers.length > 0;\r\n };\r\n /**\r\n * Initializes DOM listeners.\r\n *\r\n * @private\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.connect_ = function () {\r\n // Do nothing if running in a non-browser environment or if listeners\r\n // have been already added.\r\n if (!isBrowser || this.connected_) {\r\n return;\r\n }\r\n // Subscription to the \"Transitionend\" event is used as a workaround for\r\n // delayed transitions. This way it's possible to capture at least the\r\n // final state of an element.\r\n document.addEventListener('transitionend', this.onTransitionEnd_);\r\n window.addEventListener('resize', this.refresh);\r\n if (mutationObserverSupported) {\r\n this.mutationsObserver_ = new MutationObserver(this.refresh);\r\n this.mutationsObserver_.observe(document, {\r\n attributes: true,\r\n childList: true,\r\n characterData: true,\r\n subtree: true\r\n });\r\n }\r\n else {\r\n document.addEventListener('DOMSubtreeModified', this.refresh);\r\n this.mutationEventsAdded_ = true;\r\n }\r\n this.connected_ = true;\r\n };\r\n /**\r\n * Removes DOM listeners.\r\n *\r\n * @private\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.disconnect_ = function () {\r\n // Do nothing if running in a non-browser environment or if listeners\r\n // have been already removed.\r\n if (!isBrowser || !this.connected_) {\r\n return;\r\n }\r\n document.removeEventListener('transitionend', this.onTransitionEnd_);\r\n window.removeEventListener('resize', this.refresh);\r\n if (this.mutationsObserver_) {\r\n this.mutationsObserver_.disconnect();\r\n }\r\n if (this.mutationEventsAdded_) {\r\n document.removeEventListener('DOMSubtreeModified', this.refresh);\r\n }\r\n this.mutationsObserver_ = null;\r\n this.mutationEventsAdded_ = false;\r\n this.connected_ = false;\r\n };\r\n /**\r\n * \"Transitionend\" event handler.\r\n *\r\n * @private\r\n * @param {TransitionEvent} event\r\n * @returns {void}\r\n */\r\n ResizeObserverController.prototype.onTransitionEnd_ = function (_a) {\r\n var _b = _a.propertyName, propertyName = _b === void 0 ? '' : _b;\r\n // Detect whether transition may affect dimensions of an element.\r\n var isReflowProperty = transitionKeys.some(function (key) {\r\n return !!~propertyName.indexOf(key);\r\n });\r\n if (isReflowProperty) {\r\n this.refresh();\r\n }\r\n };\r\n /**\r\n * Returns instance of the ResizeObserverController.\r\n *\r\n * @returns {ResizeObserverController}\r\n */\r\n ResizeObserverController.getInstance = function () {\r\n if (!this.instance_) {\r\n this.instance_ = new ResizeObserverController();\r\n }\r\n return this.instance_;\r\n };\r\n /**\r\n * Holds reference to the controller's instance.\r\n *\r\n * @private {ResizeObserverController}\r\n */\r\n ResizeObserverController.instance_ = null;\r\n return ResizeObserverController;\r\n}());\n\n/**\r\n * Defines non-writable/enumerable properties of the provided target object.\r\n *\r\n * @param {Object} target - Object for which to define properties.\r\n * @param {Object} props - Properties to be defined.\r\n * @returns {Object} Target object.\r\n */\r\nvar defineConfigurable = (function (target, props) {\r\n for (var _i = 0, _a = Object.keys(props); _i < _a.length; _i++) {\r\n var key = _a[_i];\r\n Object.defineProperty(target, key, {\r\n value: props[key],\r\n enumerable: false,\r\n writable: false,\r\n configurable: true\r\n });\r\n }\r\n return target;\r\n});\n\n/**\r\n * Returns the global object associated with provided element.\r\n *\r\n * @param {Object} target\r\n * @returns {Object}\r\n */\r\nvar getWindowOf = (function (target) {\r\n // Assume that the element is an instance of Node, which means that it\r\n // has the \"ownerDocument\" property from which we can retrieve a\r\n // corresponding global object.\r\n var ownerGlobal = target && target.ownerDocument && target.ownerDocument.defaultView;\r\n // Return the local global object if it's not possible extract one from\r\n // provided element.\r\n return ownerGlobal || global$1;\r\n});\n\n// Placeholder of an empty content rectangle.\r\nvar emptyRect = createRectInit(0, 0, 0, 0);\r\n/**\r\n * Converts provided string to a number.\r\n *\r\n * @param {number|string} value\r\n * @returns {number}\r\n */\r\nfunction toFloat(value) {\r\n return parseFloat(value) || 0;\r\n}\r\n/**\r\n * Extracts borders size from provided styles.\r\n *\r\n * @param {CSSStyleDeclaration} styles\r\n * @param {...string} positions - Borders positions (top, right, ...)\r\n * @returns {number}\r\n */\r\nfunction getBordersSize(styles) {\r\n var positions = [];\r\n for (var _i = 1; _i < arguments.length; _i++) {\r\n positions[_i - 1] = arguments[_i];\r\n }\r\n return positions.reduce(function (size, position) {\r\n var value = styles['border-' + position + '-width'];\r\n return size + toFloat(value);\r\n }, 0);\r\n}\r\n/**\r\n * Extracts paddings sizes from provided styles.\r\n *\r\n * @param {CSSStyleDeclaration} styles\r\n * @returns {Object} Paddings box.\r\n */\r\nfunction getPaddings(styles) {\r\n var positions = ['top', 'right', 'bottom', 'left'];\r\n var paddings = {};\r\n for (var _i = 0, positions_1 = positions; _i < positions_1.length; _i++) {\r\n var position = positions_1[_i];\r\n var value = styles['padding-' + position];\r\n paddings[position] = toFloat(value);\r\n }\r\n return paddings;\r\n}\r\n/**\r\n * Calculates content rectangle of provided SVG element.\r\n *\r\n * @param {SVGGraphicsElement} target - Element content rectangle of which needs\r\n * to be calculated.\r\n * @returns {DOMRectInit}\r\n */\r\nfunction getSVGContentRect(target) {\r\n var bbox = target.getBBox();\r\n return createRectInit(0, 0, bbox.width, bbox.height);\r\n}\r\n/**\r\n * Calculates content rectangle of provided HTMLElement.\r\n *\r\n * @param {HTMLElement} target - Element for which to calculate the content rectangle.\r\n * @returns {DOMRectInit}\r\n */\r\nfunction getHTMLElementContentRect(target) {\r\n // Client width & height properties can't be\r\n // used exclusively as they provide rounded values.\r\n var clientWidth = target.clientWidth, clientHeight = target.clientHeight;\r\n // By this condition we can catch all non-replaced inline, hidden and\r\n // detached elements. Though elements with width & height properties less\r\n // than 0.5 will be discarded as well.\r\n //\r\n // Without it we would need to implement separate methods for each of\r\n // those cases and it's not possible to perform a precise and performance\r\n // effective test for hidden elements. E.g. even jQuery's ':visible' filter\r\n // gives wrong results for elements with width & height less than 0.5.\r\n if (!clientWidth && !clientHeight) {\r\n return emptyRect;\r\n }\r\n var styles = getWindowOf(target).getComputedStyle(target);\r\n var paddings = getPaddings(styles);\r\n var horizPad = paddings.left + paddings.right;\r\n var vertPad = paddings.top + paddings.bottom;\r\n // Computed styles of width & height are being used because they are the\r\n // only dimensions available to JS that contain non-rounded values. It could\r\n // be possible to utilize the getBoundingClientRect if only it's data wasn't\r\n // affected by CSS transformations let alone paddings, borders and scroll bars.\r\n var width = toFloat(styles.width), height = toFloat(styles.height);\r\n // Width & height include paddings and borders when the 'border-box' box\r\n // model is applied (except for IE).\r\n if (styles.boxSizing === 'border-box') {\r\n // Following conditions are required to handle Internet Explorer which\r\n // doesn't include paddings and borders to computed CSS dimensions.\r\n //\r\n // We can say that if CSS dimensions + paddings are equal to the \"client\"\r\n // properties then it's either IE, and thus we don't need to subtract\r\n // anything, or an element merely doesn't have paddings/borders styles.\r\n if (Math.round(width + horizPad) !== clientWidth) {\r\n width -= getBordersSize(styles, 'left', 'right') + horizPad;\r\n }\r\n if (Math.round(height + vertPad) !== clientHeight) {\r\n height -= getBordersSize(styles, 'top', 'bottom') + vertPad;\r\n }\r\n }\r\n // Following steps can't be applied to the document's root element as its\r\n // client[Width/Height] properties represent viewport area of the window.\r\n // Besides, it's as well not necessary as the itself neither has\r\n // rendered scroll bars nor it can be clipped.\r\n if (!isDocumentElement(target)) {\r\n // In some browsers (only in Firefox, actually) CSS width & height\r\n // include scroll bars size which can be removed at this step as scroll\r\n // bars are the only difference between rounded dimensions + paddings\r\n // and \"client\" properties, though that is not always true in Chrome.\r\n var vertScrollbar = Math.round(width + horizPad) - clientWidth;\r\n var horizScrollbar = Math.round(height + vertPad) - clientHeight;\r\n // Chrome has a rather weird rounding of \"client\" properties.\r\n // E.g. for an element with content width of 314.2px it sometimes gives\r\n // the client width of 315px and for the width of 314.7px it may give\r\n // 314px. And it doesn't happen all the time. So just ignore this delta\r\n // as a non-relevant.\r\n if (Math.abs(vertScrollbar) !== 1) {\r\n width -= vertScrollbar;\r\n }\r\n if (Math.abs(horizScrollbar) !== 1) {\r\n height -= horizScrollbar;\r\n }\r\n }\r\n return createRectInit(paddings.left, paddings.top, width, height);\r\n}\r\n/**\r\n * Checks whether provided element is an instance of the SVGGraphicsElement.\r\n *\r\n * @param {Element} target - Element to be checked.\r\n * @returns {boolean}\r\n */\r\nvar isSVGGraphicsElement = (function () {\r\n // Some browsers, namely IE and Edge, don't have the SVGGraphicsElement\r\n // interface.\r\n if (typeof SVGGraphicsElement !== 'undefined') {\r\n return function (target) { return target instanceof getWindowOf(target).SVGGraphicsElement; };\r\n }\r\n // If it's so, then check that element is at least an instance of the\r\n // SVGElement and that it has the \"getBBox\" method.\r\n // eslint-disable-next-line no-extra-parens\r\n return function (target) { return (target instanceof getWindowOf(target).SVGElement &&\r\n typeof target.getBBox === 'function'); };\r\n})();\r\n/**\r\n * Checks whether provided element is a document element ().\r\n *\r\n * @param {Element} target - Element to be checked.\r\n * @returns {boolean}\r\n */\r\nfunction isDocumentElement(target) {\r\n return target === getWindowOf(target).document.documentElement;\r\n}\r\n/**\r\n * Calculates an appropriate content rectangle for provided html or svg element.\r\n *\r\n * @param {Element} target - Element content rectangle of which needs to be calculated.\r\n * @returns {DOMRectInit}\r\n */\r\nfunction getContentRect(target) {\r\n if (!isBrowser) {\r\n return emptyRect;\r\n }\r\n if (isSVGGraphicsElement(target)) {\r\n return getSVGContentRect(target);\r\n }\r\n return getHTMLElementContentRect(target);\r\n}\r\n/**\r\n * Creates rectangle with an interface of the DOMRectReadOnly.\r\n * Spec: https://drafts.fxtf.org/geometry/#domrectreadonly\r\n *\r\n * @param {DOMRectInit} rectInit - Object with rectangle's x/y coordinates and dimensions.\r\n * @returns {DOMRectReadOnly}\r\n */\r\nfunction createReadOnlyRect(_a) {\r\n var x = _a.x, y = _a.y, width = _a.width, height = _a.height;\r\n // If DOMRectReadOnly is available use it as a prototype for the rectangle.\r\n var Constr = typeof DOMRectReadOnly !== 'undefined' ? DOMRectReadOnly : Object;\r\n var rect = Object.create(Constr.prototype);\r\n // Rectangle's properties are not writable and non-enumerable.\r\n defineConfigurable(rect, {\r\n x: x, y: y, width: width, height: height,\r\n top: y,\r\n right: x + width,\r\n bottom: height + y,\r\n left: x\r\n });\r\n return rect;\r\n}\r\n/**\r\n * Creates DOMRectInit object based on the provided dimensions and the x/y coordinates.\r\n * Spec: https://drafts.fxtf.org/geometry/#dictdef-domrectinit\r\n *\r\n * @param {number} x - X coordinate.\r\n * @param {number} y - Y coordinate.\r\n * @param {number} width - Rectangle's width.\r\n * @param {number} height - Rectangle's height.\r\n * @returns {DOMRectInit}\r\n */\r\nfunction createRectInit(x, y, width, height) {\r\n return { x: x, y: y, width: width, height: height };\r\n}\n\n/**\r\n * Class that is responsible for computations of the content rectangle of\r\n * provided DOM element and for keeping track of it's changes.\r\n */\r\nvar ResizeObservation = /** @class */ (function () {\r\n /**\r\n * Creates an instance of ResizeObservation.\r\n *\r\n * @param {Element} target - Element to be observed.\r\n */\r\n function ResizeObservation(target) {\r\n /**\r\n * Broadcasted width of content rectangle.\r\n *\r\n * @type {number}\r\n */\r\n this.broadcastWidth = 0;\r\n /**\r\n * Broadcasted height of content rectangle.\r\n *\r\n * @type {number}\r\n */\r\n this.broadcastHeight = 0;\r\n /**\r\n * Reference to the last observed content rectangle.\r\n *\r\n * @private {DOMRectInit}\r\n */\r\n this.contentRect_ = createRectInit(0, 0, 0, 0);\r\n this.target = target;\r\n }\r\n /**\r\n * Updates content rectangle and tells whether it's width or height properties\r\n * have changed since the last broadcast.\r\n *\r\n * @returns {boolean}\r\n */\r\n ResizeObservation.prototype.isActive = function () {\r\n var rect = getContentRect(this.target);\r\n this.contentRect_ = rect;\r\n return (rect.width !== this.broadcastWidth ||\r\n rect.height !== this.broadcastHeight);\r\n };\r\n /**\r\n * Updates 'broadcastWidth' and 'broadcastHeight' properties with a data\r\n * from the corresponding properties of the last observed content rectangle.\r\n *\r\n * @returns {DOMRectInit} Last observed content rectangle.\r\n */\r\n ResizeObservation.prototype.broadcastRect = function () {\r\n var rect = this.contentRect_;\r\n this.broadcastWidth = rect.width;\r\n this.broadcastHeight = rect.height;\r\n return rect;\r\n };\r\n return ResizeObservation;\r\n}());\n\nvar ResizeObserverEntry = /** @class */ (function () {\r\n /**\r\n * Creates an instance of ResizeObserverEntry.\r\n *\r\n * @param {Element} target - Element that is being observed.\r\n * @param {DOMRectInit} rectInit - Data of the element's content rectangle.\r\n */\r\n function ResizeObserverEntry(target, rectInit) {\r\n var contentRect = createReadOnlyRect(rectInit);\r\n // According to the specification following properties are not writable\r\n // and are also not enumerable in the native implementation.\r\n //\r\n // Property accessors are not being used as they'd require to define a\r\n // private WeakMap storage which may cause memory leaks in browsers that\r\n // don't support this type of collections.\r\n defineConfigurable(this, { target: target, contentRect: contentRect });\r\n }\r\n return ResizeObserverEntry;\r\n}());\n\nvar ResizeObserverSPI = /** @class */ (function () {\r\n /**\r\n * Creates a new instance of ResizeObserver.\r\n *\r\n * @param {ResizeObserverCallback} callback - Callback function that is invoked\r\n * when one of the observed elements changes it's content dimensions.\r\n * @param {ResizeObserverController} controller - Controller instance which\r\n * is responsible for the updates of observer.\r\n * @param {ResizeObserver} callbackCtx - Reference to the public\r\n * ResizeObserver instance which will be passed to callback function.\r\n */\r\n function ResizeObserverSPI(callback, controller, callbackCtx) {\r\n /**\r\n * Collection of resize observations that have detected changes in dimensions\r\n * of elements.\r\n *\r\n * @private {Array}\r\n */\r\n this.activeObservations_ = [];\r\n /**\r\n * Registry of the ResizeObservation instances.\r\n *\r\n * @private {Map}\r\n */\r\n this.observations_ = new MapShim();\r\n if (typeof callback !== 'function') {\r\n throw new TypeError('The callback provided as parameter 1 is not a function.');\r\n }\r\n this.callback_ = callback;\r\n this.controller_ = controller;\r\n this.callbackCtx_ = callbackCtx;\r\n }\r\n /**\r\n * Starts observing provided element.\r\n *\r\n * @param {Element} target - Element to be observed.\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.observe = function (target) {\r\n if (!arguments.length) {\r\n throw new TypeError('1 argument required, but only 0 present.');\r\n }\r\n // Do nothing if current environment doesn't have the Element interface.\r\n if (typeof Element === 'undefined' || !(Element instanceof Object)) {\r\n return;\r\n }\r\n if (!(target instanceof getWindowOf(target).Element)) {\r\n throw new TypeError('parameter 1 is not of type \"Element\".');\r\n }\r\n var observations = this.observations_;\r\n // Do nothing if element is already being observed.\r\n if (observations.has(target)) {\r\n return;\r\n }\r\n observations.set(target, new ResizeObservation(target));\r\n this.controller_.addObserver(this);\r\n // Force the update of observations.\r\n this.controller_.refresh();\r\n };\r\n /**\r\n * Stops observing provided element.\r\n *\r\n * @param {Element} target - Element to stop observing.\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.unobserve = function (target) {\r\n if (!arguments.length) {\r\n throw new TypeError('1 argument required, but only 0 present.');\r\n }\r\n // Do nothing if current environment doesn't have the Element interface.\r\n if (typeof Element === 'undefined' || !(Element instanceof Object)) {\r\n return;\r\n }\r\n if (!(target instanceof getWindowOf(target).Element)) {\r\n throw new TypeError('parameter 1 is not of type \"Element\".');\r\n }\r\n var observations = this.observations_;\r\n // Do nothing if element is not being observed.\r\n if (!observations.has(target)) {\r\n return;\r\n }\r\n observations.delete(target);\r\n if (!observations.size) {\r\n this.controller_.removeObserver(this);\r\n }\r\n };\r\n /**\r\n * Stops observing all elements.\r\n *\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.disconnect = function () {\r\n this.clearActive();\r\n this.observations_.clear();\r\n this.controller_.removeObserver(this);\r\n };\r\n /**\r\n * Collects observation instances the associated element of which has changed\r\n * it's content rectangle.\r\n *\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.gatherActive = function () {\r\n var _this = this;\r\n this.clearActive();\r\n this.observations_.forEach(function (observation) {\r\n if (observation.isActive()) {\r\n _this.activeObservations_.push(observation);\r\n }\r\n });\r\n };\r\n /**\r\n * Invokes initial callback function with a list of ResizeObserverEntry\r\n * instances collected from active resize observations.\r\n *\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.broadcastActive = function () {\r\n // Do nothing if observer doesn't have active observations.\r\n if (!this.hasActive()) {\r\n return;\r\n }\r\n var ctx = this.callbackCtx_;\r\n // Create ResizeObserverEntry instance for every active observation.\r\n var entries = this.activeObservations_.map(function (observation) {\r\n return new ResizeObserverEntry(observation.target, observation.broadcastRect());\r\n });\r\n this.callback_.call(ctx, entries, ctx);\r\n this.clearActive();\r\n };\r\n /**\r\n * Clears the collection of active observations.\r\n *\r\n * @returns {void}\r\n */\r\n ResizeObserverSPI.prototype.clearActive = function () {\r\n this.activeObservations_.splice(0);\r\n };\r\n /**\r\n * Tells whether observer has active observations.\r\n *\r\n * @returns {boolean}\r\n */\r\n ResizeObserverSPI.prototype.hasActive = function () {\r\n return this.activeObservations_.length > 0;\r\n };\r\n return ResizeObserverSPI;\r\n}());\n\n// Registry of internal observers. If WeakMap is not available use current shim\r\n// for the Map collection as it has all required methods and because WeakMap\r\n// can't be fully polyfilled anyway.\r\nvar observers = typeof WeakMap !== 'undefined' ? new WeakMap() : new MapShim();\r\n/**\r\n * ResizeObserver API. Encapsulates the ResizeObserver SPI implementation\r\n * exposing only those methods and properties that are defined in the spec.\r\n */\r\nvar ResizeObserver = /** @class */ (function () {\r\n /**\r\n * Creates a new instance of ResizeObserver.\r\n *\r\n * @param {ResizeObserverCallback} callback - Callback that is invoked when\r\n * dimensions of the observed elements change.\r\n */\r\n function ResizeObserver(callback) {\r\n if (!(this instanceof ResizeObserver)) {\r\n throw new TypeError('Cannot call a class as a function.');\r\n }\r\n if (!arguments.length) {\r\n throw new TypeError('1 argument required, but only 0 present.');\r\n }\r\n var controller = ResizeObserverController.getInstance();\r\n var observer = new ResizeObserverSPI(callback, controller, this);\r\n observers.set(this, observer);\r\n }\r\n return ResizeObserver;\r\n}());\r\n// Expose public methods of ResizeObserver.\r\n[\r\n 'observe',\r\n 'unobserve',\r\n 'disconnect'\r\n].forEach(function (method) {\r\n ResizeObserver.prototype[method] = function () {\r\n var _a;\r\n return (_a = observers.get(this))[method].apply(_a, arguments);\r\n };\r\n});\n\nvar index = (function () {\r\n // Export existing implementation if available.\r\n if (typeof global$1.ResizeObserver !== 'undefined') {\r\n return global$1.ResizeObserver;\r\n }\r\n return ResizeObserver;\r\n})();\n\nexport default index;\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ResizeObserver from \"resize-observer-polyfill\"\nimport {\n NEVER,\n Observable,\n Subject,\n defer,\n filter,\n finalize,\n map,\n merge,\n of,\n shareReplay,\n startWith,\n switchMap,\n tap\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Element offset\n */\nexport interface ElementSize {\n width: number /* Element width */\n height: number /* Element height */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Resize observer entry subject\n */\nconst entry$ = new Subject()\n\n/**\n * Resize observer observable\n *\n * This observable will create a `ResizeObserver` on the first subscription\n * and will automatically terminate it when there are no more subscribers.\n * It's quite important to centralize observation in a single `ResizeObserver`,\n * as the performance difference can be quite dramatic, as the link shows.\n *\n * @see https://bit.ly/3iIYfEm - Google Groups on performance\n */\nconst observer$ = defer(() => of(\n new ResizeObserver(entries => {\n for (const entry of entries)\n entry$.next(entry)\n })\n))\n .pipe(\n switchMap(observer => merge(NEVER, of(observer))\n .pipe(\n finalize(() => observer.disconnect())\n )\n ),\n shareReplay(1)\n )\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element size\n *\n * @param el - Element\n *\n * @returns Element size\n */\nexport function getElementSize(\n el: HTMLElement\n): ElementSize {\n return {\n width: el.offsetWidth,\n height: el.offsetHeight\n }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch element size\n *\n * This function returns an observable that subscribes to a single internal\n * instance of `ResizeObserver` upon subscription, and emit resize events until\n * termination. Note that this function should not be called with the same\n * element twice, as the first unsubscription will terminate observation.\n *\n * Sadly, we can't use the `DOMRect` objects returned by the observer, because\n * we need the emitted values to be consistent with `getElementSize`, which will\n * return the used values (rounded) and not actual values (unrounded). Thus, we\n * use the `offset*` properties. See the linked GitHub issue.\n *\n * @see https://bit.ly/3m0k3he - GitHub issue\n *\n * @param el - Element\n *\n * @returns Element size observable\n */\nexport function watchElementSize(\n el: HTMLElement\n): Observable {\n return observer$\n .pipe(\n tap(observer => observer.observe(el)),\n switchMap(observer => entry$\n .pipe(\n filter(({ target }) => target === el),\n finalize(() => observer.unobserve(el)),\n map(() => getElementSize(el))\n )\n ),\n startWith(getElementSize(el))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ElementSize } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve element content size (= scroll width and height)\n *\n * @param el - Element\n *\n * @returns Element content size\n */\nexport function getElementContentSize(\n el: HTMLElement\n): ElementSize {\n return {\n width: el.scrollWidth,\n height: el.scrollHeight\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n NEVER,\n Observable,\n Subject,\n defer,\n distinctUntilChanged,\n filter,\n finalize,\n map,\n merge,\n of,\n shareReplay,\n switchMap,\n tap\n} from \"rxjs\"\n\nimport {\n getElementContentSize,\n getElementSize,\n watchElementContentOffset\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Intersection observer entry subject\n */\nconst entry$ = new Subject()\n\n/**\n * Intersection observer observable\n *\n * This observable will create an `IntersectionObserver` on first subscription\n * and will automatically terminate it when there are no more subscribers.\n *\n * @see https://bit.ly/3iIYfEm - Google Groups on performance\n */\nconst observer$ = defer(() => of(\n new IntersectionObserver(entries => {\n for (const entry of entries)\n entry$.next(entry)\n }, {\n threshold: 0\n })\n))\n .pipe(\n switchMap(observer => merge(NEVER, of(observer))\n .pipe(\n finalize(() => observer.disconnect())\n )\n ),\n shareReplay(1)\n )\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch element visibility\n *\n * @param el - Element\n *\n * @returns Element visibility observable\n */\nexport function watchElementVisibility(\n el: HTMLElement\n): Observable {\n return observer$\n .pipe(\n tap(observer => observer.observe(el)),\n switchMap(observer => entry$\n .pipe(\n filter(({ target }) => target === el),\n finalize(() => observer.unobserve(el)),\n map(({ isIntersecting }) => isIntersecting)\n )\n )\n )\n}\n\n/**\n * Watch element boundary\n *\n * This function returns an observable which emits whether the bottom content\n * boundary (= scroll offset) of an element is within a certain threshold.\n *\n * @param el - Element\n * @param threshold - Threshold\n *\n * @returns Element boundary observable\n */\nexport function watchElementBoundary(\n el: HTMLElement, threshold = 16\n): Observable {\n return watchElementContentOffset(el)\n .pipe(\n map(({ y }) => {\n const visible = getElementSize(el)\n const content = getElementContentSize(el)\n return y >= (\n content.height - visible.height - threshold\n )\n }),\n distinctUntilChanged()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n fromEvent,\n map,\n startWith\n} from \"rxjs\"\n\nimport { getElement } from \"../element\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Toggle\n */\nexport type Toggle =\n | \"drawer\" /* Toggle for drawer */\n | \"search\" /* Toggle for search */\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Toggle map\n */\nconst toggles: Record = {\n drawer: getElement(\"[data-md-toggle=drawer]\"),\n search: getElement(\"[data-md-toggle=search]\")\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve the value of a toggle\n *\n * @param name - Toggle\n *\n * @returns Toggle value\n */\nexport function getToggle(name: Toggle): boolean {\n return toggles[name].checked\n}\n\n/**\n * Set toggle\n *\n * Simulating a click event seems to be the most cross-browser compatible way\n * of changing the value while also emitting a `change` event. Before, Material\n * used `CustomEvent` to programmatically change the value of a toggle, but this\n * is a much simpler and cleaner solution which doesn't require a polyfill.\n *\n * @param name - Toggle\n * @param value - Toggle value\n */\nexport function setToggle(name: Toggle, value: boolean): void {\n if (toggles[name].checked !== value)\n toggles[name].click()\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch toggle\n *\n * @param name - Toggle\n *\n * @returns Toggle value observable\n */\nexport function watchToggle(name: Toggle): Observable {\n const el = toggles[name]\n return fromEvent(el, \"change\")\n .pipe(\n map(() => el.checked),\n startWith(el.checked)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n filter,\n fromEvent,\n map,\n share\n} from \"rxjs\"\n\nimport { getActiveElement } from \"../element\"\nimport { getToggle } from \"../toggle\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Keyboard mode\n */\nexport type KeyboardMode =\n | \"global\" /* Global */\n | \"search\" /* Search is open */\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Keyboard\n */\nexport interface Keyboard {\n mode: KeyboardMode /* Keyboard mode */\n type: string /* Key type */\n claim(): void /* Key claim */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Check whether an element may receive keyboard input\n *\n * @param el - Element\n * @param type - Key type\n *\n * @returns Test result\n */\nfunction isSusceptibleToKeyboard(\n el: HTMLElement, type: string\n): boolean {\n switch (el.constructor) {\n\n /* Input elements */\n case HTMLInputElement:\n /* @ts-expect-error - omit unnecessary type cast */\n if (el.type === \"radio\")\n return /^Arrow/.test(type)\n else\n return true\n\n /* Select element and textarea */\n case HTMLSelectElement:\n case HTMLTextAreaElement:\n return true\n\n /* Everything else */\n default:\n return el.isContentEditable\n }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch keyboard\n *\n * @returns Keyboard observable\n */\nexport function watchKeyboard(): Observable {\n return fromEvent(window, \"keydown\")\n .pipe(\n filter(ev => !(ev.metaKey || ev.ctrlKey)),\n map(ev => ({\n mode: getToggle(\"search\") ? \"search\" : \"global\",\n type: ev.key,\n claim() {\n ev.preventDefault()\n ev.stopPropagation()\n }\n } as Keyboard)),\n filter(({ mode, type }) => {\n if (mode === \"global\") {\n const active = getActiveElement()\n if (typeof active !== \"undefined\")\n return !isSusceptibleToKeyboard(active, type)\n }\n return true\n }),\n share()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Subject } from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve location\n *\n * This function returns a `URL` object (and not `Location`) to normalize the\n * typings across the application. Furthermore, locations need to be tracked\n * without setting them and `Location` is a singleton which represents the\n * current location.\n *\n * @returns URL\n */\nexport function getLocation(): URL {\n return new URL(location.href)\n}\n\n/**\n * Set location\n *\n * @param url - URL to change to\n */\nexport function setLocation(url: URL): void {\n location.href = url.href\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch location\n *\n * @returns Location subject\n */\nexport function watchLocation(): Subject {\n return new Subject()\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { JSX as JSXInternal } from \"preact\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * HTML attributes\n */\ntype Attributes =\n & JSXInternal.HTMLAttributes\n & JSXInternal.SVGAttributes\n & Record\n\n/**\n * Child element\n */\ntype Child =\n | HTMLElement\n | Text\n | string\n | number\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Append a child node to an element\n *\n * @param el - Element\n * @param child - Child node(s)\n */\nfunction appendChild(el: HTMLElement, child: Child | Child[]): void {\n\n /* Handle primitive types (including raw HTML) */\n if (typeof child === \"string\" || typeof child === \"number\") {\n el.innerHTML += child.toString()\n\n /* Handle nodes */\n } else if (child instanceof Node) {\n el.appendChild(child)\n\n /* Handle nested children */\n } else if (Array.isArray(child)) {\n for (const node of child)\n appendChild(el, node)\n }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * JSX factory\n *\n * @template T - Element type\n *\n * @param tag - HTML tag\n * @param attributes - HTML attributes\n * @param children - Child elements\n *\n * @returns Element\n */\nexport function h(\n tag: T, attributes?: Attributes | null, ...children: Child[]\n): HTMLElementTagNameMap[T]\n\nexport function h(\n tag: string, attributes?: Attributes | null, ...children: Child[]\n): T\n\nexport function h(\n tag: string, attributes?: Attributes | null, ...children: Child[]\n): T {\n const el = document.createElement(tag)\n\n /* Set attributes, if any */\n if (attributes)\n for (const attr of Object.keys(attributes)) {\n if (typeof attributes[attr] === \"undefined\")\n continue\n\n /* Set default attribute or boolean */\n if (typeof attributes[attr] !== \"boolean\")\n el.setAttribute(attr, attributes[attr])\n else\n el.setAttribute(attr, \"\")\n }\n\n /* Append child nodes */\n for (const child of children)\n appendChild(el, child)\n\n /* Return element */\n return el as T\n}\n\n/* ----------------------------------------------------------------------------\n * Namespace\n * ------------------------------------------------------------------------- */\n\nexport declare namespace h {\n namespace JSX {\n type Element = HTMLElement\n type IntrinsicElements = JSXInternal.IntrinsicElements\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Truncate a string after the given number of characters\n *\n * This is not a very reasonable approach, since the summaries kind of suck.\n * It would be better to create something more intelligent, highlighting the\n * search occurrences and making a better summary out of it, but this note was\n * written three years ago, so who knows if we'll ever fix it.\n *\n * @param value - Value to be truncated\n * @param n - Number of characters\n *\n * @returns Truncated value\n */\nexport function truncate(value: string, n: number): string {\n let i = n\n if (value.length > i) {\n while (value[i] !== \" \" && --i > 0) { /* keep eating */ }\n return `${value.substring(0, i)}...`\n }\n return value\n}\n\n/**\n * Round a number for display with repository facts\n *\n * This is a reverse-engineered version of GitHub's weird rounding algorithm\n * for stars, forks and all other numbers. While all numbers below `1,000` are\n * returned as-is, bigger numbers are converted to fixed numbers:\n *\n * - `1,049` => `1k`\n * - `1,050` => `1.1k`\n * - `1,949` => `1.9k`\n * - `1,950` => `2k`\n *\n * @param value - Original value\n *\n * @returns Rounded value\n */\nexport function round(value: number): string {\n if (value > 999) {\n const digits = +((value - 950) % 1000 > 99)\n return `${((value + 0.000001) / 1000).toFixed(digits)}k`\n } else {\n return value.toString()\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n filter,\n fromEvent,\n map,\n shareReplay,\n startWith\n} from \"rxjs\"\n\nimport { getOptionalElement } from \"~/browser\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve location hash\n *\n * @returns Location hash\n */\nexport function getLocationHash(): string {\n return location.hash.substring(1)\n}\n\n/**\n * Set location hash\n *\n * Setting a new fragment identifier via `location.hash` will have no effect\n * if the value doesn't change. When a new fragment identifier is set, we want\n * the browser to target the respective element at all times, which is why we\n * use this dirty little trick.\n *\n * @param hash - Location hash\n */\nexport function setLocationHash(hash: string): void {\n const el = h(\"a\", { href: hash })\n el.addEventListener(\"click\", ev => ev.stopPropagation())\n el.click()\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch location hash\n *\n * @returns Location hash observable\n */\nexport function watchLocationHash(): Observable {\n return fromEvent(window, \"hashchange\")\n .pipe(\n map(getLocationHash),\n startWith(getLocationHash()),\n filter(hash => hash.length > 0),\n shareReplay(1)\n )\n}\n\n/**\n * Watch location target\n *\n * @returns Location target observable\n */\nexport function watchLocationTarget(): Observable {\n return watchLocationHash()\n .pipe(\n map(id => getOptionalElement(`[id=\"${id}\"]`)!),\n filter(el => typeof el !== \"undefined\")\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n fromEvent,\n fromEventPattern,\n map,\n merge,\n startWith,\n switchMap\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch media query\n *\n * Note that although `MediaQueryList.addListener` is deprecated we have to\n * use it, because it's the only way to ensure proper downward compatibility.\n *\n * @see https://bit.ly/3dUBH2m - GitHub issue\n *\n * @param query - Media query\n *\n * @returns Media observable\n */\nexport function watchMedia(query: string): Observable {\n const media = matchMedia(query)\n return fromEventPattern(next => (\n media.addListener(() => next(media.matches))\n ))\n .pipe(\n startWith(media.matches)\n )\n}\n\n/**\n * Watch print mode\n *\n * @returns Print observable\n */\nexport function watchPrint(): Observable {\n const media = matchMedia(\"print\")\n return merge(\n fromEvent(window, \"beforeprint\").pipe(map(() => true)),\n fromEvent(window, \"afterprint\").pipe(map(() => false))\n )\n .pipe(\n startWith(media.matches)\n )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Toggle an observable with a media observable\n *\n * @template T - Data type\n *\n * @param query$ - Media observable\n * @param factory - Observable factory\n *\n * @returns Toggled observable\n */\nexport function at(\n query$: Observable, factory: () => Observable\n): Observable {\n return query$\n .pipe(\n switchMap(active => active ? factory() : EMPTY)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n catchError,\n from,\n map,\n of,\n shareReplay,\n switchMap,\n throwError\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch the given URL\n *\n * If the request fails (e.g. when dispatched from `file://` locations), the\n * observable will complete without emitting a value.\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Response observable\n */\nexport function request(\n url: URL | string, options: RequestInit = { credentials: \"same-origin\" }\n): Observable {\n return from(fetch(`${url}`, options))\n .pipe(\n catchError(() => EMPTY),\n switchMap(res => res.status !== 200\n ? throwError(() => new Error(res.statusText))\n : of(res)\n )\n )\n}\n\n/**\n * Fetch JSON from the given URL\n *\n * @template T - Data type\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function requestJSON(\n url: URL | string, options?: RequestInit\n): Observable {\n return request(url, options)\n .pipe(\n switchMap(res => res.json()),\n shareReplay(1)\n )\n}\n\n/**\n * Fetch XML from the given URL\n *\n * @param url - Request URL\n * @param options - Options\n *\n * @returns Data observable\n */\nexport function requestXML(\n url: URL | string, options?: RequestInit\n): Observable {\n const dom = new DOMParser()\n return request(url, options)\n .pipe(\n switchMap(res => res.text()),\n map(res => dom.parseFromString(res, \"text/xml\")),\n shareReplay(1)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n defer,\n finalize,\n fromEvent,\n map,\n merge,\n switchMap,\n take,\n throwError\n} from \"rxjs\"\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create and load a `script` element\n *\n * This function returns an observable that will emit when the script was\n * successfully loaded, or throw an error if it didn't.\n *\n * @param src - Script URL\n *\n * @returns Script observable\n */\nexport function watchScript(src: string): Observable {\n const script = h(\"script\", { src })\n return defer(() => {\n document.head.appendChild(script)\n return merge(\n fromEvent(script, \"load\"),\n fromEvent(script, \"error\")\n .pipe(\n switchMap(() => (\n throwError(() => new ReferenceError(`Invalid script: ${src}`))\n ))\n )\n )\n .pipe(\n map(() => undefined),\n finalize(() => document.head.removeChild(script)),\n take(1)\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n fromEvent,\n map,\n merge,\n startWith\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport offset\n */\nexport interface ViewportOffset {\n x: number /* Horizontal offset */\n y: number /* Vertical offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve viewport offset\n *\n * On iOS Safari, viewport offset can be negative due to overflow scrolling.\n * As this may induce strange behaviors downstream, we'll just limit it to 0.\n *\n * @returns Viewport offset\n */\nexport function getViewportOffset(): ViewportOffset {\n return {\n x: Math.max(0, scrollX),\n y: Math.max(0, scrollY)\n }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport offset\n *\n * @returns Viewport offset observable\n */\nexport function watchViewportOffset(): Observable {\n return merge(\n fromEvent(window, \"scroll\", { passive: true }),\n fromEvent(window, \"resize\", { passive: true })\n )\n .pipe(\n map(getViewportOffset),\n startWith(getViewportOffset())\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n fromEvent,\n map,\n startWith\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport size\n */\nexport interface ViewportSize {\n width: number /* Viewport width */\n height: number /* Viewport height */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve viewport size\n *\n * @returns Viewport size\n */\nexport function getViewportSize(): ViewportSize {\n return {\n width: innerWidth,\n height: innerHeight\n }\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport size\n *\n * @returns Viewport size observable\n */\nexport function watchViewportSize(): Observable {\n return fromEvent(window, \"resize\", { passive: true })\n .pipe(\n map(getViewportSize),\n startWith(getViewportSize())\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n combineLatest,\n map,\n shareReplay\n} from \"rxjs\"\n\nimport {\n ViewportOffset,\n watchViewportOffset\n} from \"../offset\"\nimport {\n ViewportSize,\n watchViewportSize\n} from \"../size\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Viewport\n */\nexport interface Viewport {\n offset: ViewportOffset /* Viewport offset */\n size: ViewportSize /* Viewport size */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport\n *\n * @returns Viewport observable\n */\nexport function watchViewport(): Observable {\n return combineLatest([\n watchViewportOffset(),\n watchViewportSize()\n ])\n .pipe(\n map(([offset, size]) => ({ offset, size })),\n shareReplay(1)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n combineLatest,\n distinctUntilKeyChanged,\n map\n} from \"rxjs\"\n\nimport { Header } from \"~/components\"\n\nimport { getElementOffset } from \"../../element\"\nimport { Viewport } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
/* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch viewport relative to element\n *\n * @param el - Element\n * @param options - Options\n *\n * @returns Viewport observable\n */\nexport function watchViewportAt(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n const size$ = viewport$\n .pipe(\n distinctUntilKeyChanged(\"size\")\n )\n\n /* Compute element offset */\n const offset$ = combineLatest([size$, header$])\n .pipe(\n map(() => getElementOffset(el))\n )\n\n /* Compute relative viewport, return hot observable */\n return combineLatest([header$, viewport$, offset$])\n .pipe(\n map(([{ height }, { offset, size }, { x, y }]) => ({\n offset: {\n x: offset.x - x,\n y: offset.y - y + height\n },\n size\n }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n fromEvent,\n map,\n share,\n switchMap,\n tap,\n throttle\n} from \"rxjs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Worker message\n */\nexport interface WorkerMessage {\n type: unknown /* Message type */\n data?: unknown /* Message data */\n}\n\n/**\n * Worker handler\n *\n * @template T - Message type\n */\nexport interface WorkerHandler<\n T extends WorkerMessage\n> {\n tx$: Subject /* Message transmission subject */\n rx$: Observable /* Message receive observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n *\n * @template T - Worker message type\n */\ninterface WatchOptions {\n tx$: Observable /* Message transmission observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch a web worker\n *\n * This function returns an observable that sends all values emitted by the\n * message observable to the web worker. Web worker communication is expected\n * to be bidirectional (request-response) and synchronous. Messages that are\n * emitted during a pending request are throttled, the last one is emitted.\n *\n * @param worker - Web worker\n * @param options - Options\n *\n * @returns Worker message observable\n */\nexport function watchWorker(\n worker: Worker, { tx$ }: WatchOptions\n): Observable {\n\n /* Intercept messages from worker-like objects */\n const rx$ = fromEvent(worker, \"message\")\n .pipe(\n map(({ data }) => data as T)\n )\n\n /* Send and receive messages, return hot observable */\n return tx$\n .pipe(\n throttle(() => rx$, { leading: true, trailing: true }),\n tap(message => worker.postMessage(message)),\n switchMap(() => rx$),\n share()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { getElement, getLocation } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Feature flag\n */\nexport type Flag =\n | \"content.code.annotate\" /* Code annotations */\n | \"content.tabs.link\" /* Link content tabs */\n | \"header.autohide\" /* Hide header */\n | \"navigation.expand\" /* Automatic expansion */\n | \"navigation.indexes\" /* Section pages */\n | \"navigation.instant\" /* Instant loading */\n | \"navigation.sections\" /* Section navigation */\n | \"navigation.tabs\" /* Tabs navigation */\n | \"navigation.tabs.sticky\" /* Tabs navigation (sticky) */\n | \"navigation.top\" /* Back-to-top button */\n | \"navigation.tracking\" /* Anchor tracking */\n | \"search.highlight\" /* Search highlighting */\n | \"search.share\" /* Search sharing */\n | \"search.suggest\" /* Search suggestions */\n | \"toc.integrate\" /* Integrated table of contents */\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Translation\n */\nexport type Translation =\n | \"clipboard.copy\" /* Copy to clipboard */\n | \"clipboard.copied\" /* Copied to clipboard */\n | \"search.config.lang\" /* Search language */\n | \"search.config.pipeline\" /* Search pipeline */\n | \"search.config.separator\" /* Search separator */\n | \"search.placeholder\" /* Search */\n | \"search.result.placeholder\" /* Type to start searching */\n | \"search.result.none\" /* No matching documents */\n | \"search.result.one\" /* 1 matching document */\n | \"search.result.other\" /* # matching documents */\n | \"search.result.more.one\" /* 1 more on this page */\n | \"search.result.more.other\" /* # more on this page */\n | \"search.result.term.missing\" /* Missing */\n | \"select.version.title\" /* Version selector */\n\n/**\n * Translations\n */\nexport type Translations = Record\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Versioning\n */\nexport interface Versioning {\n provider: \"mike\" /* Version provider */\n default?: string /* Default version */\n}\n\n/**\n * Configuration\n */\nexport interface Config {\n base: string /* Base URL */\n features: Flag[] /* Feature flags */\n translations: Translations /* Translations */\n search: string /* Search worker URL */\n version?: Versioning /* Versioning */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve global configuration and make base URL absolute\n */\nconst script = getElement(\"#__config\")\nconst config: Config = JSON.parse(script.textContent!)\nconfig.base = `${new URL(config.base, getLocation())}`\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve global configuration\n *\n * @returns Global configuration\n */\nexport function configuration(): Config {\n return config\n}\n\n/**\n * Check whether a feature flag is enabled\n *\n * @param flag - Feature flag\n *\n * @returns Test result\n */\nexport function feature(flag: Flag): boolean {\n return config.features.includes(flag)\n}\n\n/**\n * Retrieve the translation for the given key\n *\n * @param key - Key to be translated\n * @param value - Positional value, if any\n *\n * @returns Translation\n */\nexport function translation(\n key: Translation, value?: string | number\n): string {\n return typeof value !== \"undefined\"\n ? config.translations[key].replace(\"#\", value.toString())\n : config.translations[key]\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { getElement, getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Component type\n */\nexport type ComponentType =\n | \"announce\" /* Announcement bar */\n | \"container\" /* Container */\n | \"content\" /* Content */\n | \"dialog\" /* Dialog */\n | \"header\" /* Header */\n | \"header-title\" /* Header title */\n | \"header-topic\" /* Header topic */\n | \"main\" /* Main area */\n | \"outdated\" /* Version warning */\n | \"palette\" /* Color palette */\n | \"search\" /* Search */\n | \"search-query\" /* Search input */\n | \"search-result\" /* Search results */\n | \"search-share\" /* Search sharing */\n | \"search-suggest\" /* Search suggestions */\n | \"sidebar\" /* Sidebar */\n | \"skip\" /* Skip link */\n | \"source\" /* Repository information */\n | \"tabs\" /* Navigation tabs */\n | \"toc\" /* Table of contents */\n | \"top\" /* Back-to-top button */\n\n/**\n * Component\n *\n * @template T - Component type\n * @template U - Reference type\n */\nexport type Component<\n T extends {} = {},\n U extends HTMLElement = HTMLElement\n> =\n T & {\n ref: U /* Component reference */\n }\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Component type map\n */\ninterface ComponentTypeMap {\n \"announce\": HTMLElement /* Announcement bar */\n \"container\": HTMLElement /* Container */\n \"content\": HTMLElement /* Content */\n \"dialog\": HTMLElement /* Dialog */\n \"header\": HTMLElement /* Header */\n \"header-title\": HTMLElement /* Header title */\n \"header-topic\": HTMLElement /* Header topic */\n \"main\": HTMLElement /* Main area */\n \"outdated\": HTMLElement /* Version warning */\n \"palette\": HTMLElement /* Color palette */\n \"search\": HTMLElement /* Search */\n \"search-query\": HTMLInputElement /* Search input */\n \"search-result\": HTMLElement /* Search results */\n \"search-share\": HTMLAnchorElement /* Search sharing */\n \"search-suggest\": HTMLElement /* Search suggestions */\n \"sidebar\": HTMLElement /* Sidebar */\n \"skip\": HTMLAnchorElement /* Skip link */\n \"source\": HTMLAnchorElement /* Repository information */\n \"tabs\": HTMLElement /* Navigation tabs */\n \"toc\": HTMLElement /* Table of contents */\n \"top\": HTMLAnchorElement /* Back-to-top button */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Retrieve the element for a given component or throw a reference error\n *\n * @template T - Component type\n *\n * @param type - Component type\n * @param node - Node of reference\n *\n * @returns Element\n */\nexport function getComponentElement(\n type: T, node: ParentNode = document\n): ComponentTypeMap[T] {\n return getElement(`[data-md-component=${type}]`, node)\n}\n\n/**\n * Retrieve all elements for a given component\n *\n * @template T - Component type\n *\n * @param type - Component type\n * @param node - Node of reference\n *\n * @returns Elements\n */\nexport function getComponentElements(\n type: T, node: ParentNode = document\n): ComponentTypeMap[T][] {\n return getElements(`[data-md-component=${type}]`, node)\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ClipboardJS from \"clipboard\"\nimport {\n EMPTY,\n Observable,\n Subject,\n defer,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n finalize,\n map,\n mergeWith,\n switchMap,\n take,\n takeLast,\n takeUntil,\n tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n getElementContentSize,\n watchElementSize,\n watchElementVisibility\n} from \"~/browser\"\nimport { renderClipboardButton } from \"~/templates\"\n\nimport { Component } from \"../../../_\"\nimport {\n Annotation,\n mountAnnotationList\n} from \"../../annotation\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Code block\n */\nexport interface CodeBlock {\n scrollable: boolean /* Code block overflows */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n print$: Observable /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Global sequence number for Clipboard.js integration\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Find candidate list element directly following a code block\n *\n * @param el - Code block element\n *\n * @returns List element or nothing\n */\nfunction findCandidateList(el: HTMLElement): HTMLElement | undefined {\n if (el.nextElementSibling) {\n const sibling = el.nextElementSibling as HTMLElement\n if (sibling.tagName === \"OL\")\n return sibling\n\n /* Skip empty paragraphs - see https://bit.ly/3r4ZJ2O */\n else if (sibling.tagName === \"P\" && !sibling.children.length)\n return findCandidateList(sibling)\n }\n\n /* Everything else */\n return undefined\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch code block\n *\n * This function monitors size changes of the viewport, as well as switches of\n * content tabs with embedded code blocks, as both may trigger overflow.\n *\n * @param el - Code block element\n *\n * @returns Code block observable\n */\nexport function watchCodeBlock(\n el: HTMLElement\n): Observable {\n return watchElementSize(el)\n .pipe(\n map(({ width }) => {\n const content = getElementContentSize(el)\n return {\n scrollable: content.width > width\n }\n }),\n distinctUntilKeyChanged(\"scrollable\")\n )\n}\n\n/**\n * Mount code block\n *\n * This function ensures that an overflowing code block is focusable through\n * keyboard, so it can be scrolled without a mouse to improve on accessibility.\n * Furthermore, if code annotations are enabled, they are mounted if and only\n * if the code block is currently visible, e.g., not in a hidden content tab.\n *\n * @param el - Code block element\n * @param options - Options\n *\n * @returns Code block and annotation component observable\n */\nexport function mountCodeBlock(\n el: HTMLElement, options: MountOptions\n): Observable> {\n const { matches: hover } = matchMedia(\"(hover)\")\n\n /* Defer mounting of code block - see https://bit.ly/3vHVoVD */\n const factory$ = defer(() => {\n const push$ = new Subject()\n push$.subscribe(({ scrollable }) => {\n if (scrollable && hover)\n el.setAttribute(\"tabindex\", \"0\")\n else\n el.removeAttribute(\"tabindex\")\n })\n\n /* Render button for Clipboard.js integration */\n if (ClipboardJS.isSupported()) {\n const parent = el.closest(\"pre\")!\n parent.id = `__code_${++sequence}`\n parent.insertBefore(\n renderClipboardButton(parent.id),\n el\n )\n }\n\n /* Handle code annotations */\n const container = el.closest(\".highlight\")\n if (container instanceof HTMLElement) {\n const list = findCandidateList(container)\n\n /* Mount code annotations, if enabled */\n if (typeof list !== \"undefined\" && (\n container.classList.contains(\"annotate\") ||\n feature(\"content.code.annotate\")\n )) {\n const annotations$ = mountAnnotationList(list, el, options)\n\n /* Create and return component */\n return watchCodeBlock(el)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state })),\n mergeWith(\n watchElementSize(container)\n .pipe(\n takeUntil(push$.pipe(takeLast(1))),\n map(({ width, height }) => width && height),\n distinctUntilChanged(),\n switchMap(active => active ? annotations$ : EMPTY)\n )\n )\n )\n }\n }\n\n /* Create and return component */\n return watchCodeBlock(el)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n\n /* Mount code block on first sight */\n return watchElementVisibility(el)\n .pipe(\n filter(visible => visible),\n take(1),\n switchMap(() => factory$)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render an empty annotation\n *\n * @param id - Annotation identifier\n *\n * @returns Element\n */\nexport function renderAnnotation(id: number): HTMLElement {\n return (\n \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { translation } from \"~/_\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a 'copy-to-clipboard' button\n *\n * @param id - Unique identifier\n *\n * @returns Element\n */\nexport function renderClipboardButton(id: string): HTMLElement {\n return (\n code`}\n >\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ComponentChild } from \"preact\"\n\nimport { feature, translation } from \"~/_\"\nimport {\n SearchDocument,\n SearchMetadata,\n SearchResultItem\n} from \"~/integrations/search\"\nimport { h, truncate } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Render flag\n */\nconst enum Flag {\n TEASER = 1, /* Render teaser */\n PARENT = 2 /* Render as parent */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper function\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a search document\n *\n * @param document - Search document\n * @param flag - Render flags\n *\n * @returns Element\n */\nfunction renderSearchDocument(\n document: SearchDocument & SearchMetadata, flag: Flag\n): HTMLElement {\n const parent = flag & Flag.PARENT\n const teaser = flag & Flag.TEASER\n\n /* Render missing query terms */\n const missing = Object.keys(document.terms)\n .filter(key => !document.terms[key])\n .reduce((list, key) => [\n ...list, {key}, \" \"\n ], [])\n .slice(0, -1)\n\n /* Assemble query string for highlighting */\n const url = new URL(document.location)\n if (feature(\"search.highlight\"))\n url.searchParams.set(\"h\", Object.entries(document.terms)\n .filter(([, match]) => match)\n .reduce((highlight, [value]) => `${highlight} ${value}`.trim(), \"\")\n )\n\n /* Render article or section, depending on flags */\n return (\n \n \n {parent > 0 &&
}\n

{document.title}

\n {teaser > 0 && document.text.length > 0 &&\n

\n {truncate(document.text, 320)}\n

\n }\n {document.tags && document.tags.map(tag => (\n {tag}\n ))}\n {teaser > 0 && missing.length > 0 &&\n

\n {translation(\"search.result.term.missing\")}: {...missing}\n

\n }\n \n \n )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a search result\n *\n * @param result - Search result\n *\n * @returns Element\n */\nexport function renderSearchResultItem(\n result: SearchResultItem\n): HTMLElement {\n const threshold = result[0].score\n const docs = [...result]\n\n /* Find and extract parent article */\n const parent = docs.findIndex(doc => !doc.location.includes(\"#\"))\n const [article] = docs.splice(parent, 1)\n\n /* Determine last index above threshold */\n let index = docs.findIndex(doc => doc.score < threshold)\n if (index === -1)\n index = docs.length\n\n /* Partition sections */\n const best = docs.slice(0, index)\n const more = docs.slice(index)\n\n /* Render children */\n const children = [\n renderSearchDocument(article, Flag.PARENT | +(!parent && index === 0)),\n ...best.map(section => renderSearchDocument(section, Flag.TEASER)),\n ...more.length ? [\n
\n \n {more.length > 0 && more.length === 1\n ? translation(\"search.result.more.one\")\n : translation(\"search.result.more.other\", more.length)\n }\n \n {...more.map(section => renderSearchDocument(section, Flag.TEASER))}\n
\n ] : []\n ]\n\n /* Render search result */\n return (\n
  • \n {children}\n
    • \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { SourceFacts } from \"~/components\"\nimport { h, round } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render repository facts\n *\n * @param facts - Repository facts\n *\n * @returns Element\n */\nexport function renderSourceFacts(facts: SourceFacts): HTMLElement {\n return (\n
      \n {Object.entries(facts).map(([key, value]) => (\n
    • \n {typeof value === \"number\" ? round(value) : value}\n
      • \n ))}\n
    \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Tabbed control type\n */\ntype TabbedControlType =\n | \"prev\"\n | \"next\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render control for content tabs\n *\n * @param type - Control type\n *\n * @returns Element\n */\nexport function renderTabbedControl(\n type: TabbedControlType\n): HTMLElement {\n const classes = `tabbed-control tabbed-control--${type}`\n return (\n \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a table inside a wrapper to improve scrolling on mobile\n *\n * @param table - Table element\n *\n * @returns Element\n */\nexport function renderTable(table: HTMLElement): HTMLElement {\n return (\n
    \n
    \n {table}\n
    \n
    \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { configuration, translation } from \"~/_\"\nimport { h } from \"~/utilities\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Version\n */\nexport interface Version {\n version: string /* Version identifier */\n title: string /* Version title */\n aliases: string[] /* Version aliases */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a version\n *\n * @param version - Version\n *\n * @returns Element\n */\nfunction renderVersion(version: Version): HTMLElement {\n const config = configuration()\n\n /* Ensure trailing slash, see https://bit.ly/3rL5u3f */\n const url = new URL(`../${version.version}/`, config.base)\n return (\n
  • \n \n {version.title}\n \n
    • \n )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Render a version selector\n *\n * @param versions - Versions\n * @param active - Active version\n *\n * @returns Element\n */\nexport function renderVersionSelector(\n versions: Version[], active: Version\n): HTMLElement {\n return (\n
    \n \n {active.title}\n \n
      \n {versions.map(renderVersion)}\n
    \n
    \n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n Subject,\n animationFrameScheduler,\n combineLatest,\n defer,\n finalize,\n fromEvent,\n map,\n switchMap,\n take,\n takeLast,\n takeUntil,\n tap,\n throttleTime\n} from \"rxjs\"\n\nimport {\n ElementOffset,\n getElement,\n getElementSize,\n watchElementContentOffset,\n watchElementFocus,\n watchElementOffset,\n watchElementVisibility\n} from \"~/browser\"\n\nimport { Component } from \"../../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Annotation\n */\nexport interface Annotation {\n active: boolean /* Annotation is active */\n offset: ElementOffset /* Annotation offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch annotation\n *\n * @param el - Annotation element\n * @param container - Containing element\n *\n * @returns Annotation observable\n */\nexport function watchAnnotation(\n el: HTMLElement, container: HTMLElement\n): Observable {\n const offset$ = defer(() => combineLatest([\n watchElementOffset(el),\n watchElementContentOffset(container)\n ]))\n .pipe(\n map(([{ x, y }, scroll]) => {\n const { width } = getElementSize(el)\n return ({\n x: x - scroll.x + width / 2,\n y: y - scroll.y\n })\n })\n )\n\n /* Actively watch annotation on focus */\n return watchElementFocus(el)\n .pipe(\n switchMap(active => offset$\n .pipe(\n map(offset => ({ active, offset })),\n take(+!active || Infinity)\n )\n )\n )\n}\n\n/**\n * Mount annotation\n *\n * @param el - Annotation element\n * @param container - Containing element\n *\n * @returns Annotation component observable\n */\nexport function mountAnnotation(\n el: HTMLElement, container: HTMLElement\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe({\n\n /* Handle emission */\n next({ offset }) {\n el.style.setProperty(\"--md-tooltip-x\", `${offset.x}px`)\n el.style.setProperty(\"--md-tooltip-y\", `${offset.y}px`)\n },\n\n /* Handle complete */\n complete() {\n el.style.removeProperty(\"--md-tooltip-x\")\n el.style.removeProperty(\"--md-tooltip-y\")\n }\n })\n\n /* Start animation only when annotation is visible */\n const done$ = push$.pipe(takeLast(1))\n watchElementVisibility(el)\n .pipe(\n takeUntil(done$)\n )\n .subscribe(visible => {\n el.toggleAttribute(\"data-md-visible\", visible)\n })\n\n /* Track relative origin of tooltip */\n push$\n .pipe(\n throttleTime(500, animationFrameScheduler),\n map(() => container.getBoundingClientRect()),\n map(({ x }) => x)\n )\n .subscribe({\n\n /* Handle emission */\n next(origin) {\n if (origin)\n el.style.setProperty(\"--md-tooltip-0\", `${-origin}px`)\n else\n el.style.removeProperty(\"--md-tooltip-0\")\n },\n\n /* Handle complete */\n complete() {\n el.style.removeProperty(\"--md-tooltip-0\")\n }\n })\n\n /* Close open annotation on click */\n const index = getElement(\":scope > :last-child\", el)\n const blur$ = fromEvent(index, \"mousedown\", { once: true })\n push$\n .pipe(\n switchMap(({ active }) => active ? blur$ : EMPTY),\n tap(ev => ev.preventDefault())\n )\n .subscribe(() => el.blur())\n\n /* Create and return component */\n return watchAnnotation(el, container)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n Subject,\n defer,\n finalize,\n merge,\n share,\n takeLast,\n takeUntil\n} from \"rxjs\"\n\nimport {\n getElement,\n getElements,\n getOptionalElement\n} from \"~/browser\"\nimport { renderAnnotation } from \"~/templates\"\n\nimport { Component } from \"../../../_\"\nimport {\n Annotation,\n mountAnnotation\n} from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n print$: Observable /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Find all annotation markers in the given code block\n *\n * @param container - Containing element\n *\n * @returns Annotation markers\n */\nfunction findAnnotationMarkers(container: HTMLElement): Text[] {\n const markers: Text[] = []\n for (const comment of getElements(\".c, .c1, .cm\", container)) {\n let match: RegExpExecArray | null\n\n /* Split text at marker and add to list */\n let text = comment.firstChild as Text\n if (text instanceof Text)\n while ((match = /\\((\\d+)\\)/.exec(text.textContent!))) {\n const marker = text.splitText(match.index)\n text = marker.splitText(match[0].length)\n markers.push(marker)\n }\n }\n return markers\n}\n\n/**\n * Swap the child nodes of two elements\n *\n * @param source - Source element\n * @param target - Target element\n */\nfunction swap(source: HTMLElement, target: HTMLElement): void {\n target.append(...Array.from(source.childNodes))\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount annotation list\n *\n * This function analyzes the containing code block and checks for markers\n * referring to elements in the given annotation list. If no markers are found,\n * the list is left untouched. Otherwise, list elements are rendered as\n * annotations inside the code block.\n *\n * @param el - Annotation list element\n * @param container - Containing element\n * @param options - Options\n *\n * @returns Annotation component observable\n */\nexport function mountAnnotationList(\n el: HTMLElement, container: HTMLElement, { print$ }: MountOptions\n): Observable> {\n\n /* Find and replace all markers with empty annotations */\n const annotations = new Map()\n for (const marker of findAnnotationMarkers(container)) {\n const [, id] = marker.textContent!.match(/\\((\\d+)\\)/)!\n if (getOptionalElement(`li:nth-child(${id})`, el)) {\n annotations.set(+id, renderAnnotation(+id))\n marker.replaceWith(annotations.get(+id)!)\n }\n }\n\n /* Keep list if there are no annotations to render */\n if (annotations.size === 0)\n return EMPTY\n\n /* Create and return component */\n return defer(() => {\n const done$ = new Subject()\n\n /* Handle print mode - see https://bit.ly/3rgPdpt */\n print$\n .pipe(\n takeUntil(done$.pipe(takeLast(1)))\n )\n .subscribe(active => {\n el.hidden = !active\n\n /* Show annotations in code block or list (print) */\n for (const [id, annotation] of annotations) {\n const inner = getElement(\".md-typeset\", annotation)\n const child = getElement(`li:nth-child(${id})`, el)\n if (!active)\n swap(child, inner)\n else\n swap(inner, child)\n }\n })\n\n /* Create and return component */\n return merge(...[...annotations]\n .map(([, annotation]) => (\n mountAnnotation(annotation, container)\n ))\n )\n .pipe(\n finalize(() => done$.complete()),\n share()\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n map,\n of,\n shareReplay,\n tap\n} from \"rxjs\"\n\nimport { watchScript } from \"~/browser\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../../_\"\n\nimport themeCSS from \"./index.css\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mermaid diagram\n */\nexport interface Mermaid {}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Mermaid instance observable\n */\nlet mermaid$: Observable\n\n/**\n * Global sequence number for diagrams\n */\nlet sequence = 0\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch Mermaid script\n *\n * @returns Mermaid scripts observable\n */\nfunction fetchScripts(): Observable {\n return typeof mermaid === \"undefined\" || mermaid instanceof Element\n ? watchScript(\"https://unpkg.com/mermaid@9.0.1/dist/mermaid.min.js\")\n : of(undefined)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount Mermaid diagram\n *\n * @param el - Code block element\n *\n * @returns Mermaid diagram component observable\n */\nexport function mountMermaid(\n el: HTMLElement\n): Observable> {\n el.classList.remove(\"mermaid\") // Hack: mitigate https://bit.ly/3CiN6Du\n mermaid$ ||= fetchScripts()\n .pipe(\n tap(() => mermaid.initialize({\n startOnLoad: false,\n themeCSS\n })),\n map(() => undefined),\n shareReplay(1)\n )\n\n /* Render diagram */\n mermaid$.subscribe(() => {\n el.classList.add(\"mermaid\") // Hack: mitigate https://bit.ly/3CiN6Du\n const id = `__mermaid_${sequence++}`\n const host = h(\"div\", { class: \"mermaid\" })\n mermaid.mermaidAPI.render(id, el.textContent, (svg: string) => {\n\n /* Create a shadow root and inject diagram */\n const shadow = host.attachShadow({ mode: \"closed\" })\n shadow.innerHTML = svg\n\n /* Replace code block with diagram */\n el.replaceWith(host)\n })\n })\n\n /* Create and return component */\n return mermaid$\n .pipe(\n map(() => ({ ref: el }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n defer,\n filter,\n finalize,\n map,\n merge,\n tap\n} from \"rxjs\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Details\n */\nexport interface Details {\n action: \"open\" | \"close\" /* Details state */\n reveal?: boolean /* Details is revealed */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n target$: Observable /* Location target observable */\n print$: Observable /* Media print observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n target$: Observable /* Location target observable */\n print$: Observable /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch details\n *\n * @param el - Details element\n * @param options - Options\n *\n * @returns Details observable\n */\nexport function watchDetails(\n el: HTMLDetailsElement, { target$, print$ }: WatchOptions\n): Observable
    {\n let open = true\n return merge(\n\n /* Open and focus details on location target */\n target$\n .pipe(\n map(target => target.closest(\"details:not([open])\")!),\n filter(details => el === details),\n map(() => ({\n action: \"open\", reveal: true\n }) as Details)\n ),\n\n /* Open details on print and close afterwards */\n print$\n .pipe(\n filter(active => active || !open),\n tap(() => open = el.open),\n map(active => ({\n action: active ? \"open\" : \"close\"\n }) as Details)\n )\n )\n}\n\n/**\n * Mount details\n *\n * This function ensures that `details` tags are opened on anchor jumps and\n * prior to printing, so the whole content of the page is visible.\n *\n * @param el - Details element\n * @param options - Options\n *\n * @returns Details component observable\n */\nexport function mountDetails(\n el: HTMLDetailsElement, options: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject
    ()\n push$.subscribe(({ action, reveal }) => {\n if (action === \"open\")\n el.setAttribute(\"open\", \"\")\n else\n el.removeAttribute(\"open\")\n if (reveal)\n el.scrollIntoView()\n })\n\n /* Create and return component */\n return watchDetails(el, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Observable, of } from \"rxjs\"\n\nimport { renderTable } from \"~/templates\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Data table\n */\nexport interface DataTable {}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Sentinel for replacement\n */\nconst sentinel = h(\"table\")\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount data table\n *\n * This function wraps a data table in another scrollable container, so it can\n * be smoothly scrolled on smaller screen sizes and won't break the layout.\n *\n * @param el - Data table element\n *\n * @returns Data table component observable\n */\nexport function mountDataTable(\n el: HTMLElement\n): Observable> {\n el.replaceWith(sentinel)\n sentinel.replaceWith(renderTable(el))\n\n /* Create and return component */\n return of({ ref: el })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n animationFrameScheduler,\n asyncScheduler,\n auditTime,\n combineLatest,\n defer,\n finalize,\n fromEvent,\n map,\n merge,\n skip,\n startWith,\n subscribeOn,\n takeLast,\n takeUntil,\n tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n getElement,\n getElementContentOffset,\n getElementContentSize,\n getElementOffset,\n getElementSize,\n getElements,\n watchElementContentOffset,\n watchElementSize\n} from \"~/browser\"\nimport { renderTabbedControl } from \"~/templates\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Content tabs\n */\nexport interface ContentTabs {\n active: HTMLLabelElement /* Active tab label */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch content tabs\n *\n * @param el - Content tabs element\n *\n * @returns Content tabs observable\n */\nexport function watchContentTabs(\n el: HTMLElement\n): Observable {\n const inputs = getElements(\":scope > input\", el)\n const initial = inputs.find(input => input.checked) || inputs[0]\n return merge(...inputs.map(input => fromEvent(input, \"change\")\n .pipe(\n map(() => getElement(`label[for=\"${input.id}\"]`))\n )\n ))\n .pipe(\n startWith(getElement(`label[for=\"${initial.id}\"]`)),\n map(active => ({ active }))\n )\n}\n\n/**\n * Mount content tabs\n *\n * This function scrolls the active tab into view. While this functionality is\n * provided by browsers as part of `scrollInfoView`, browsers will always also\n * scroll the vertical axis, which we do not want. Thus, we decided to provide\n * this functionality ourselves.\n *\n * @param el - Content tabs element\n *\n * @returns Content tabs component observable\n */\nexport function mountContentTabs(\n el: HTMLElement\n): Observable> {\n\n /* Render content tab previous button for pagination */\n const prev = renderTabbedControl(\"prev\")\n el.append(prev)\n\n /* Render content tab next button for pagination */\n const next = renderTabbedControl(\"next\")\n el.append(next)\n\n /* Mount component on subscription */\n const container = getElement(\".tabbed-labels\", el)\n return defer(() => {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n combineLatest([push$, watchElementSize(el)])\n .pipe(\n auditTime(1, animationFrameScheduler),\n takeUntil(done$)\n )\n .subscribe({\n\n /* Handle emission */\n next([{ active }, size]) {\n const offset = getElementOffset(active)\n const { width } = getElementSize(active)\n\n /* Set tab indicator offset and width */\n el.style.setProperty(\"--md-indicator-x\", `${offset.x}px`)\n el.style.setProperty(\"--md-indicator-width\", `${width}px`)\n\n /* Scroll container to active content tab */\n const content = getElementContentOffset(container)\n if (\n offset.x < content.x ||\n offset.x + width > content.x + size.width\n )\n container.scrollTo({\n left: Math.max(0, offset.x - 16),\n behavior: \"smooth\"\n })\n },\n\n /* Handle complete */\n complete() {\n el.style.removeProperty(\"--md-indicator-x\")\n el.style.removeProperty(\"--md-indicator-width\")\n }\n })\n\n /* Hide content tab buttons on borders */\n combineLatest([\n watchElementContentOffset(container),\n watchElementSize(container)\n ])\n .pipe(\n takeUntil(done$)\n )\n .subscribe(([offset, size]) => {\n const content = getElementContentSize(container)\n prev.hidden = offset.x < 16\n next.hidden = offset.x > content.width - size.width - 16\n })\n\n /* Paginate content tab container on click */\n merge(\n fromEvent(prev, \"click\").pipe(map(() => -1)),\n fromEvent(next, \"click\").pipe(map(() => +1))\n )\n .pipe(\n takeUntil(done$)\n )\n .subscribe(direction => {\n const { width } = getElementSize(container)\n container.scrollBy({\n left: width * direction,\n behavior: \"smooth\"\n })\n })\n\n /* Set up linking of content tabs, if enabled */\n if (feature(\"content.tabs.link\"))\n push$.pipe(skip(1))\n .subscribe(({ active }) => {\n const tab = active.innerText.trim()\n for (const set of getElements(\"[data-tabs]\"))\n for (const input of getElements(\n \":scope > input\", set\n )) {\n const label = getElement(`label[for=\"${input.id}\"]`)\n if (label.innerText.trim() === tab) {\n input.click()\n break\n }\n }\n\n /* Persist active tabs in local storage */\n const tabs = __md_get(\"__tabs\") || []\n __md_set(\"__tabs\", [...new Set([tab, ...tabs])])\n })\n\n /* Create and return component */\n return watchContentTabs(el)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n .pipe(\n subscribeOn(asyncScheduler)\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Observable, merge } from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Annotation } from \"../annotation\"\nimport {\n CodeBlock,\n Mermaid,\n mountCodeBlock,\n mountMermaid\n} from \"../code\"\nimport {\n Details,\n mountDetails\n} from \"../details\"\nimport {\n DataTable,\n mountDataTable\n} from \"../table\"\nimport {\n ContentTabs,\n mountContentTabs\n} from \"../tabs\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Content\n */\nexport type Content =\n | Annotation\n | ContentTabs\n | CodeBlock\n | Mermaid\n | DataTable\n | Details\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n target$: Observable /* Location target observable */\n print$: Observable /* Media print observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount content\n *\n * This function mounts all components that are found in the content of the\n * actual article, including code blocks, data tables and details.\n *\n * @param el - Content element\n * @param options - Options\n *\n * @returns Content component observable\n */\nexport function mountContent(\n el: HTMLElement, { target$, print$ }: MountOptions\n): Observable> {\n return merge(\n\n /* Code blocks */\n ...getElements(\"pre:not(.mermaid) > code\", el)\n .map(child => mountCodeBlock(child, { print$ })),\n\n /* Mermaid diagrams */\n ...getElements(\"pre.mermaid\", el)\n .map(child => mountMermaid(child)),\n\n /* Data tables */\n ...getElements(\"table:not([class])\", el)\n .map(child => mountDataTable(child)),\n\n /* Details */\n ...getElements(\"details\", el)\n .map(child => mountDetails(child, { target$, print$ })),\n\n /* Content tabs */\n ...getElements(\"[data-tabs]\", el)\n .map(child => mountContentTabs(child))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n defer,\n delay,\n finalize,\n map,\n merge,\n of,\n switchMap,\n tap\n} from \"rxjs\"\n\nimport { getElement } from \"~/browser\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Dialog\n */\nexport interface Dialog {\n message: string /* Dialog message */\n active: boolean /* Dialog is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n alert$: Subject /* Alert subject */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n alert$: Subject /* Alert subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch dialog\n *\n * @param _el - Dialog element\n * @param options - Options\n *\n * @returns Dialog observable\n */\nexport function watchDialog(\n _el: HTMLElement, { alert$ }: WatchOptions\n): Observable {\n return alert$\n .pipe(\n switchMap(message => merge(\n of(true),\n of(false).pipe(delay(2000))\n )\n .pipe(\n map(active => ({ message, active }))\n )\n )\n )\n}\n\n/**\n * Mount dialog\n *\n * This function reveals the dialog in the right corner when a new alert is\n * emitted through the subject that is passed as part of the options.\n *\n * @param el - Dialog element\n * @param options - Options\n *\n * @returns Dialog component observable\n */\nexport function mountDialog(\n el: HTMLElement, options: MountOptions\n): Observable> {\n const inner = getElement(\".md-typeset\", el)\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(({ message, active }) => {\n el.classList.toggle(\"md-dialog--active\", active)\n inner.textContent = message\n })\n\n /* Create and return component */\n return watchDialog(el, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n combineLatest,\n combineLatestWith,\n defer,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n map,\n of,\n shareReplay,\n startWith,\n switchMap,\n takeLast,\n takeUntil\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n Viewport,\n watchElementSize,\n watchToggle\n} from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Main } from \"../../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Header\n */\nexport interface Header {\n height: number /* Header visible height */\n hidden: boolean /* Header is hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n main$: Observable
    /* Main area observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Compute whether the header is hidden\n *\n * If the user scrolls past a certain threshold, the header can be hidden when\n * scrolling down, and shown when scrolling up.\n *\n * @param options - Options\n *\n * @returns Toggle observable\n */\nfunction isHidden({ viewport$ }: WatchOptions): Observable {\n if (!feature(\"header.autohide\"))\n return of(false)\n\n /* Compute direction and turning point */\n const direction$ = viewport$\n .pipe(\n map(({ offset: { y } }) => y),\n bufferCount(2, 1),\n map(([a, b]) => [a < b, b] as const),\n distinctUntilKeyChanged(0)\n )\n\n /* Compute whether header should be hidden */\n const hidden$ = combineLatest([viewport$, direction$])\n .pipe(\n filter(([{ offset }, [, y]]) => Math.abs(y - offset.y) > 100),\n map(([, [direction]]) => direction),\n distinctUntilChanged()\n )\n\n /* Compute threshold for hiding */\n const search$ = watchToggle(\"search\")\n return combineLatest([viewport$, search$])\n .pipe(\n map(([{ offset }, search]) => offset.y > 400 && !search),\n distinctUntilChanged(),\n switchMap(active => active ? hidden$ : of(false)),\n startWith(false)\n )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch header\n *\n * @param el - Header element\n * @param options - Options\n *\n * @returns Header observable\n */\nexport function watchHeader(\n el: HTMLElement, options: WatchOptions\n): Observable
    {\n return defer(() => combineLatest([\n watchElementSize(el),\n isHidden(options)\n ]))\n .pipe(\n map(([{ height }, hidden]) => ({\n height,\n hidden\n })),\n distinctUntilChanged((a, b) => (\n a.height === b.height &&\n a.hidden === b.hidden\n )),\n shareReplay(1)\n )\n}\n\n/**\n * Mount header\n *\n * This function manages the different states of the header, i.e. whether it's\n * hidden or rendered with a shadow. This depends heavily on the main area.\n *\n * @param el - Header element\n * @param options - Options\n *\n * @returns Header component observable\n */\nexport function mountHeader(\n el: HTMLElement, { header$, main$ }: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject
    ()\n const done$ = push$.pipe(takeLast(1))\n push$\n .pipe(\n distinctUntilKeyChanged(\"active\"),\n combineLatestWith(header$)\n )\n .subscribe(([{ active }, { hidden }]) => {\n el.classList.toggle(\"md-header--shadow\", active && !hidden)\n el.hidden = hidden\n })\n\n /* Link to main area */\n main$.subscribe(push$)\n\n /* Create and return component */\n return header$\n .pipe(\n takeUntil(done$),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n Subject,\n defer,\n distinctUntilKeyChanged,\n finalize,\n map,\n tap\n} from \"rxjs\"\n\nimport {\n Viewport,\n getElementSize,\n getOptionalElement,\n watchViewportAt\n} from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { Header } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Header\n */\nexport interface HeaderTitle {\n active: boolean /* Header title is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch header title\n *\n * @param el - Heading element\n * @param options - Options\n *\n * @returns Header title observable\n */\nexport function watchHeaderTitle(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n return watchViewportAt(el, { viewport$, header$ })\n .pipe(\n map(({ offset: { y } }) => {\n const { height } = getElementSize(el)\n return {\n active: y >= height\n }\n }),\n distinctUntilKeyChanged(\"active\")\n )\n}\n\n/**\n * Mount header title\n *\n * This function swaps the header title from the site title to the title of the\n * current page when the user scrolls past the first headline.\n *\n * @param el - Header title element\n * @param options - Options\n *\n * @returns Header title component observable\n */\nexport function mountHeaderTitle(\n el: HTMLElement, options: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(({ active }) => {\n el.classList.toggle(\"md-header__title--active\", active)\n })\n\n /* Obtain headline, if any */\n const heading = getOptionalElement(\"article h1\")\n if (typeof heading === \"undefined\")\n return EMPTY\n\n /* Create and return component */\n return watchHeaderTitle(heading, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n combineLatest,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n map,\n switchMap\n} from \"rxjs\"\n\nimport {\n Viewport,\n watchElementSize\n} from \"~/browser\"\n\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Main area\n */\nexport interface Main {\n offset: number /* Main area top offset */\n height: number /* Main area visible height */\n active: boolean /* Main area is active */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch main area\n *\n * This function returns an observable that computes the visual parameters of\n * the main area which depends on the viewport vertical offset and height, as\n * well as the height of the header element, if the header is fixed.\n *\n * @param el - Main area element\n * @param options - Options\n *\n * @returns Main area observable\n */\nexport function watchMain(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable
    {\n\n /* Compute necessary adjustment for header */\n const adjust$ = header$\n .pipe(\n map(({ height }) => height),\n distinctUntilChanged()\n )\n\n /* Compute the main area's top and bottom borders */\n const border$ = adjust$\n .pipe(\n switchMap(() => watchElementSize(el)\n .pipe(\n map(({ height }) => ({\n top: el.offsetTop,\n bottom: el.offsetTop + height\n })),\n distinctUntilKeyChanged(\"bottom\")\n )\n )\n )\n\n /* Compute the main area's offset, visible height and if we scrolled past */\n return combineLatest([adjust$, border$, viewport$])\n .pipe(\n map(([header, { top, bottom }, { offset: { y }, size: { height } }]) => {\n height = Math.max(0, height\n - Math.max(0, top - y, header)\n - Math.max(0, height + y - bottom)\n )\n return {\n offset: top - header,\n height,\n active: top - header <= y\n }\n }),\n distinctUntilChanged((a, b) => (\n a.offset === b.offset &&\n a.height === b.height &&\n a.active === b.active\n ))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n asyncScheduler,\n defer,\n finalize,\n fromEvent,\n map,\n mergeMap,\n observeOn,\n of,\n shareReplay,\n startWith,\n tap\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\nimport { Component } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Palette colors\n */\nexport interface PaletteColor {\n scheme?: string /* Color scheme */\n primary?: string /* Primary color */\n accent?: string /* Accent color */\n}\n\n/**\n * Palette\n */\nexport interface Palette {\n index: number /* Palette index */\n color: PaletteColor /* Palette colors */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch color palette\n *\n * @param inputs - Color palette element\n *\n * @returns Color palette observable\n */\nexport function watchPalette(\n inputs: HTMLInputElement[]\n): Observable {\n const current = __md_get(\"__palette\") || {\n index: inputs.findIndex(input => matchMedia(\n input.getAttribute(\"data-md-color-media\")!\n ).matches)\n }\n\n /* Emit changes in color palette */\n return of(...inputs)\n .pipe(\n mergeMap(input => fromEvent(input, \"change\")\n .pipe(\n map(() => input)\n )\n ),\n startWith(inputs[Math.max(0, current.index)]),\n map(input => ({\n index: inputs.indexOf(input),\n color: {\n scheme: input.getAttribute(\"data-md-color-scheme\"),\n primary: input.getAttribute(\"data-md-color-primary\"),\n accent: input.getAttribute(\"data-md-color-accent\")\n }\n } as Palette)),\n shareReplay(1)\n )\n}\n\n/**\n * Mount color palette\n *\n * @param el - Color palette element\n *\n * @returns Color palette component observable\n */\nexport function mountPalette(\n el: HTMLElement\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(palette => {\n document.body.setAttribute(\"data-md-color-switching\", \"\")\n\n /* Set color palette */\n for (const [key, value] of Object.entries(palette.color))\n document.body.setAttribute(`data-md-color-${key}`, value)\n\n /* Toggle visibility */\n for (let index = 0; index < inputs.length; index++) {\n const label = inputs[index].nextElementSibling\n if (label instanceof HTMLElement)\n label.hidden = palette.index !== index\n }\n\n /* Persist preference in local storage */\n __md_set(\"__palette\", palette)\n })\n\n /* Revert transition durations after color switch */\n push$.pipe(observeOn(asyncScheduler))\n .subscribe(() => {\n document.body.removeAttribute(\"data-md-color-switching\")\n })\n\n /* Create and return component */\n const inputs = getElements(\"input\", el)\n return watchPalette(inputs)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport ClipboardJS from \"clipboard\"\nimport {\n Observable,\n Subject,\n map,\n tap\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport { getElement } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n alert$: Subject /* Alert subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Extract text to copy\n *\n * @param el - HTML element\n *\n * @returns Extracted text\n */\nfunction extract(el: HTMLElement): string {\n el.setAttribute(\"data-md-copying\", \"\")\n const text = el.innerText\n el.removeAttribute(\"data-md-copying\")\n return text\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up Clipboard.js integration\n *\n * @param options - Options\n */\nexport function setupClipboardJS(\n { alert$ }: SetupOptions\n): void {\n if (ClipboardJS.isSupported()) {\n new Observable(subscriber => {\n new ClipboardJS(\"[data-clipboard-target], [data-clipboard-text]\", {\n text: el => (\n el.getAttribute(\"data-clipboard-text\")! ||\n extract(getElement(\n el.getAttribute(\"data-clipboard-target\")!\n ))\n )\n })\n .on(\"success\", ev => subscriber.next(ev))\n })\n .pipe(\n tap(ev => {\n const trigger = ev.trigger as HTMLElement\n trigger.focus()\n }),\n map(() => translation(\"clipboard.copied\"))\n )\n .subscribe(alert$)\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n catchError,\n defaultIfEmpty,\n map,\n of,\n tap\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport { getElements, requestXML } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Sitemap, i.e. a list of URLs\n */\nexport type Sitemap = string[]\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Preprocess a list of URLs\n *\n * This function replaces the `site_url` in the sitemap with the actual base\n * URL, to allow instant loading to work in occasions like Netlify previews.\n *\n * @param urls - URLs\n *\n * @returns URL path parts\n */\nfunction preprocess(urls: Sitemap): Sitemap {\n if (urls.length < 2)\n return [\"\"]\n\n /* Take the first two URLs and remove everything after the last slash */\n const [root, next] = [...urls]\n .sort((a, b) => a.length - b.length)\n .map(url => url.replace(/[^/]+$/, \"\"))\n\n /* Compute common prefix */\n let index = 0\n if (root === next)\n index = root.length\n else\n while (root.charCodeAt(index) === next.charCodeAt(index))\n index++\n\n /* Remove common prefix and return in original order */\n return urls.map(url => url.replace(root.slice(0, index), \"\"))\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch the sitemap for the given base URL\n *\n * @param base - Base URL\n *\n * @returns Sitemap observable\n */\nexport function fetchSitemap(base?: URL): Observable {\n const cached = __md_get(\"__sitemap\", sessionStorage, base)\n if (cached) {\n return of(cached)\n } else {\n const config = configuration()\n return requestXML(new URL(\"sitemap.xml\", base || config.base))\n .pipe(\n map(sitemap => preprocess(getElements(\"loc\", sitemap)\n .map(node => node.textContent!)\n )),\n catchError(() => EMPTY), // @todo refactor instant loading\n defaultIfEmpty([]),\n tap(sitemap => __md_set(\"__sitemap\", sitemap, sessionStorage, base))\n )\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n NEVER,\n Observable,\n Subject,\n bufferCount,\n catchError,\n concatMap,\n debounceTime,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n fromEvent,\n map,\n merge,\n of,\n sample,\n share,\n skip,\n skipUntil,\n switchMap\n} from \"rxjs\"\n\nimport { configuration, feature } from \"~/_\"\nimport {\n Viewport,\n ViewportOffset,\n getElements,\n getOptionalElement,\n request,\n setLocation,\n setLocationHash\n} from \"~/browser\"\nimport { getComponentElement } from \"~/components\"\nimport { h } from \"~/utilities\"\n\nimport { fetchSitemap } from \"../sitemap\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * History state\n */\nexport interface HistoryState {\n url: URL /* State URL */\n offset?: ViewportOffset /* State viewport offset */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n document$: Subject /* Document subject */\n location$: Subject /* Location subject */\n viewport$: Observable /* Viewport observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up instant loading\n *\n * When fetching, theoretically, we could use `responseType: \"document\"`, but\n * since all MkDocs links are relative, we need to make sure that the current\n * location matches the document we just loaded. Otherwise any relative links\n * in the document could use the old location.\n *\n * This is the reason why we need to synchronize history events and the process\n * of fetching the document for navigation changes (except `popstate` events):\n *\n * 1. Fetch document via `XMLHTTPRequest`\n * 2. Set new location via `history.pushState`\n * 3. Parse and emit fetched document\n *\n * For `popstate` events, we must not use `history.pushState`, or the forward\n * history will be irreversibly overwritten. In case the request fails, the\n * location change is dispatched regularly.\n *\n * @param options - Options\n */\nexport function setupInstantLoading(\n { document$, location$, viewport$ }: SetupOptions\n): void {\n const config = configuration()\n if (location.protocol === \"file:\")\n return\n\n /* Disable automatic scroll restoration */\n if (\"scrollRestoration\" in history) {\n history.scrollRestoration = \"manual\"\n\n /* Hack: ensure that reloads restore viewport offset */\n fromEvent(window, \"beforeunload\")\n .subscribe(() => {\n history.scrollRestoration = \"auto\"\n })\n }\n\n /* Hack: ensure absolute favicon link to omit 404s when switching */\n const favicon = getOptionalElement(\"link[rel=icon]\")\n if (typeof favicon !== \"undefined\")\n favicon.href = favicon.href\n\n /* Intercept internal navigation */\n const push$ = fetchSitemap()\n .pipe(\n map(paths => paths.map(path => `${new URL(path, config.base)}`)),\n switchMap(urls => fromEvent(document.body, \"click\")\n .pipe(\n filter(ev => !ev.metaKey && !ev.ctrlKey),\n switchMap(ev => {\n if (ev.target instanceof Element) {\n const el = ev.target.closest(\"a\")\n if (el && !el.target) {\n const url = new URL(el.href)\n\n /* Canonicalize URL */\n url.search = \"\"\n url.hash = \"\"\n\n /* Check if URL should be intercepted */\n if (\n url.pathname !== location.pathname &&\n urls.includes(url.toString())\n ) {\n ev.preventDefault()\n return of({\n url: new URL(el.href)\n })\n }\n }\n }\n return NEVER\n })\n )\n ),\n share()\n )\n\n /* Intercept history back and forward */\n const pop$ = fromEvent(window, \"popstate\")\n .pipe(\n filter(ev => ev.state !== null),\n map(ev => ({\n url: new URL(location.href),\n offset: ev.state\n })),\n share()\n )\n\n /* Emit location change */\n merge(push$, pop$)\n .pipe(\n distinctUntilChanged((a, b) => a.url.href === b.url.href),\n map(({ url }) => url)\n )\n .subscribe(location$)\n\n /* Fetch document via `XMLHTTPRequest` */\n const response$ = location$\n .pipe(\n distinctUntilKeyChanged(\"pathname\"),\n switchMap(url => request(url.href)\n .pipe(\n catchError(() => {\n setLocation(url)\n return NEVER\n })\n )\n ),\n share()\n )\n\n /* Set new location via `history.pushState` */\n push$\n .pipe(\n sample(response$)\n )\n .subscribe(({ url }) => {\n history.pushState({}, \"\", `${url}`)\n })\n\n /* Parse and emit fetched document */\n const dom = new DOMParser()\n response$\n .pipe(\n switchMap(res => res.text()),\n map(res => dom.parseFromString(res, \"text/html\"))\n )\n .subscribe(document$)\n\n /* Replace meta tags and components */\n document$\n .pipe(\n skip(1)\n )\n .subscribe(replacement => {\n for (const selector of [\n\n /* Meta tags */\n \"title\",\n \"link[rel=canonical]\",\n \"meta[name=author]\",\n \"meta[name=description]\",\n\n /* Components */\n \"[data-md-component=announce]\",\n \"[data-md-component=container]\",\n \"[data-md-component=header-topic]\",\n \"[data-md-component=outdated]\",\n \"[data-md-component=logo]\",\n \"[data-md-component=skip]\",\n ...feature(\"navigation.tabs.sticky\")\n ? [\"[data-md-component=tabs]\"]\n : []\n ]) {\n const source = getOptionalElement(selector)\n const target = getOptionalElement(selector, replacement)\n if (\n typeof source !== \"undefined\" &&\n typeof target !== \"undefined\"\n ) {\n source.replaceWith(target)\n }\n }\n })\n\n /* Re-evaluate scripts */\n document$\n .pipe(\n skip(1),\n map(() => getComponentElement(\"container\")),\n switchMap(el => getElements(\"script\", el)),\n concatMap(el => {\n const script = h(\"script\")\n if (el.src) {\n for (const name of el.getAttributeNames())\n script.setAttribute(name, el.getAttribute(name)!)\n el.replaceWith(script)\n\n /* Complete when script is loaded */\n return new Observable(observer => {\n script.onload = () => observer.complete()\n })\n\n /* Complete immediately */\n } else {\n script.textContent = el.textContent\n el.replaceWith(script)\n return EMPTY\n }\n })\n )\n .subscribe()\n\n /* Emit history state change */\n merge(push$, pop$)\n .pipe(\n sample(document$)\n )\n .subscribe(({ url, offset }) => {\n if (url.hash && !offset) {\n setLocationHash(url.hash)\n } else {\n window.scrollTo(0, offset?.y || 0)\n }\n })\n\n /* Debounce update of viewport offset */\n viewport$\n .pipe(\n skipUntil(push$),\n debounceTime(250),\n distinctUntilKeyChanged(\"offset\")\n )\n .subscribe(({ offset }) => {\n history.replaceState(offset, \"\")\n })\n\n /* Set viewport offset from history */\n merge(push$, pop$)\n .pipe(\n bufferCount(2, 1),\n filter(([a, b]) => a.url.pathname === b.url.pathname),\n map(([, state]) => state)\n )\n .subscribe(({ offset }) => {\n window.scrollTo(0, offset?.y || 0)\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexDocument } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search document\n */\nexport interface SearchDocument extends SearchIndexDocument {\n parent?: SearchIndexDocument /* Parent article */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search document mapping\n */\nexport type SearchDocumentMap = Map\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search document mapping\n *\n * @param docs - Search index documents\n *\n * @returns Search document map\n */\nexport function setupSearchDocumentMap(\n docs: SearchIndexDocument[]\n): SearchDocumentMap {\n const documents = new Map()\n const parents = new Set()\n for (const doc of docs) {\n const [path, hash] = doc.location.split(\"#\")\n\n /* Extract location, title and tags */\n const location = doc.location\n const title = doc.title\n const tags = doc.tags\n\n /* Escape and cleanup text */\n const text = escapeHTML(doc.text)\n .replace(/\\s+(?=[,.:;!?])/g, \"\")\n .replace(/\\s+/g, \" \")\n\n /* Handle section */\n if (hash) {\n const parent = documents.get(path)!\n\n /* Ignore first section, override article */\n if (!parents.has(parent)) {\n parent.title = doc.title\n parent.text = text\n\n /* Remember that we processed the article */\n parents.add(parent)\n\n /* Add subsequent section */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n parent\n })\n }\n\n /* Add article */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n ...tags && { tags }\n })\n }\n }\n return documents\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexConfig } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlight function\n *\n * @param value - Value\n *\n * @returns Highlighted value\n */\nexport type SearchHighlightFn = (value: string) => string\n\n/**\n * Search highlight factory function\n *\n * @param query - Query value\n *\n * @returns Search highlight function\n */\nexport type SearchHighlightFactoryFn = (query: string) => SearchHighlightFn\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search highlighter\n *\n * @param config - Search index configuration\n * @param escape - Whether to escape HTML\n *\n * @returns Search highlight factory function\n */\nexport function setupSearchHighlighter(\n config: SearchIndexConfig, escape: boolean\n): SearchHighlightFactoryFn {\n const separator = new RegExp(config.separator, \"img\")\n const highlight = (_: unknown, data: string, term: string) => {\n return `${data}${term}`\n }\n\n /* Return factory function */\n return (query: string) => {\n query = query\n .replace(/[\\s*+\\-:~^]+/g, \" \")\n .trim()\n\n /* Create search term match expression */\n const match = new RegExp(`(^|${config.separator})(${\n query\n .replace(/[|\\\\{}()[\\]^$+*?.-]/g, \"\\\\$&\")\n .replace(separator, \"|\")\n })`, \"img\")\n\n /* Highlight string value */\n return value => (\n escape\n ? escapeHTML(value)\n : value\n )\n .replace(match, highlight)\n .replace(/<\\/mark>(\\s+)]*>/img, \"$1\")\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search transformation function\n *\n * @param value - Query value\n *\n * @returns Transformed query value\n */\nexport type SearchTransformFn = (value: string) => string\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Default transformation function\n *\n * 1. Search for terms in quotation marks and prepend a `+` modifier to denote\n * that the resulting document must contain all terms, converting the query\n * to an `AND` query (as opposed to the default `OR` behavior). While users\n * may expect terms enclosed in quotation marks to map to span queries, i.e.\n * for which order is important, Lunr.js doesn't support them, so the best\n * we can do is to convert the terms to an `AND` query.\n *\n * 2. Replace control characters which are not located at the beginning of the\n * query or preceded by white space, or are not followed by a non-whitespace\n * character or are at the end of the query string. Furthermore, filter\n * unmatched quotation marks.\n *\n * 3. Trim excess whitespace from left and right.\n *\n * @param query - Query value\n *\n * @returns Transformed query value\n */\nexport function defaultTransform(query: string): string {\n return query\n .split(/\"([^\"]+)\"/g) /* => 1 */\n .map((terms, index) => index & 1\n ? terms.replace(/^\\b|^(?![^\\x00-\\x7F]|$)|\\s+/g, \" +\")\n : terms\n )\n .join(\"\")\n .replace(/\"|(?:^|\\s+)[*+\\-:^~]+(?=\\s+|$)/g, \"\") /* => 2 */\n .trim() /* => 3 */\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { SearchIndex, SearchResult } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search message type\n */\nexport const enum SearchMessageType {\n SETUP, /* Search index setup */\n READY, /* Search index ready */\n QUERY, /* Search query */\n RESULT /* Search results */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Message containing the data necessary to setup the search index\n */\nexport interface SearchSetupMessage {\n type: SearchMessageType.SETUP /* Message type */\n data: SearchIndex /* Message data */\n}\n\n/**\n * Message indicating the search index is ready\n */\nexport interface SearchReadyMessage {\n type: SearchMessageType.READY /* Message type */\n}\n\n/**\n * Message containing a search query\n */\nexport interface SearchQueryMessage {\n type: SearchMessageType.QUERY /* Message type */\n data: string /* Message data */\n}\n\n/**\n * Message containing results for a search query\n */\nexport interface SearchResultMessage {\n type: SearchMessageType.RESULT /* Message type */\n data: SearchResult /* Message data */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Message exchanged with the search worker\n */\nexport type SearchMessage =\n | SearchSetupMessage\n | SearchReadyMessage\n | SearchQueryMessage\n | SearchResultMessage\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Type guard for search setup messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchSetupMessage(\n message: SearchMessage\n): message is SearchSetupMessage {\n return message.type === SearchMessageType.SETUP\n}\n\n/**\n * Type guard for search ready messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchReadyMessage(\n message: SearchMessage\n): message is SearchReadyMessage {\n return message.type === SearchMessageType.READY\n}\n\n/**\n * Type guard for search query messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchQueryMessage(\n message: SearchMessage\n): message is SearchQueryMessage {\n return message.type === SearchMessageType.QUERY\n}\n\n/**\n * Type guard for search result messages\n *\n * @param message - Search worker message\n *\n * @returns Test result\n */\nexport function isSearchResultMessage(\n message: SearchMessage\n): message is SearchResultMessage {\n return message.type === SearchMessageType.RESULT\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n ObservableInput,\n Subject,\n from,\n map,\n share\n} from \"rxjs\"\n\nimport { configuration, feature, translation } from \"~/_\"\nimport { WorkerHandler, watchWorker } from \"~/browser\"\n\nimport { SearchIndex } from \"../../_\"\nimport {\n SearchOptions,\n SearchPipeline\n} from \"../../options\"\nimport {\n SearchMessage,\n SearchMessageType,\n SearchSetupMessage,\n isSearchResultMessage\n} from \"../message\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search worker\n */\nexport type SearchWorker = WorkerHandler\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up search index\n *\n * @param data - Search index\n *\n * @returns Search index\n */\nfunction setupSearchIndex({ config, docs }: SearchIndex): SearchIndex {\n\n /* Override default language with value from translation */\n if (config.lang.length === 1 && config.lang[0] === \"en\")\n config.lang = [\n translation(\"search.config.lang\")\n ]\n\n /* Override default separator with value from translation */\n if (config.separator === \"[\\\\s\\\\-]+\")\n config.separator = translation(\"search.config.separator\")\n\n /* Set pipeline from translation */\n const pipeline = translation(\"search.config.pipeline\")\n .split(/\\s*,\\s*/)\n .filter(Boolean) as SearchPipeline\n\n /* Determine search options */\n const options: SearchOptions = {\n pipeline,\n suggestions: feature(\"search.suggest\")\n }\n\n /* Return search index after defaulting */\n return { config, docs, options }\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up search worker\n *\n * This function creates a web worker to set up and query the search index,\n * which is done using Lunr.js. The index must be passed as an observable to\n * enable hacks like _localsearch_ via search index embedding as JSON.\n *\n * @param url - Worker URL\n * @param index - Search index observable input\n *\n * @returns Search worker\n */\nexport function setupSearchWorker(\n url: string, index: ObservableInput\n): SearchWorker {\n const config = configuration()\n const worker = new Worker(url)\n\n /* Create communication channels and resolve relative links */\n const tx$ = new Subject()\n const rx$ = watchWorker(worker, { tx$ })\n .pipe(\n map(message => {\n if (isSearchResultMessage(message)) {\n for (const result of message.data.items)\n for (const document of result)\n document.location = `${new URL(document.location, config.base)}`\n }\n return message\n }),\n share()\n )\n\n /* Set up search index */\n from(index)\n .pipe(\n map(data => ({\n type: SearchMessageType.SETUP,\n data: setupSearchIndex(data)\n } as SearchSetupMessage))\n )\n .subscribe(tx$.next.bind(tx$))\n\n /* Return search worker */\n return { tx$, rx$ }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Subject,\n catchError,\n combineLatest,\n filter,\n fromEvent,\n map,\n of,\n switchMap,\n withLatestFrom\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n getElement,\n getLocation,\n requestJSON,\n setLocation\n} from \"~/browser\"\nimport { getComponentElements } from \"~/components\"\nimport {\n Version,\n renderVersionSelector\n} from \"~/templates\"\n\nimport { fetchSitemap } from \"../sitemap\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Setup options\n */\ninterface SetupOptions {\n document$: Subject /* Document subject */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Set up version selector\n *\n * @param options - Options\n */\nexport function setupVersionSelector(\n { document$ }: SetupOptions\n): void {\n const config = configuration()\n const versions$ = requestJSON(\n new URL(\"../versions.json\", config.base)\n )\n .pipe(\n catchError(() => EMPTY) // @todo refactor instant loading\n )\n\n /* Determine current version */\n const current$ = versions$\n .pipe(\n map(versions => {\n const [, current] = config.base.match(/([^/]+)\\/?$/)!\n return versions.find(({ version, aliases }) => (\n version === current || aliases.includes(current)\n )) || versions[0]\n })\n )\n\n /* Intercept inter-version navigation */\n versions$\n .pipe(\n map(versions => new Map(versions.map(version => [\n `${new URL(`../${version.version}/`, config.base)}`,\n version\n ]))),\n switchMap(urls => fromEvent(document.body, \"click\")\n .pipe(\n filter(ev => !ev.metaKey && !ev.ctrlKey),\n withLatestFrom(current$),\n switchMap(([ev, current]) => {\n if (ev.target instanceof Element) {\n const el = ev.target.closest(\"a\")\n if (el && !el.target && urls.has(el.href)) {\n const url = el.href\n // This is a temporary hack to detect if a version inside the\n // version selector or on another part of the site was clicked.\n // If we're inside the version selector, we definitely want to\n // find the same page, as we might have different deployments\n // due to aliases. However, if we're outside the version\n // selector, we must abort here, because we might otherwise\n // interfere with instant loading. We need to refactor this\n // at some point together with instant loading.\n //\n // See https://github.com/squidfunk/mkdocs-material/issues/4012\n if (!ev.target.closest(\".md-version\")) {\n const version = urls.get(url)!\n if (version === current)\n return EMPTY\n }\n ev.preventDefault()\n return of(url)\n }\n }\n return EMPTY\n }),\n switchMap(url => {\n const { version } = urls.get(url)!\n return fetchSitemap(new URL(url))\n .pipe(\n map(sitemap => {\n const location = getLocation()\n const path = location.href.replace(config.base, \"\")\n return sitemap.includes(path)\n ? new URL(`../${version}/${path}`, config.base)\n : new URL(url)\n })\n )\n })\n )\n )\n )\n .subscribe(url => setLocation(url))\n\n /* Render version selector and warning */\n combineLatest([versions$, current$])\n .subscribe(([versions, current]) => {\n const topic = getElement(\".md-header__topic\")\n topic.appendChild(renderVersionSelector(versions, current))\n })\n\n /* Integrate outdated version banner with instant loading */\n document$.pipe(switchMap(() => current$))\n .subscribe(current => {\n\n /* Check if version state was already determined */\n let outdated = __md_get(\"__outdated\", sessionStorage)\n if (outdated === null) {\n const latest = config.version?.default || \"latest\"\n outdated = !current.aliases.includes(latest)\n\n /* Persist version state in session storage */\n __md_set(\"__outdated\", outdated, sessionStorage)\n }\n\n /* Unhide outdated version banner */\n if (outdated)\n for (const warning of getComponentElements(\"outdated\"))\n warning.hidden = false\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n combineLatest,\n delay,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n filter,\n finalize,\n fromEvent,\n map,\n merge,\n share,\n shareReplay,\n startWith,\n take,\n takeLast,\n takeUntil,\n tap\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport {\n getLocation,\n setToggle,\n watchElementFocus,\n watchToggle\n} from \"~/browser\"\nimport {\n SearchMessageType,\n SearchQueryMessage,\n SearchWorker,\n defaultTransform,\n isSearchReadyMessage\n} from \"~/integrations\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search query\n */\nexport interface SearchQuery {\n value: string /* Query value */\n focus: boolean /* Query focus */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch search query\n *\n * Note that the focus event which triggers re-reading the current query value\n * is delayed by `1ms` so the input's empty state is allowed to propagate.\n *\n * @param el - Search query element\n * @param worker - Search worker\n *\n * @returns Search query observable\n */\nexport function watchSearchQuery(\n el: HTMLInputElement, { rx$ }: SearchWorker\n): Observable {\n const fn = __search?.transform || defaultTransform\n\n /* Immediately show search dialog */\n const { searchParams } = getLocation()\n if (searchParams.has(\"q\"))\n setToggle(\"search\", true)\n\n /* Intercept query parameter (deep link) */\n const param$ = rx$\n .pipe(\n filter(isSearchReadyMessage),\n take(1),\n map(() => searchParams.get(\"q\") || \"\")\n )\n\n /* Remove query parameter when search is closed */\n watchToggle(\"search\")\n .pipe(\n filter(active => !active),\n take(1)\n )\n .subscribe(() => {\n const url = new URL(location.href)\n url.searchParams.delete(\"q\")\n history.replaceState({}, \"\", `${url}`)\n })\n\n /* Set query from parameter */\n param$.subscribe(value => { // TODO: not ideal - find a better way\n if (value) {\n el.value = value\n el.focus()\n }\n })\n\n /* Intercept focus and input events */\n const focus$ = watchElementFocus(el)\n const value$ = merge(\n fromEvent(el, \"keyup\"),\n fromEvent(el, \"focus\").pipe(delay(1)),\n param$\n )\n .pipe(\n map(() => fn(el.value)),\n startWith(\"\"),\n distinctUntilChanged(),\n )\n\n /* Combine into single observable */\n return combineLatest([value$, focus$])\n .pipe(\n map(([value, focus]) => ({ value, focus })),\n shareReplay(1)\n )\n}\n\n/**\n * Mount search query\n *\n * @param el - Search query element\n * @param worker - Search worker\n *\n * @returns Search query component observable\n */\nexport function mountSearchQuery(\n el: HTMLInputElement, { tx$, rx$ }: SearchWorker\n): Observable> {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n\n /* Handle value changes */\n push$\n .pipe(\n distinctUntilKeyChanged(\"value\"),\n map(({ value }): SearchQueryMessage => ({\n type: SearchMessageType.QUERY,\n data: value\n }))\n )\n .subscribe(tx$.next.bind(tx$))\n\n /* Handle focus changes */\n push$\n .pipe(\n distinctUntilKeyChanged(\"focus\")\n )\n .subscribe(({ focus }) => {\n if (focus) {\n setToggle(\"search\", focus)\n el.placeholder = \"\"\n } else {\n el.placeholder = translation(\"search.placeholder\")\n }\n })\n\n /* Handle reset */\n fromEvent(el.form!, \"reset\")\n .pipe(\n takeUntil(done$)\n )\n .subscribe(() => el.focus())\n\n /* Create and return component */\n return watchSearchQuery(el, { tx$, rx$ })\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state })),\n share()\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n filter,\n finalize,\n map,\n merge,\n of,\n skipUntil,\n switchMap,\n take,\n tap,\n withLatestFrom,\n zipWith\n} from \"rxjs\"\n\nimport { translation } from \"~/_\"\nimport {\n getElement,\n watchElementBoundary\n} from \"~/browser\"\nimport {\n SearchResult,\n SearchWorker,\n isSearchReadyMessage,\n isSearchResultMessage\n} from \"~/integrations\"\nimport { renderSearchResultItem } from \"~/templates\"\nimport { round } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\nimport { SearchQuery } from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n query$: Observable /* Search query observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search result list\n *\n * This function performs a lazy rendering of the search results, depending on\n * the vertical offset of the search result container.\n *\n * @param el - Search result list element\n * @param worker - Search worker\n * @param options - Options\n *\n * @returns Search result list component observable\n */\nexport function mountSearchResult(\n el: HTMLElement, { rx$ }: SearchWorker, { query$ }: MountOptions\n): Observable> {\n const push$ = new Subject()\n const boundary$ = watchElementBoundary(el.parentElement!)\n .pipe(\n filter(Boolean)\n )\n\n /* Retrieve nested components */\n const meta = getElement(\":scope > :first-child\", el)\n const list = getElement(\":scope > :last-child\", el)\n\n /* Wait until search is ready */\n const ready$ = rx$\n .pipe(\n filter(isSearchReadyMessage),\n take(1)\n )\n\n /* Update search result metadata */\n push$\n .pipe(\n withLatestFrom(query$),\n skipUntil(ready$)\n )\n .subscribe(([{ items }, { value }]) => {\n if (value) {\n switch (items.length) {\n\n /* No results */\n case 0:\n meta.textContent = translation(\"search.result.none\")\n break\n\n /* One result */\n case 1:\n meta.textContent = translation(\"search.result.one\")\n break\n\n /* Multiple result */\n default:\n meta.textContent = translation(\n \"search.result.other\",\n round(items.length)\n )\n }\n } else {\n meta.textContent = translation(\"search.result.placeholder\")\n }\n })\n\n /* Update search result list */\n push$\n .pipe(\n tap(() => list.innerHTML = \"\"),\n switchMap(({ items }) => merge(\n of(...items.slice(0, 10)),\n of(...items.slice(10))\n .pipe(\n bufferCount(4),\n zipWith(boundary$),\n switchMap(([chunk]) => chunk)\n )\n ))\n )\n .subscribe(result => list.appendChild(\n renderSearchResultItem(result)\n ))\n\n /* Filter search result message */\n const result$ = rx$\n .pipe(\n filter(isSearchResultMessage),\n map(({ data }) => data)\n )\n\n /* Create and return component */\n return result$\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n finalize,\n fromEvent,\n map,\n tap\n} from \"rxjs\"\n\nimport { getLocation } from \"~/browser\"\n\nimport { Component } from \"../../_\"\nimport { SearchQuery } from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search sharing\n */\nexport interface SearchShare {\n url: URL /* Deep link for sharing */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n query$: Observable /* Search query observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n query$: Observable /* Search query observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search sharing\n *\n * @param _el - Search sharing element\n * @param options - Options\n *\n * @returns Search sharing observable\n */\nexport function watchSearchShare(\n _el: HTMLElement, { query$ }: WatchOptions\n): Observable {\n return query$\n .pipe(\n map(({ value }) => {\n const url = getLocation()\n url.hash = \"\"\n url.searchParams.delete(\"h\")\n url.searchParams.set(\"q\", value)\n return { url }\n })\n )\n}\n\n/**\n * Mount search sharing\n *\n * @param el - Search sharing element\n * @param options - Options\n *\n * @returns Search sharing component observable\n */\nexport function mountSearchShare(\n el: HTMLAnchorElement, options: MountOptions\n): Observable> {\n const push$ = new Subject()\n push$.subscribe(({ url }) => {\n el.setAttribute(\"data-clipboard-text\", el.href)\n el.href = `${url}`\n })\n\n /* Prevent following of link */\n fromEvent(el, \"click\")\n .subscribe(ev => ev.preventDefault())\n\n /* Create and return component */\n return watchSearchShare(el, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n asyncScheduler,\n combineLatestWith,\n distinctUntilChanged,\n filter,\n finalize,\n fromEvent,\n map,\n merge,\n observeOn,\n tap\n} from \"rxjs\"\n\nimport { Keyboard } from \"~/browser\"\nimport {\n SearchResult,\n SearchWorker,\n isSearchResultMessage\n} from \"~/integrations\"\n\nimport { Component, getComponentElement } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search suggestions\n */\nexport interface SearchSuggest {}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n keyboard$: Observable /* Keyboard observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search suggestions\n *\n * This function will perform a lazy rendering of the search results, depending\n * on the vertical offset of the search result container.\n *\n * @param el - Search result list element\n * @param worker - Search worker\n * @param options - Options\n *\n * @returns Search result list component observable\n */\nexport function mountSearchSuggest(\n el: HTMLElement, { rx$ }: SearchWorker, { keyboard$ }: MountOptions\n): Observable> {\n const push$ = new Subject()\n\n /* Retrieve query component and track all changes */\n const query = getComponentElement(\"search-query\")\n const query$ = merge(\n fromEvent(query, \"keydown\"),\n fromEvent(query, \"focus\")\n )\n .pipe(\n observeOn(asyncScheduler),\n map(() => query.value),\n distinctUntilChanged(),\n )\n\n /* Update search suggestions */\n push$\n .pipe(\n combineLatestWith(query$),\n map(([{ suggestions }, value]) => {\n const words = value.split(/([\\s-]+)/)\n if (suggestions?.length && words[words.length - 1]) {\n const last = suggestions[suggestions.length - 1]\n if (last.startsWith(words[words.length - 1]))\n words[words.length - 1] = last\n } else {\n words.length = 0\n }\n return words\n })\n )\n .subscribe(words => el.innerHTML = words\n .join(\"\")\n .replace(/\\s/g, \" \")\n )\n\n /* Set up search keyboard handlers */\n keyboard$\n .pipe(\n filter(({ mode }) => mode === \"search\")\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Right arrow: accept current suggestion */\n case \"ArrowRight\":\n if (\n el.innerText.length &&\n query.selectionStart === query.value.length\n )\n query.value = el.innerText\n break\n }\n })\n\n /* Filter search result message */\n const result$ = rx$\n .pipe(\n filter(isSearchResultMessage),\n map(({ data }) => data)\n )\n\n /* Create and return component */\n return result$\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(() => ({ ref: el }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n NEVER,\n Observable,\n ObservableInput,\n filter,\n merge,\n mergeWith,\n sample,\n take\n} from \"rxjs\"\n\nimport { configuration } from \"~/_\"\nimport {\n Keyboard,\n getActiveElement,\n getElements,\n setToggle\n} from \"~/browser\"\nimport {\n SearchIndex,\n SearchResult,\n isSearchQueryMessage,\n isSearchReadyMessage,\n setupSearchWorker\n} from \"~/integrations\"\n\nimport {\n Component,\n getComponentElement,\n getComponentElements\n} from \"../../_\"\nimport {\n SearchQuery,\n mountSearchQuery\n} from \"../query\"\nimport { mountSearchResult } from \"../result\"\nimport {\n SearchShare,\n mountSearchShare\n} from \"../share\"\nimport {\n SearchSuggest,\n mountSearchSuggest\n} from \"../suggest\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search\n */\nexport type Search =\n | SearchQuery\n | SearchResult\n | SearchShare\n | SearchSuggest\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n index$: ObservableInput /* Search index observable */\n keyboard$: Observable /* Keyboard observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search\n *\n * This function sets up the search functionality, including the underlying\n * web worker and all keyboard bindings.\n *\n * @param el - Search element\n * @param options - Options\n *\n * @returns Search component observable\n */\nexport function mountSearch(\n el: HTMLElement, { index$, keyboard$ }: MountOptions\n): Observable> {\n const config = configuration()\n try {\n const url = __search?.worker || config.search\n const worker = setupSearchWorker(url, index$)\n\n /* Retrieve query and result components */\n const query = getComponentElement(\"search-query\", el)\n const result = getComponentElement(\"search-result\", el)\n\n /* Re-emit query when search is ready */\n const { tx$, rx$ } = worker\n tx$\n .pipe(\n filter(isSearchQueryMessage),\n sample(rx$.pipe(filter(isSearchReadyMessage))),\n take(1)\n )\n .subscribe(tx$.next.bind(tx$))\n\n /* Set up search keyboard handlers */\n keyboard$\n .pipe(\n filter(({ mode }) => mode === \"search\")\n )\n .subscribe(key => {\n const active = getActiveElement()\n switch (key.type) {\n\n /* Enter: go to first (best) result */\n case \"Enter\":\n if (active === query) {\n const anchors = new Map()\n for (const anchor of getElements(\n \":first-child [href]\", result\n )) {\n const article = anchor.firstElementChild!\n anchors.set(anchor, parseFloat(\n article.getAttribute(\"data-md-score\")!\n ))\n }\n\n /* Go to result with highest score, if any */\n if (anchors.size) {\n const [[best]] = [...anchors].sort(([, a], [, b]) => b - a)\n best.click()\n }\n\n /* Otherwise omit form submission */\n key.claim()\n }\n break\n\n /* Escape or Tab: close search */\n case \"Escape\":\n case \"Tab\":\n setToggle(\"search\", false)\n query.blur()\n break\n\n /* Vertical arrows: select previous or next search result */\n case \"ArrowUp\":\n case \"ArrowDown\":\n if (typeof active === \"undefined\") {\n query.focus()\n } else {\n const els = [query, ...getElements(\n \":not(details) > [href], summary, details[open] [href]\",\n result\n )]\n const i = Math.max(0, (\n Math.max(0, els.indexOf(active)) + els.length + (\n key.type === \"ArrowUp\" ? -1 : +1\n )\n ) % els.length)\n els[i].focus()\n }\n\n /* Prevent scrolling of page */\n key.claim()\n break\n\n /* All other keys: hand to search query */\n default:\n if (query !== getActiveElement())\n query.focus()\n }\n })\n\n /* Set up global keyboard handlers */\n keyboard$\n .pipe(\n filter(({ mode }) => mode === \"global\"),\n )\n .subscribe(key => {\n switch (key.type) {\n\n /* Open search and select query */\n case \"f\":\n case \"s\":\n case \"/\":\n query.focus()\n query.select()\n\n /* Prevent scrolling of page */\n key.claim()\n break\n }\n })\n\n /* Create and return component */\n const query$ = mountSearchQuery(query, worker)\n const result$ = mountSearchResult(result, worker, { query$ })\n return merge(query$, result$)\n .pipe(\n mergeWith(\n\n /* Search sharing */\n ...getComponentElements(\"search-share\", el)\n .map(child => mountSearchShare(child, { query$ })),\n\n /* Search suggestions */\n ...getComponentElements(\"search-suggest\", el)\n .map(child => mountSearchSuggest(child, worker, { keyboard$ }))\n )\n )\n\n /* Gracefully handle broken search */\n } catch (err) {\n el.hidden = true\n return NEVER\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n ObservableInput,\n combineLatest,\n filter,\n map,\n startWith\n} from \"rxjs\"\n\nimport { getLocation } from \"~/browser\"\nimport {\n SearchIndex,\n setupSearchHighlighter\n} from \"~/integrations\"\nimport { h } from \"~/utilities\"\n\nimport { Component } from \"../../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlighting\n */\nexport interface SearchHighlight {\n nodes: Map /* Map of replacements */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount options\n */\ninterface MountOptions {\n index$: ObservableInput /* Search index observable */\n location$: Observable /* Location observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Mount search highlighting\n *\n * @param el - Content element\n * @param options - Options\n *\n * @returns Search highlighting component observable\n */\nexport function mountSearchHiglight(\n el: HTMLElement, { index$, location$ }: MountOptions\n): Observable> {\n return combineLatest([\n index$,\n location$\n .pipe(\n startWith(getLocation()),\n filter(url => !!url.searchParams.get(\"h\"))\n )\n ])\n .pipe(\n map(([index, url]) => setupSearchHighlighter(index.config, true)(\n url.searchParams.get(\"h\")!\n )),\n map(fn => {\n const nodes = new Map()\n\n /* Traverse text nodes and collect matches */\n const it = document.createNodeIterator(el, NodeFilter.SHOW_TEXT)\n for (let node = it.nextNode(); node; node = it.nextNode()) {\n if (node.parentElement?.offsetHeight) {\n const original = node.textContent!\n const replaced = fn(original)\n if (replaced.length > original.length)\n nodes.set(node as ChildNode, replaced)\n }\n }\n\n /* Replace original nodes with matches */\n for (const [node, text] of nodes) {\n const { childNodes } = h(\"span\", null, text)\n node.replaceWith(...Array.from(childNodes))\n }\n\n /* Return component */\n return { ref: el, nodes }\n })\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n animationFrameScheduler,\n auditTime,\n combineLatest,\n defer,\n distinctUntilChanged,\n finalize,\n map,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\nimport {\n Viewport,\n getElement,\n getElementOffset\n} from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Sidebar\n */\nexport interface Sidebar {\n height: number /* Sidebar height */\n locked: boolean /* Sidebar is locked */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n main$: Observable
    /* Main area observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n main$: Observable
    /* Main area observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch sidebar\n *\n * This function returns an observable that computes the visual parameters of\n * the sidebar which depends on the vertical viewport offset, as well as the\n * height of the main area. When the page is scrolled beyond the header, the\n * sidebar is locked and fills the remaining space.\n *\n * @param el - Sidebar element\n * @param options - Options\n *\n * @returns Sidebar observable\n */\nexport function watchSidebar(\n el: HTMLElement, { viewport$, main$ }: WatchOptions\n): Observable {\n const parent = el.parentElement!\n const adjust =\n parent.offsetTop -\n parent.parentElement!.offsetTop\n\n /* Compute the sidebar's available height and if it should be locked */\n return combineLatest([main$, viewport$])\n .pipe(\n map(([{ offset, height }, { offset: { y } }]) => {\n height = height\n + Math.min(adjust, Math.max(0, y - offset))\n - adjust\n return {\n height,\n locked: y >= offset + adjust\n }\n }),\n distinctUntilChanged((a, b) => (\n a.height === b.height &&\n a.locked === b.locked\n ))\n )\n}\n\n/**\n * Mount sidebar\n *\n * This function doesn't set the height of the actual sidebar, but of its first\n * child \u2013 the `.md-sidebar__scrollwrap` element in order to mitigiate jittery\n * sidebars when the footer is scrolled into view. At some point we switched\n * from `absolute` / `fixed` positioning to `sticky` positioning, significantly\n * reducing jitter in some browsers (respectively Firefox and Safari) when\n * scrolling from the top. However, top-aligned sticky positioning means that\n * the sidebar snaps to the bottom when the end of the container is reached.\n * This is what leads to the mentioned jitter, as the sidebar's height may be\n * updated too slowly.\n *\n * This behaviour can be mitigiated by setting the height of the sidebar to `0`\n * while preserving the padding, and the height on its first element.\n *\n * @param el - Sidebar element\n * @param options - Options\n *\n * @returns Sidebar component observable\n */\nexport function mountSidebar(\n el: HTMLElement, { header$, ...options }: MountOptions\n): Observable> {\n const inner = getElement(\".md-sidebar__scrollwrap\", el)\n const { y } = getElementOffset(inner)\n return defer(() => {\n const push$ = new Subject()\n push$\n .pipe(\n auditTime(0, animationFrameScheduler),\n withLatestFrom(header$)\n )\n .subscribe({\n\n /* Handle emission */\n next([{ height }, { height: offset }]) {\n inner.style.height = `${height - 2 * y}px`\n el.style.top = `${offset}px`\n },\n\n /* Handle complete */\n complete() {\n inner.style.height = \"\"\n el.style.top = \"\"\n }\n })\n\n /* Create and return component */\n return watchSidebar(el, options)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { Repo, User } from \"github-types\"\nimport {\n EMPTY,\n Observable,\n catchError,\n defaultIfEmpty,\n map,\n zip\n} from \"rxjs\"\n\nimport { requestJSON } from \"~/browser\"\n\nimport { SourceFacts } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * GitHub release (partial)\n */\ninterface Release {\n tag_name: string /* Tag name */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch GitHub repository facts\n *\n * @param user - GitHub user or organization\n * @param repo - GitHub repository\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFactsFromGitHub(\n user: string, repo?: string\n): Observable {\n if (typeof repo !== \"undefined\") {\n const url = `https://api.github.com/repos/${user}/${repo}`\n return zip(\n\n /* Fetch version */\n requestJSON(`${url}/releases/latest`)\n .pipe(\n catchError(() => EMPTY), // @todo refactor instant loading\n map(release => ({\n version: release.tag_name\n })),\n defaultIfEmpty({})\n ),\n\n /* Fetch stars and forks */\n requestJSON(url)\n .pipe(\n catchError(() => EMPTY), // @todo refactor instant loading\n map(info => ({\n stars: info.stargazers_count,\n forks: info.forks_count\n })),\n defaultIfEmpty({})\n )\n )\n .pipe(\n map(([release, info]) => ({ ...release, ...info }))\n )\n\n /* User or organization */\n } else {\n const url = `https://api.github.com/users/${user}`\n return requestJSON(url)\n .pipe(\n map(info => ({\n repositories: info.public_repos\n })),\n defaultIfEmpty({})\n )\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { ProjectSchema } from \"gitlab\"\nimport {\n EMPTY,\n Observable,\n catchError,\n defaultIfEmpty,\n map\n} from \"rxjs\"\n\nimport { requestJSON } from \"~/browser\"\n\nimport { SourceFacts } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch GitLab repository facts\n *\n * @param base - GitLab base\n * @param project - GitLab project\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFactsFromGitLab(\n base: string, project: string\n): Observable {\n const url = `https://${base}/api/v4/projects/${encodeURIComponent(project)}`\n return requestJSON(url)\n .pipe(\n catchError(() => EMPTY), // @todo refactor instant loading\n map(({ star_count, forks_count }) => ({\n stars: star_count,\n forks: forks_count\n })),\n defaultIfEmpty({})\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport { EMPTY, Observable } from \"rxjs\"\n\nimport { fetchSourceFactsFromGitHub } from \"../github\"\nimport { fetchSourceFactsFromGitLab } from \"../gitlab\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository facts for repositories\n */\nexport interface RepositoryFacts {\n stars?: number /* Number of stars */\n forks?: number /* Number of forks */\n version?: string /* Latest version */\n}\n\n/**\n * Repository facts for organizations\n */\nexport interface OrganizationFacts {\n repositories?: number /* Number of repositories */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Repository facts\n */\nexport type SourceFacts =\n | RepositoryFacts\n | OrganizationFacts\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch repository facts\n *\n * @param url - Repository URL\n *\n * @returns Repository facts observable\n */\nexport function fetchSourceFacts(\n url: string\n): Observable {\n const [type] = url.match(/(git(?:hub|lab))/i) || []\n switch (type.toLowerCase()) {\n\n /* GitHub repository */\n case \"github\":\n const [, user, repo] = url.match(/^.+github\\.com\\/([^/]+)\\/?([^/]+)?/i)!\n return fetchSourceFactsFromGitHub(user, repo)\n\n /* GitLab repository */\n case \"gitlab\":\n const [, base, slug] = url.match(/^.+?([^/]*gitlab[^/]+)\\/(.+?)\\/?$/i)!\n return fetchSourceFactsFromGitLab(base, slug)\n\n /* Everything else */\n default:\n return EMPTY\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n EMPTY,\n Observable,\n Subject,\n catchError,\n defer,\n filter,\n finalize,\n map,\n of,\n shareReplay,\n tap\n} from \"rxjs\"\n\nimport { getElement } from \"~/browser\"\nimport { renderSourceFacts } from \"~/templates\"\n\nimport { Component } from \"../../_\"\nimport {\n SourceFacts,\n fetchSourceFacts\n} from \"../facts\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository information\n */\nexport interface Source {\n facts: SourceFacts /* Repository facts */\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Repository information observable\n */\nlet fetch$: Observable\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch repository information\n *\n * This function tries to read the repository facts from session storage, and\n * if unsuccessful, fetches them from the underlying provider.\n *\n * @param el - Repository information element\n *\n * @returns Repository information observable\n */\nexport function watchSource(\n el: HTMLAnchorElement\n): Observable {\n return fetch$ ||= defer(() => {\n const cached = __md_get(\"__source\", sessionStorage)\n if (cached)\n return of(cached)\n else\n return fetchSourceFacts(el.href)\n .pipe(\n tap(facts => __md_set(\"__source\", facts, sessionStorage))\n )\n })\n .pipe(\n catchError(() => EMPTY),\n filter(facts => Object.keys(facts).length > 0),\n map(facts => ({ facts })),\n shareReplay(1)\n )\n}\n\n/**\n * Mount repository information\n *\n * @param el - Repository information element\n *\n * @returns Repository information component observable\n */\nexport function mountSource(\n el: HTMLAnchorElement\n): Observable> {\n const inner = getElement(\":scope > :last-child\", el)\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe(({ facts }) => {\n inner.appendChild(renderSourceFacts(facts))\n inner.classList.add(\"md-source__repository--active\")\n })\n\n /* Create and return component */\n return watchSource(el)\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n defer,\n distinctUntilKeyChanged,\n finalize,\n map,\n of,\n switchMap,\n tap\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n Viewport,\n watchElementSize,\n watchViewportAt\n} from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Navigation tabs\n */\nexport interface Tabs {\n hidden: boolean /* Navigation tabs are hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch navigation tabs\n *\n * @param el - Navigation tabs element\n * @param options - Options\n *\n * @returns Navigation tabs observable\n */\nexport function watchTabs(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n return watchElementSize(document.body)\n .pipe(\n switchMap(() => watchViewportAt(el, { header$, viewport$ })),\n map(({ offset: { y } }) => {\n return {\n hidden: y >= 10\n }\n }),\n distinctUntilKeyChanged(\"hidden\")\n )\n}\n\n/**\n * Mount navigation tabs\n *\n * This function hides the navigation tabs when scrolling past the threshold\n * and makes them reappear in a nice CSS animation when scrolling back up.\n *\n * @param el - Navigation tabs element\n * @param options - Options\n *\n * @returns Navigation tabs component observable\n */\nexport function mountTabs(\n el: HTMLElement, options: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n push$.subscribe({\n\n /* Handle emission */\n next({ hidden }) {\n el.hidden = hidden\n },\n\n /* Handle complete */\n complete() {\n el.hidden = false\n }\n })\n\n /* Create and return component */\n return (\n feature(\"navigation.tabs.sticky\")\n ? of({ hidden: false })\n : watchTabs(el, options)\n )\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n combineLatestWith,\n debounceTime,\n defer,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n finalize,\n map,\n of,\n repeat,\n scan,\n share,\n skip,\n startWith,\n switchMap,\n takeLast,\n takeUntil,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\nimport { feature } from \"~/_\"\nimport {\n Viewport,\n getElement,\n getElements,\n getLocation,\n getOptionalElement,\n watchElementSize\n} from \"~/browser\"\n\nimport {\n Component,\n getComponentElement\n} from \"../_\"\nimport { Header } from \"../header\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Table of contents\n */\nexport interface TableOfContents {\n prev: HTMLAnchorElement[][] /* Anchors (previous) */\n next: HTMLAnchorElement[][] /* Anchors (next) */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n target$: Observable /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch table of contents\n *\n * This is effectively a scroll spy implementation which will account for the\n * fixed header and automatically re-calculate anchor offsets when the viewport\n * is resized. The returned observable will only emit if the table of contents\n * needs to be repainted.\n *\n * This implementation tracks an anchor element's entire path starting from its\n * level up to the top-most anchor element, e.g. `[h3, h2, h1]`. Although the\n * Material theme currently doesn't make use of this information, it enables\n * the styling of the entire hierarchy through customization.\n *\n * Note that the current anchor is the last item of the `prev` anchor list.\n *\n * @param el - Table of contents element\n * @param options - Options\n *\n * @returns Table of contents observable\n */\nexport function watchTableOfContents(\n el: HTMLElement, { viewport$, header$ }: WatchOptions\n): Observable {\n const table = new Map()\n\n /* Compute anchor-to-target mapping */\n const anchors = getElements(\"[href^=\\\\#]\", el)\n for (const anchor of anchors) {\n const id = decodeURIComponent(anchor.hash.substring(1))\n const target = getOptionalElement(`[id=\"${id}\"]`)\n if (typeof target !== \"undefined\")\n table.set(anchor, target)\n }\n\n /* Compute necessary adjustment for header */\n const adjust$ = header$\n .pipe(\n distinctUntilKeyChanged(\"height\"),\n map(({ height }) => {\n const main = getComponentElement(\"main\")\n const grid = getElement(\":scope > :first-child\", main)\n return height + 0.8 * (\n grid.offsetTop -\n main.offsetTop\n )\n }),\n share()\n )\n\n /* Compute partition of previous and next anchors */\n const partition$ = watchElementSize(document.body)\n .pipe(\n distinctUntilKeyChanged(\"height\"),\n\n /* Build index to map anchor paths to vertical offsets */\n switchMap(body => defer(() => {\n let path: HTMLAnchorElement[] = []\n return of([...table].reduce((index, [anchor, target]) => {\n while (path.length) {\n const last = table.get(path[path.length - 1])!\n if (last.tagName >= target.tagName) {\n path.pop()\n } else {\n break\n }\n }\n\n /* If the current anchor is hidden, continue with its parent */\n let offset = target.offsetTop\n while (!offset && target.parentElement) {\n target = target.parentElement\n offset = target.offsetTop\n }\n\n /* Map reversed anchor path to vertical offset */\n return index.set(\n [...path = [...path, anchor]].reverse(),\n offset\n )\n }, new Map()))\n })\n .pipe(\n\n /* Sort index by vertical offset (see https://bit.ly/30z6QSO) */\n map(index => new Map([...index].sort(([, a], [, b]) => a - b))),\n combineLatestWith(adjust$),\n\n /* Re-compute partition when viewport offset changes */\n switchMap(([index, adjust]) => viewport$\n .pipe(\n scan(([prev, next], { offset: { y }, size }) => {\n const last = y + size.height >= Math.floor(body.height)\n\n /* Look forward */\n while (next.length) {\n const [, offset] = next[0]\n if (offset - adjust < y || last) {\n prev = [...prev, next.shift()!]\n } else {\n break\n }\n }\n\n /* Look backward */\n while (prev.length) {\n const [, offset] = prev[prev.length - 1]\n if (offset - adjust >= y && !last) {\n next = [prev.pop()!, ...next]\n } else {\n break\n }\n }\n\n /* Return partition */\n return [prev, next]\n }, [[], [...index]]),\n distinctUntilChanged((a, b) => (\n a[0] === b[0] &&\n a[1] === b[1]\n ))\n )\n )\n )\n )\n )\n\n /* Compute and return anchor list migrations */\n return partition$\n .pipe(\n map(([prev, next]) => ({\n prev: prev.map(([path]) => path),\n next: next.map(([path]) => path)\n })),\n\n /* Extract anchor list migrations */\n startWith({ prev: [], next: [] }),\n bufferCount(2, 1),\n map(([a, b]) => {\n\n /* Moving down */\n if (a.prev.length < b.prev.length) {\n return {\n prev: b.prev.slice(Math.max(0, a.prev.length - 1), b.prev.length),\n next: []\n }\n\n /* Moving up */\n } else {\n return {\n prev: b.prev.slice(-1),\n next: b.next.slice(0, b.next.length - a.next.length)\n }\n }\n })\n )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount table of contents\n *\n * @param el - Table of contents element\n * @param options - Options\n *\n * @returns Table of contents component observable\n */\nexport function mountTableOfContents(\n el: HTMLElement, { viewport$, header$, target$ }: MountOptions\n): Observable> {\n return defer(() => {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n push$.subscribe(({ prev, next }) => {\n\n /* Look forward */\n for (const [anchor] of next) {\n anchor.classList.remove(\"md-nav__link--passed\")\n anchor.classList.remove(\"md-nav__link--active\")\n }\n\n /* Look backward */\n for (const [index, [anchor]] of prev.entries()) {\n anchor.classList.add(\"md-nav__link--passed\")\n anchor.classList.toggle(\n \"md-nav__link--active\",\n index === prev.length - 1\n )\n }\n })\n\n /* Set up anchor tracking, if enabled */\n if (feature(\"navigation.tracking\"))\n viewport$\n .pipe(\n takeUntil(done$),\n distinctUntilKeyChanged(\"offset\"),\n debounceTime(250),\n skip(1),\n takeUntil(target$.pipe(skip(1))),\n repeat({ delay: 250 }),\n withLatestFrom(push$)\n )\n .subscribe(([, { prev }]) => {\n const url = getLocation()\n\n /* Set hash fragment to active anchor */\n const anchor = prev[prev.length - 1]\n if (anchor && anchor.length) {\n const [active] = anchor\n const { hash } = new URL(active.href)\n if (url.hash !== hash) {\n url.hash = hash\n history.replaceState({}, \"\", `${url}`)\n }\n\n /* Reset anchor when at the top */\n } else {\n url.hash = \"\"\n history.replaceState({}, \"\", `${url}`)\n }\n })\n\n /* Create and return component */\n return watchTableOfContents(el, { viewport$, header$ })\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n Subject,\n bufferCount,\n combineLatest,\n distinctUntilChanged,\n distinctUntilKeyChanged,\n endWith,\n finalize,\n map,\n repeat,\n skip,\n takeLast,\n takeUntil,\n tap\n} from \"rxjs\"\n\nimport { Viewport } from \"~/browser\"\n\nimport { Component } from \"../_\"\nimport { Header } from \"../header\"\nimport { Main } from \"../main\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Back-to-top button\n */\nexport interface BackToTop {\n hidden: boolean /* Back-to-top button is hidden */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch options\n */\ninterface WatchOptions {\n viewport$: Observable /* Viewport observable */\n main$: Observable
    /* Main area observable */\n target$: Observable /* Location target observable */\n}\n\n/**\n * Mount options\n */\ninterface MountOptions {\n viewport$: Observable /* Viewport observable */\n header$: Observable
    /* Header observable */\n main$: Observable
    /* Main area observable */\n target$: Observable /* Location target observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Watch back-to-top\n *\n * @param _el - Back-to-top element\n * @param options - Options\n *\n * @returns Back-to-top observable\n */\nexport function watchBackToTop(\n _el: HTMLElement, { viewport$, main$, target$ }: WatchOptions\n): Observable {\n\n /* Compute direction */\n const direction$ = viewport$\n .pipe(\n map(({ offset: { y } }) => y),\n bufferCount(2, 1),\n map(([a, b]) => a > b && b > 0),\n distinctUntilChanged()\n )\n\n /* Compute whether main area is active */\n const active$ = main$\n .pipe(\n map(({ active }) => active)\n )\n\n /* Compute threshold for hiding */\n return combineLatest([active$, direction$])\n .pipe(\n map(([active, direction]) => !(active && direction)),\n distinctUntilChanged(),\n takeUntil(target$.pipe(skip(1))),\n endWith(true),\n repeat({ delay: 250 }),\n map(hidden => ({ hidden }))\n )\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Mount back-to-top\n *\n * @param el - Back-to-top element\n * @param options - Options\n *\n * @returns Back-to-top component observable\n */\nexport function mountBackToTop(\n el: HTMLElement, { viewport$, header$, main$, target$ }: MountOptions\n): Observable> {\n const push$ = new Subject()\n const done$ = push$.pipe(takeLast(1))\n push$.subscribe({\n\n /* Handle emission */\n next({ hidden }) {\n el.hidden = hidden\n if (hidden) {\n el.setAttribute(\"tabindex\", \"-1\")\n el.blur()\n } else {\n el.removeAttribute(\"tabindex\")\n }\n },\n\n /* Handle complete */\n complete() {\n el.style.top = \"\"\n el.hidden = true\n el.removeAttribute(\"tabindex\")\n }\n })\n\n /* Watch header height */\n header$\n .pipe(\n takeUntil(done$),\n distinctUntilKeyChanged(\"height\")\n )\n .subscribe(({ height }) => {\n el.style.top = `${height + 16}px`\n })\n\n /* Create and return component */\n return watchBackToTop(el, { viewport$, main$, target$ })\n .pipe(\n tap(state => push$.next(state)),\n finalize(() => push$.complete()),\n map(state => ({ ref: el, ...state }))\n )\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n fromEvent,\n map,\n mergeMap,\n switchMap,\n takeWhile,\n tap,\n withLatestFrom\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n document$: Observable /* Document observable */\n tablet$: Observable /* Media tablet observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch indeterminate checkboxes\n *\n * This function replaces the indeterminate \"pseudo state\" with the actual\n * indeterminate state, which is used to keep navigation always expanded.\n *\n * @param options - Options\n */\nexport function patchIndeterminate(\n { document$, tablet$ }: PatchOptions\n): void {\n document$\n .pipe(\n switchMap(() => getElements(\n // @todo `data-md-state` is deprecated and removed in v9\n \".md-toggle--indeterminate, [data-md-state=indeterminate]\"\n )),\n tap(el => {\n el.indeterminate = true\n el.checked = false\n }),\n mergeMap(el => fromEvent(el, \"change\")\n .pipe(\n takeWhile(() => el.classList.contains(\"md-toggle--indeterminate\")),\n map(() => el)\n )\n ),\n withLatestFrom(tablet$)\n )\n .subscribe(([el, tablet]) => {\n el.classList.remove(\"md-toggle--indeterminate\")\n if (tablet)\n el.checked = false\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n filter,\n fromEvent,\n map,\n mergeMap,\n switchMap,\n tap\n} from \"rxjs\"\n\nimport { getElements } from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n document$: Observable /* Document observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Check whether the given device is an Apple device\n *\n * @returns Test result\n */\nfunction isAppleDevice(): boolean {\n return /(iPad|iPhone|iPod)/.test(navigator.userAgent)\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch all elements with `data-md-scrollfix` attributes\n *\n * This is a year-old patch which ensures that overflow scrolling works at the\n * top and bottom of containers on iOS by ensuring a `1px` scroll offset upon\n * the start of a touch event.\n *\n * @see https://bit.ly/2SCtAOO - Original source\n *\n * @param options - Options\n */\nexport function patchScrollfix(\n { document$ }: PatchOptions\n): void {\n document$\n .pipe(\n switchMap(() => getElements(\"[data-md-scrollfix]\")),\n tap(el => el.removeAttribute(\"data-md-scrollfix\")),\n filter(isAppleDevice),\n mergeMap(el => fromEvent(el, \"touchstart\")\n .pipe(\n map(() => el)\n )\n )\n )\n .subscribe(el => {\n const top = el.scrollTop\n\n /* We're at the top of the container */\n if (top === 0) {\n el.scrollTop = 1\n\n /* We're at the bottom of the container */\n } else if (top + el.offsetHeight === el.scrollHeight) {\n el.scrollTop = top - 1\n }\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n Observable,\n combineLatest,\n delay,\n map,\n of,\n switchMap,\n withLatestFrom\n} from \"rxjs\"\n\nimport {\n Viewport,\n watchToggle\n} from \"~/browser\"\n\n/* ----------------------------------------------------------------------------\n * Helper types\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch options\n */\ninterface PatchOptions {\n viewport$: Observable /* Viewport observable */\n tablet$: Observable /* Media tablet observable */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Patch the document body to lock when search is open\n *\n * For mobile and tablet viewports, the search is rendered full screen, which\n * leads to scroll leaking when at the top or bottom of the search result. This\n * function locks the body when the search is in full screen mode, and restores\n * the scroll position when leaving.\n *\n * @param options - Options\n */\nexport function patchScrolllock(\n { viewport$, tablet$ }: PatchOptions\n): void {\n combineLatest([watchToggle(\"search\"), tablet$])\n .pipe(\n map(([active, tablet]) => active && !tablet),\n switchMap(active => of(active)\n .pipe(\n delay(active ? 400 : 100)\n )\n ),\n withLatestFrom(viewport$)\n )\n .subscribe(([active, { offset: { y }}]) => {\n if (active) {\n document.body.setAttribute(\"data-md-scrolllock\", \"\")\n document.body.style.top = `-${y}px`\n } else {\n const value = -1 * parseInt(document.body.style.top, 10)\n document.body.removeAttribute(\"data-md-scrolllock\")\n document.body.style.top = \"\"\n if (value)\n window.scrollTo(0, value)\n }\n })\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Polyfills\n * ------------------------------------------------------------------------- */\n\n/* Polyfill `Object.entries` */\nif (!Object.entries)\n Object.entries = function (obj: object) {\n const data: [string, string][] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n data.push([key, obj[key]])\n\n /* Return entries */\n return data\n }\n\n/* Polyfill `Object.values` */\nif (!Object.values)\n Object.values = function (obj: object) {\n const data: string[] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n 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- "names": [] -} diff --git a/assets/javascripts/lunr/min/lunr.ar.min.js b/assets/javascripts/lunr/min/lunr.ar.min.js deleted file mode 100644 index 248ddc5..0000000 --- a/assets/javascripts/lunr/min/lunr.ar.min.js +++ /dev/null @@ -1 +0,0 @@ -!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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nu når og også om op os over på selv sig sin sine sit skal skulle som sådan thi til ud under var vi vil ville vor være været".split(" ")),e.Pipeline.registerFunction(e.da.stopWordFilter,"stopWordFilter-da")}}); \ No newline at end of file diff --git a/assets/javascripts/lunr/min/lunr.de.min.js b/assets/javascripts/lunr/min/lunr.de.min.js deleted file mode 100644 index f3b5c10..0000000 --- a/assets/javascripts/lunr/min/lunr.de.min.js +++ /dev/null @@ -1,18 +0,0 @@ -/*! - * Lunr languages, `German` language - * https://github.com/MihaiValentin/lunr-languages - * - * Copyright 2014, Mihai Valentin - * http://www.mozilla.org/MPL/ - */ -/*! - * based on - * Snowball JavaScript Library v0.3 - * http://code.google.com/p/urim/ - * http://snowball.tartarus.org/ - * - * Copyright 2010, Oleg Mazko - * http://www.mozilla.org/MPL/ - */ - -!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 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Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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andere anderem anderen anderer anderes anderm andern anderr anders auch auf aus bei bin bis bist da damit dann das dasselbe dazu daß dein deine deinem deinen deiner deines dem demselben den denn denselben der derer derselbe derselben des desselben dessen dich die dies diese dieselbe dieselben diesem diesen dieser dieses dir doch dort du durch ein eine einem einen einer eines einig einige einigem einigen einiger einiges einmal er es etwas euch euer eure eurem euren eurer eures für gegen gewesen hab habe haben hat hatte hatten hier hin hinter ich ihm ihn ihnen ihr ihre ihrem ihren ihrer ihres im in indem ins ist jede jedem jeden jeder jedes jene jenem jenen jener jenes jetzt kann kein keine keinem keinen keiner keines können könnte machen man manche manchem manchen mancher manches mein meine meinem meinen meiner meines mich mir mit muss musste nach nicht nichts noch nun nur ob oder ohne sehr sein seine seinem seinen seiner seines selbst sich sie sind so solche solchem solchen solcher solches soll sollte sondern sonst um und uns unse unsem unsen unser unses unter viel vom von vor war waren warst was weg weil weiter welche welchem welchen welcher welches wenn werde werden wie wieder will wir wird wirst wo wollen wollte während würde würden zu zum zur zwar zwischen über".split(" ")),e.Pipeline.registerFunction(e.de.stopWordFilter,"stopWordFilter-de")}}); \ No newline at end of file diff --git a/assets/javascripts/lunr/min/lunr.du.min.js b/assets/javascripts/lunr/min/lunr.du.min.js deleted file mode 100644 index 49a0f3f..0000000 --- a/assets/javascripts/lunr/min/lunr.du.min.js +++ /dev/null @@ -1,18 +0,0 @@ -/*! - * Lunr languages, `Dutch` language - * https://github.com/MihaiValentin/lunr-languages - * - * Copyright 2014, Mihai Valentin - * http://www.mozilla.org/MPL/ - */ -/*! - * based on - * Snowball JavaScript Library v0.3 - * http://code.google.com/p/urim/ - * http://snowball.tartarus.org/ - * - * Copyright 2010, Oleg Mazko - * http://www.mozilla.org/MPL/ - */ - 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")),e.Pipeline.registerFunction(e.ro.stopWordFilter,"stopWordFilter-ro")}}); \ No newline at end of file diff --git a/assets/javascripts/lunr/min/lunr.ru.min.js b/assets/javascripts/lunr/min/lunr.ru.min.js deleted file mode 100644 index 186cc48..0000000 --- a/assets/javascripts/lunr/min/lunr.ru.min.js +++ /dev/null @@ -1,18 +0,0 @@ -/*! - * Lunr languages, `Russian` language - * https://github.com/MihaiValentin/lunr-languages - * - * Copyright 2014, Mihai Valentin - * http://www.mozilla.org/MPL/ - */ -/*! - * based on - * Snowball JavaScript Library v0.3 - * http://code.google.com/p/urim/ - * http://snowball.tartarus.org/ - * - * Copyright 2010, Oleg Mazko - * http://www.mozilla.org/MPL/ - */ - -!function(e,n){"function"==typeof define&&define.amd?define(n):"object"==typeof exports?module.exports=n():n()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. 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n()&&Dr.find_among_b(ar,2)}function p(){return n()&&Dr.find_among_b(mr,4)}function g(){return n()&&Dr.find_among_b(dr,2)}function y(){return n()&&Dr.find_among_b(fr,4)}function z(){return n()&&Dr.find_among_b(br,2)}function v(){return n()&&Dr.find_among_b(wr,2)&&c()}function h(){return Dr.eq_s_b(2,"ki")}function q(){return n()&&Dr.find_among_b(_r,2)&&o()}function C(){return n()&&Dr.find_among_b(kr,4)&&c()}function P(){return n()&&Dr.find_among_b(pr,4)}function F(){return n()&&Dr.find_among_b(gr,4)&&c()}function S(){return Dr.find_among_b(yr,4)}function W(){return n()&&Dr.find_among_b(zr,2)}function L(){return n()&&Dr.find_among_b(vr,4)}function x(){return n()&&Dr.find_among_b(hr,8)}function A(){return Dr.find_among_b(qr,2)}function E(){return n()&&Dr.find_among_b(Cr,32)&&c()}function j(){return Dr.find_among_b(Pr,8)&&c()}function T(){return n()&&Dr.find_among_b(Fr,4)&&c()}function Z(){return Dr.eq_s_b(3,"ken")&&c()}function B(){var r=Dr.limit-Dr.cursor;return!(T()||(Dr.cursor=Dr.limit-r,E()||(Dr.cursor=Dr.limit-r,j()||(Dr.cursor=Dr.limit-r,Z()))))}function D(){if(A()){var r=Dr.limit-Dr.cursor;if(S()||(Dr.cursor=Dr.limit-r,W()||(Dr.cursor=Dr.limit-r,C()||(Dr.cursor=Dr.limit-r,P()||(Dr.cursor=Dr.limit-r,F()||(Dr.cursor=Dr.limit-r))))),T())return!1}return!0}function G(){if(W()){Dr.bra=Dr.cursor,Dr.slice_del();var r=Dr.limit-Dr.cursor;return Dr.ket=Dr.cursor,x()||(Dr.cursor=Dr.limit-r,E()||(Dr.cursor=Dr.limit-r,j()||(Dr.cursor=Dr.limit-r,T()||(Dr.cursor=Dr.limit-r)))),nr=!1,!1}return!0}function H(){if(!L())return!0;var r=Dr.limit-Dr.cursor;return!E()&&(Dr.cursor=Dr.limit-r,!j())}function I(){var r,i=Dr.limit-Dr.cursor;return!(S()||(Dr.cursor=Dr.limit-i,F()||(Dr.cursor=Dr.limit-i,P()||(Dr.cursor=Dr.limit-i,C()))))||(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,T()||(Dr.cursor=Dr.limit-r),!1)}function J(){var r,i=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,nr=!0,B()&&(Dr.cursor=Dr.limit-i,D()&&(Dr.cursor=Dr.limit-i,G()&&(Dr.cursor=Dr.limit-i,H()&&(Dr.cursor=Dr.limit-i,I()))))){if(Dr.cursor=Dr.limit-i,!x())return;Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,r=Dr.limit-Dr.cursor,S()||(Dr.cursor=Dr.limit-r,W()||(Dr.cursor=Dr.limit-r,C()||(Dr.cursor=Dr.limit-r,P()||(Dr.cursor=Dr.limit-r,F()||(Dr.cursor=Dr.limit-r))))),T()||(Dr.cursor=Dr.limit-r)}Dr.bra=Dr.cursor,Dr.slice_del()}function K(){var r,i,e,n;if(Dr.ket=Dr.cursor,h()){if(r=Dr.limit-Dr.cursor,p())return Dr.bra=Dr.cursor,Dr.slice_del(),i=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,W()?(Dr.bra=Dr.cursor,Dr.slice_del(),K()):(Dr.cursor=Dr.limit-i,a()&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()))),!0;if(Dr.cursor=Dr.limit-r,w()){if(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,e=Dr.limit-Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else{if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,!a()&&(Dr.cursor=Dr.limit-e,!m()&&(Dr.cursor=Dr.limit-e,!K())))return!0;Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())}return!0}if(Dr.cursor=Dr.limit-r,g()){if(n=Dr.limit-Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else if(Dr.cursor=Dr.limit-n,m())Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K());else if(Dr.cursor=Dr.limit-n,!K())return!1;return!0}}return!1}function M(r){if(Dr.ket=Dr.cursor,!g()&&(Dr.cursor=Dr.limit-r,!k()))return!1;var i=Dr.limit-Dr.cursor;if(d())Dr.bra=Dr.cursor,Dr.slice_del();else if(Dr.cursor=Dr.limit-i,m())Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K());else if(Dr.cursor=Dr.limit-i,!K())return!1;return!0}function N(r){if(Dr.ket=Dr.cursor,!z()&&(Dr.cursor=Dr.limit-r,!b()))return!1;var i=Dr.limit-Dr.cursor;return!(!m()&&(Dr.cursor=Dr.limit-i,!d()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()),!0)}function O(){var r,i=Dr.limit-Dr.cursor;return Dr.ket=Dr.cursor,!(!w()&&(Dr.cursor=Dr.limit-i,!v()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,!(!W()||(Dr.bra=Dr.cursor,Dr.slice_del(),!K()))||(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!(a()||(Dr.cursor=Dr.limit-r,m()||(Dr.cursor=Dr.limit-r,K())))||(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()),!0)))}function Q(){var r,i,e=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,!p()&&(Dr.cursor=Dr.limit-e,!f()&&(Dr.cursor=Dr.limit-e,!_())))return!1;if(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,r=Dr.limit-Dr.cursor,a())Dr.bra=Dr.cursor,Dr.slice_del(),i=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,W()||(Dr.cursor=Dr.limit-i);else if(Dr.cursor=Dr.limit-r,!W())return!0;return Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,K(),!0}function R(){var r,i,e=Dr.limit-Dr.cursor;if(Dr.ket=Dr.cursor,W())return Dr.bra=Dr.cursor,Dr.slice_del(),void K();if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,q())if(Dr.bra=Dr.cursor,Dr.slice_del(),r=Dr.limit-Dr.cursor,Dr.ket=Dr.cursor,d())Dr.bra=Dr.cursor,Dr.slice_del();else{if(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!a()&&(Dr.cursor=Dr.limit-r,!m())){if(Dr.cursor=Dr.limit-r,Dr.ket=Dr.cursor,!W())return;if(Dr.bra=Dr.cursor,Dr.slice_del(),!K())return}Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())}else if(Dr.cursor=Dr.limit-e,!M(e)&&(Dr.cursor=Dr.limit-e,!N(e))){if(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,y())return Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,i=Dr.limit-Dr.cursor,void(a()?(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K())):(Dr.cursor=Dr.limit-i,W()?(Dr.bra=Dr.cursor,Dr.slice_del(),K()):(Dr.cursor=Dr.limit-i,K())));if(Dr.cursor=Dr.limit-e,!O()){if(Dr.cursor=Dr.limit-e,d())return Dr.bra=Dr.cursor,void Dr.slice_del();Dr.cursor=Dr.limit-e,K()||(Dr.cursor=Dr.limit-e,Q()||(Dr.cursor=Dr.limit-e,Dr.ket=Dr.cursor,(a()||(Dr.cursor=Dr.limit-e,m()))&&(Dr.bra=Dr.cursor,Dr.slice_del(),Dr.ket=Dr.cursor,W()&&(Dr.bra=Dr.cursor,Dr.slice_del(),K()))))}}}function U(){var r;if(Dr.ket=Dr.cursor,r=Dr.find_among_b(Sr,4))switch(Dr.bra=Dr.cursor,r){case 1:Dr.slice_from("p");break;case 2:Dr.slice_from("ç");break;case 3:Dr.slice_from("t");break;case 4:Dr.slice_from("k")}}function V(){for(;;){var r=Dr.limit-Dr.cursor;if(Dr.in_grouping_b(Wr,97,305)){Dr.cursor=Dr.limit-r;break}if(Dr.cursor=Dr.limit-r,Dr.cursor<=Dr.limit_backward)return!1;Dr.cursor--}return!0}function X(r,i,e){if(Dr.cursor=Dr.limit-r,V()){var n=Dr.limit-Dr.cursor;if(!Dr.eq_s_b(1,i)&&(Dr.cursor=Dr.limit-n,!Dr.eq_s_b(1,e)))return!0;Dr.cursor=Dr.limit-r;var t=Dr.cursor;return Dr.insert(Dr.cursor,Dr.cursor,e),Dr.cursor=t,!1}return!0}function Y(){var r=Dr.limit-Dr.cursor;(Dr.eq_s_b(1,"d")||(Dr.cursor=Dr.limit-r,Dr.eq_s_b(1,"g")))&&X(r,"a","ı")&&X(r,"e","i")&&X(r,"o","u")&&X(r,"ö","ü")}function $(){for(var r,i=Dr.cursor,e=2;;){for(r=Dr.cursor;!Dr.in_grouping(Wr,97,305);){if(Dr.cursor>=Dr.limit)return Dr.cursor=r,!(e>0)&&(Dr.cursor=i,!0);Dr.cursor++}e--}}function rr(r,i,e){for(;!Dr.eq_s(i,e);){if(Dr.cursor>=Dr.limit)return!0;Dr.cursor++}return(tr=i)!=Dr.limit||(Dr.cursor=r,!1)}function ir(){var r=Dr.cursor;return!rr(r,2,"ad")||(Dr.cursor=r,!rr(r,5,"soyad"))}function er(){var r=Dr.cursor;return!ir()&&(Dr.limit_backward=r,Dr.cursor=Dr.limit,Y(),Dr.cursor=Dr.limit,U(),!0)}var nr,tr,ur=[new i("m",-1,-1),new i("n",-1,-1),new i("miz",-1,-1),new i("niz",-1,-1),new i("muz",-1,-1),new i("nuz",-1,-1),new i("müz",-1,-1),new i("nüz",-1,-1),new i("mız",-1,-1),new i("nız",-1,-1)],or=[new i("leri",-1,-1),new i("ları",-1,-1)],sr=[new i("ni",-1,-1),new i("nu",-1,-1),new i("nü",-1,-1),new i("nı",-1,-1)],cr=[new i("in",-1,-1),new i("un",-1,-1),new i("ün",-1,-1),new i("ın",-1,-1)],lr=[new i("a",-1,-1),new i("e",-1,-1)],ar=[new i("na",-1,-1),new i("ne",-1,-1)],mr=[new i("da",-1,-1),new i("ta",-1,-1),new i("de",-1,-1),new i("te",-1,-1)],dr=[new i("nda",-1,-1),new i("nde",-1,-1)],fr=[new i("dan",-1,-1),new i("tan",-1,-1),new i("den",-1,-1),new i("ten",-1,-1)],br=[new i("ndan",-1,-1),new i("nden",-1,-1)],wr=[new i("la",-1,-1),new i("le",-1,-1)],_r=[new i("ca",-1,-1),new i("ce",-1,-1)],kr=[new i("im",-1,-1),new i("um",-1,-1),new i("üm",-1,-1),new i("ım",-1,-1)],pr=[new 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i("dün",-1,-1),new i("tün",-1,-1),new i("dın",-1,-1),new i("tın",-1,-1),new i("du",-1,-1),new i("tu",-1,-1),new i("dü",-1,-1),new i("tü",-1,-1),new i("dı",-1,-1),new i("tı",-1,-1)],Pr=[new i("sa",-1,-1),new i("se",-1,-1),new i("sak",-1,-1),new i("sek",-1,-1),new i("sam",-1,-1),new i("sem",-1,-1),new i("san",-1,-1),new i("sen",-1,-1)],Fr=[new i("miş",-1,-1),new i("muş",-1,-1),new i("müş",-1,-1),new i("mış",-1,-1)],Sr=[new i("b",-1,1),new i("c",-1,2),new i("d",-1,3),new i("ğ",-1,4)],Wr=[17,65,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,32,8,0,0,0,0,0,0,1],Lr=[1,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,8,0,0,0,0,0,0,1],xr=[1,64,16,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1],Ar=[17,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,130],Er=[1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1],jr=[17],Tr=[65],Zr=[65],Br=[["a",xr,97,305],["e",Ar,101,252],["ı",Er,97,305],["i",jr,101,105],["o",Tr,111,117],["ö",Zr,246,252],["u",Tr,111,117]],Dr=new e;this.setCurrent=function(r){Dr.setCurrent(r)},this.getCurrent=function(){return Dr.getCurrent()},this.stem=function(){return!!($()&&(Dr.limit_backward=Dr.cursor,Dr.cursor=Dr.limit,J(),Dr.cursor=Dr.limit,nr&&(R(),Dr.cursor=Dr.limit_backward,er())))}};return function(r){return"function"==typeof r.update?r.update(function(r){return n.setCurrent(r),n.stem(),n.getCurrent()}):(n.setCurrent(r),n.stem(),n.getCurrent())}}(),r.Pipeline.registerFunction(r.tr.stemmer,"stemmer-tr"),r.tr.stopWordFilter=r.generateStopWordFilter("acaba altmış altı ama ancak arada aslında ayrıca bana bazı belki ben benden beni benim beri beş bile bin bir biri birkaç birkez birçok birşey birşeyi biz bizden bize bizi bizim bu buna bunda bundan bunlar bunları bunların bunu bunun burada böyle böylece da daha dahi de defa değil diye diğer doksan dokuz dolayı dolayısıyla dört edecek eden ederek edilecek ediliyor edilmesi ediyor elli en etmesi etti ettiği ettiğini eğer gibi göre halen hangi hatta hem henüz hep hepsi her herhangi herkesin hiç hiçbir iki ile ilgili ise itibaren itibariyle için işte kadar karşın katrilyon kendi kendilerine kendini kendisi kendisine kendisini kez ki kim kimden kime kimi kimse kırk milyar milyon mu mü mı nasıl ne neden nedenle nerde nerede nereye niye niçin o olan olarak oldu olduklarını olduğu olduğunu olmadı olmadığı olmak olması olmayan olmaz olsa olsun olup olur olursa oluyor on ona ondan onlar onlardan onları onların onu onun otuz oysa pek rağmen sadece sanki sekiz seksen sen senden seni senin siz sizden sizi sizin tarafından trilyon tüm var vardı ve veya ya yani yapacak yapmak yaptı yaptıkları yaptığı yaptığını yapılan yapılması yapıyor yedi yerine yetmiş yine yirmi yoksa yüz zaten çok çünkü öyle üzere üç şey şeyden şeyi şeyler şu şuna şunda şundan şunları şunu şöyle".split(" ")),r.Pipeline.registerFunction(r.tr.stopWordFilter,"stopWordFilter-tr")}}); \ No newline at end of file diff --git a/assets/javascripts/lunr/min/lunr.vi.min.js b/assets/javascripts/lunr/min/lunr.vi.min.js deleted file mode 100644 index 22aed28..0000000 --- a/assets/javascripts/lunr/min/lunr.vi.min.js +++ /dev/null @@ -1 +0,0 @@ -!function(e,r){"function"==typeof define&&define.amd?define(r):"object"==typeof exports?module.exports=r():r()(e.lunr)}(this,function(){return function(e){if(void 0===e)throw new Error("Lunr is not present. Please include / require Lunr before this script.");if(void 0===e.stemmerSupport)throw new Error("Lunr stemmer support is not present. 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- this.strOffset++; - } else { - this.isError = true; - } - return this; - }, - isError: false, - tag: "SINSYM", - w: 1, - type: "SINSYM"}; - } -} - - -var LatinRules = [WordRule, SpaceRule, SingleSymbolRule, NumberRule]; - -module.exports = LatinRules; - -},{}],4:[function(require,module,exports){ -var _ = require("underscore") - , WordcutCore = require("./wordcut_core"); -var PathInfoBuilder = { - - /* - buildByPartAcceptors: function(path, acceptors, i) { - var - var genInfos = partAcceptors.reduce(function(genInfos, acceptor) { - - }, []); - - return genInfos; - } - */ - - buildByAcceptors: function(path, finalAcceptors, i) { - var self = this; - var infos = finalAcceptors.map(function(acceptor) { - var p = i - acceptor.strOffset + 1 - , _info = path[p]; - - var info = {p: p, - mw: _info.mw + (acceptor.mw === undefined ? 0 : acceptor.mw), - w: acceptor.w + _info.w, - unk: (acceptor.unk ? acceptor.unk : 0) + _info.unk, - type: acceptor.type}; - - if (acceptor.type == "PART") { - for(var j = p + 1; j <= i; j++) { - path[j].merge = p; - } - info.merge = p; - } - - return info; - }); - return infos.filter(function(info) { return info; }); - }, - - fallback: function(path, leftBoundary, text, i) { - var _info = path[leftBoundary]; - if (text[i].match(/[\u0E48-\u0E4E]/)) { - if (leftBoundary != 0) - leftBoundary = path[leftBoundary].p; - return {p: leftBoundary, - mw: 0, - w: 1 + _info.w, - unk: 1 + _info.unk, - type: "UNK"}; -/* } else if(leftBoundary > 0 && path[leftBoundary].type !== "UNK") { - leftBoundary = path[leftBoundary].p; - return {p: leftBoundary, - w: 1 + _info.w, - unk: 1 + _info.unk, - type: "UNK"}; */ - } else { - return {p: leftBoundary, - mw: _info.mw, - w: 1 + _info.w, - unk: 1 + _info.unk, - type: "UNK"}; - } - }, - - build: function(path, finalAcceptors, i, leftBoundary, text) { - var basicPathInfos = this.buildByAcceptors(path, finalAcceptors, i); - if (basicPathInfos.length > 0) { - return basicPathInfos; - } else { - return [this.fallback(path, leftBoundary, text, i)]; - } - } -}; - -module.exports = function() { - return _.clone(PathInfoBuilder); -} - -},{"./wordcut_core":8,"underscore":25}],5:[function(require,module,exports){ -var _ = require("underscore"); - - -var PathSelector = { - selectPath: function(paths) { - var path = paths.reduce(function(selectedPath, path) { - if (selectedPath == null) { - return path; - } else { - if (path.unk < selectedPath.unk) - return path; - if (path.unk == selectedPath.unk) { - if (path.mw < selectedPath.mw) - return path - if (path.mw == selectedPath.mw) { - if (path.w < selectedPath.w) - return path; - } - } - return selectedPath; - } - }, null); - return path; - }, - - createPath: function() { - return [{p:null, w:0, unk:0, type: "INIT", mw:0}]; - } -}; - -module.exports = function() { - return _.clone(PathSelector); -}; - -},{"underscore":25}],6:[function(require,module,exports){ -function isMatch(pat, offset, ch) { - if (pat.length <= offset) - return false; - var _ch = pat[offset]; - return _ch == ch || - (_ch.match(/[กข]/) && ch.match(/[ก-ฮ]/)) || - (_ch.match(/[มบ]/) && ch.match(/[ก-ฮ]/)) || - (_ch.match(/\u0E49/) && ch.match(/[\u0E48-\u0E4B]/)); -} - -var Rule0 = { - pat: "เหก็ม", - createAcceptor: function(tag) { - return {strOffset: 0, - isFinal: false, - transit: function(ch) { - if (isMatch(Rule0.pat, this.strOffset,ch)) { - this.isFinal = (this.strOffset + 1 == Rule0.pat.length); - this.strOffset++; - } else { - this.isError = true; - } - return this; - }, - isError: false, - tag: "THAI_RULE", - type: "THAI_RULE", - w: 1}; - } -}; - -var PartRule = { - createAcceptor: function(tag) { - return {strOffset: 0, - patterns: [ - "แก", "เก", "ก้", "กก์", "กา", "กี", "กิ", "กืก" - ], - isFinal: false, - transit: function(ch) { - var offset = this.strOffset; - this.patterns = this.patterns.filter(function(pat) { - return isMatch(pat, offset, ch); - }); - - if (this.patterns.length > 0) { - var len = 1 + offset; - this.isFinal = this.patterns.some(function(pat) { - return pat.length == len; - }); - this.strOffset++; - } else { - this.isError = true; - } - return this; - }, - isError: false, - tag: "PART", - type: "PART", - unk: 1, - w: 1}; - } -}; - -var ThaiRules = [Rule0, PartRule]; - -module.exports = ThaiRules; - -},{}],7:[function(require,module,exports){ -var sys = require("sys") - , WordcutDict = require("./dict") - , WordcutCore = require("./wordcut_core") - , PathInfoBuilder = require("./path_info_builder") - , PathSelector = require("./path_selector") - , Acceptors = require("./acceptors") - , latinRules = require("./latin_rules") - , thaiRules = require("./thai_rules") - , _ = require("underscore"); - - -var Wordcut = Object.create(WordcutCore); -Wordcut.defaultPathInfoBuilder = PathInfoBuilder; -Wordcut.defaultPathSelector = PathSelector; -Wordcut.defaultAcceptors = Acceptors; -Wordcut.defaultLatinRules = latinRules; -Wordcut.defaultThaiRules = thaiRules; -Wordcut.defaultDict = WordcutDict; - - -Wordcut.initNoDict = function(dict_path) { - var self = this; - self.pathInfoBuilder = new self.defaultPathInfoBuilder; - self.pathSelector = new self.defaultPathSelector; - self.acceptors = new self.defaultAcceptors; - self.defaultLatinRules.forEach(function(rule) { - self.acceptors.creators.push(rule); - }); - self.defaultThaiRules.forEach(function(rule) { - self.acceptors.creators.push(rule); - }); -}; - -Wordcut.init = function(dict_path, withDefault, additionalWords) { - withDefault = withDefault || false; - this.initNoDict(); - var dict = _.clone(this.defaultDict); - dict.init(dict_path, withDefault, additionalWords); - this.acceptors.creators.push(dict); -}; - -module.exports = Wordcut; - -},{"./acceptors":1,"./dict":2,"./latin_rules":3,"./path_info_builder":4,"./path_selector":5,"./thai_rules":6,"./wordcut_core":8,"sys":28,"underscore":25}],8:[function(require,module,exports){ -var WordcutCore = { - - buildPath: function(text) { - var self = this - , path = self.pathSelector.createPath() - , leftBoundary = 0; - self.acceptors.reset(); - for (var i = 0; i < text.length; i++) { - var ch = text[i]; - self.acceptors.transit(ch); - - var possiblePathInfos = self - .pathInfoBuilder - .build(path, - self.acceptors.getFinalAcceptors(), - i, - leftBoundary, - text); - var selectedPath = self.pathSelector.selectPath(possiblePathInfos) - - path.push(selectedPath); - if (selectedPath.type !== "UNK") { - leftBoundary = i; - } - } - return path; - }, - - pathToRanges: function(path) { - var e = path.length - 1 - , ranges = []; - - while (e > 0) { - var info = path[e] - , s = info.p; - - if (info.merge !== undefined && ranges.length > 0) { - var r = ranges[ranges.length - 1]; - r.s = info.merge; - s = r.s; - } else { - ranges.push({s:s, e:e}); - } - e = s; - } - return ranges.reverse(); - }, - - rangesToText: function(text, ranges, delimiter) { - return ranges.map(function(r) { - return text.substring(r.s, r.e); - }).join(delimiter); - }, - - cut: function(text, delimiter) { - var path = this.buildPath(text) - , ranges = this.pathToRanges(path); - return this - .rangesToText(text, ranges, - (delimiter === undefined ? "|" : delimiter)); - }, - - cutIntoRanges: function(text, noText) { - var path = this.buildPath(text) - , ranges = this.pathToRanges(path); - - if (!noText) { - ranges.forEach(function(r) { - r.text = text.substring(r.s, r.e); - }); - } - return ranges; - }, - - cutIntoArray: function(text) { - var path = this.buildPath(text) - , ranges = this.pathToRanges(path); - - return ranges.map(function(r) { - return text.substring(r.s, r.e) - }); - } -}; - -module.exports = WordcutCore; - -},{}],9:[function(require,module,exports){ -// http://wiki.commonjs.org/wiki/Unit_Testing/1.0 -// -// THIS IS NOT TESTED NOR LIKELY TO WORK OUTSIDE V8! -// -// Originally from narwhal.js (http://narwhaljs.org) -// Copyright (c) 2009 Thomas Robinson <280north.com> -// -// Permission is hereby granted, free of charge, to any person obtaining a copy -// of this software and associated documentation files (the 'Software'), to -// deal in the Software without restriction, including without limitation the -// rights to use, copy, modify, merge, publish, distribute, sublicense, and/or -// sell copies of the Software, and to permit persons to whom the Software is -// furnished to do so, subject to the following conditions: -// -// The above copyright notice and this permission notice shall be included in -// all copies or substantial portions of the Software. -// -// THE SOFTWARE IS PROVIDED 'AS IS', WITHOUT WARRANTY OF ANY KIND, EXPRESS OR -// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, -// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE -// AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN -// ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION -// WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. - -// when used in node, this will actually load the util module we depend on -// versus loading the builtin util module as happens otherwise -// this is a bug in node module loading as far as I am concerned -var util = require('util/'); - -var pSlice = Array.prototype.slice; -var hasOwn = Object.prototype.hasOwnProperty; - -// 1. The assert module provides functions that throw -// AssertionError's when particular conditions are not met. The -// assert module must conform to the following interface. - -var assert = module.exports = ok; - -// 2. The AssertionError is defined in assert. -// new assert.AssertionError({ message: message, -// actual: actual, -// expected: expected }) - -assert.AssertionError = function AssertionError(options) { - this.name = 'AssertionError'; - this.actual = options.actual; - this.expected = options.expected; - this.operator = options.operator; - if (options.message) { - this.message = options.message; - this.generatedMessage = false; - } else { - this.message = getMessage(this); - this.generatedMessage = true; - } - var stackStartFunction = options.stackStartFunction || fail; - - if (Error.captureStackTrace) { - Error.captureStackTrace(this, stackStartFunction); - } - else { - // non v8 browsers so we can have a stacktrace - var err = new Error(); - if (err.stack) { - var out = err.stack; - - // try to strip useless frames - var fn_name = stackStartFunction.name; - var idx = out.indexOf('\n' + fn_name); - if (idx >= 0) { - // once we have located the function frame - // we need to strip out everything before it (and its line) - var next_line = out.indexOf('\n', idx + 1); - out = out.substring(next_line + 1); - } - - this.stack = out; - } - } -}; - -// assert.AssertionError instanceof Error -util.inherits(assert.AssertionError, Error); - -function replacer(key, value) { - if (util.isUndefined(value)) { - return '' + value; - } - if (util.isNumber(value) && !isFinite(value)) { - return value.toString(); - } - if (util.isFunction(value) || util.isRegExp(value)) { - return value.toString(); - } - return value; -} - -function truncate(s, n) { - if (util.isString(s)) { - return s.length < n ? s : s.slice(0, n); - } else { - return s; - } -} - -function getMessage(self) { - return truncate(JSON.stringify(self.actual, replacer), 128) + ' ' + - self.operator + ' ' + - truncate(JSON.stringify(self.expected, replacer), 128); -} - -// At present only the three keys mentioned above are used and -// understood by the spec. Implementations or sub modules can pass -// other keys to the AssertionError's constructor - they will be -// ignored. - -// 3. All of the following functions must throw an AssertionError -// when a corresponding condition is not met, with a message that -// may be undefined if not provided. All assertion methods provide -// both the actual and expected values to the assertion error for -// display purposes. - -function fail(actual, expected, message, operator, stackStartFunction) { - throw new assert.AssertionError({ - message: message, - actual: actual, - expected: expected, - operator: operator, - stackStartFunction: stackStartFunction - }); -} - -// EXTENSION! allows for well behaved errors defined elsewhere. -assert.fail = fail; - -// 4. Pure assertion tests whether a value is truthy, as determined -// by !!guard. -// assert.ok(guard, message_opt); -// This statement is equivalent to assert.equal(true, !!guard, -// message_opt);. To test strictly for the value true, use -// assert.strictEqual(true, guard, message_opt);. - -function ok(value, message) { - if (!value) fail(value, true, message, '==', assert.ok); -} -assert.ok = ok; - -// 5. The equality assertion tests shallow, coercive equality with -// ==. -// assert.equal(actual, expected, message_opt); - -assert.equal = function equal(actual, expected, message) { - if (actual != expected) fail(actual, expected, message, '==', assert.equal); -}; - -// 6. The non-equality assertion tests for whether two objects are not equal -// with != assert.notEqual(actual, expected, message_opt); - -assert.notEqual = function notEqual(actual, expected, message) { - if (actual == expected) { - fail(actual, expected, message, '!=', assert.notEqual); - } -}; - -// 7. The equivalence assertion tests a deep equality relation. -// assert.deepEqual(actual, expected, message_opt); - -assert.deepEqual = function deepEqual(actual, expected, message) { - if (!_deepEqual(actual, expected)) { - fail(actual, expected, message, 'deepEqual', assert.deepEqual); - } -}; - -function _deepEqual(actual, expected) { - // 7.1. All identical values are equivalent, as determined by ===. - if (actual === expected) { - return true; - - } else if (util.isBuffer(actual) && util.isBuffer(expected)) { - if (actual.length != expected.length) return false; - - for (var i = 0; i < actual.length; i++) { - if (actual[i] !== expected[i]) return false; - } - - return true; - - // 7.2. If the expected value is a Date object, the actual value is - // equivalent if it is also a Date object that refers to the same time. - } else if (util.isDate(actual) && util.isDate(expected)) { - return actual.getTime() === expected.getTime(); - - // 7.3 If the expected value is a RegExp object, the actual value is - // equivalent if it is also a RegExp object with the same source and - // properties (`global`, `multiline`, `lastIndex`, `ignoreCase`). - } else if (util.isRegExp(actual) && util.isRegExp(expected)) { - return actual.source === expected.source && - actual.global === expected.global && - actual.multiline === expected.multiline && - actual.lastIndex === expected.lastIndex && - actual.ignoreCase === expected.ignoreCase; - - // 7.4. Other pairs that do not both pass typeof value == 'object', - // equivalence is determined by ==. - } else if (!util.isObject(actual) && !util.isObject(expected)) { - return actual == expected; - - // 7.5 For all other Object pairs, including Array objects, equivalence is - // determined by having the same number of owned properties (as verified - // with Object.prototype.hasOwnProperty.call), the same set of keys - // (although not necessarily the same order), equivalent values for every - // corresponding key, and an identical 'prototype' property. Note: this - // accounts for both named and indexed properties on Arrays. - } else { - return objEquiv(actual, expected); - } -} - -function isArguments(object) { - return Object.prototype.toString.call(object) == '[object Arguments]'; -} - -function objEquiv(a, b) { - if (util.isNullOrUndefined(a) || util.isNullOrUndefined(b)) - return false; - // an identical 'prototype' property. - if (a.prototype !== b.prototype) return false; - // if one is a primitive, the other must be same - if (util.isPrimitive(a) || util.isPrimitive(b)) { - return a === b; - } - var aIsArgs = isArguments(a), - bIsArgs = isArguments(b); - if ((aIsArgs && !bIsArgs) || (!aIsArgs && bIsArgs)) - return false; - if (aIsArgs) { - a = pSlice.call(a); - b = pSlice.call(b); - return _deepEqual(a, b); - } - var ka = objectKeys(a), - kb = objectKeys(b), - key, i; - // having the same number of owned properties (keys incorporates - // hasOwnProperty) - if (ka.length != kb.length) - return false; - //the same set of keys (although not necessarily the same order), - ka.sort(); - kb.sort(); - //~~~cheap key test - for (i = ka.length - 1; i >= 0; i--) { - if (ka[i] != kb[i]) - return false; - } - //equivalent values for every corresponding key, and - //~~~possibly expensive deep test - for (i = ka.length - 1; i >= 0; i--) { - key = ka[i]; - if (!_deepEqual(a[key], b[key])) return false; - } - return true; -} - -// 8. The non-equivalence assertion tests for any deep inequality. -// assert.notDeepEqual(actual, expected, message_opt); - -assert.notDeepEqual = function notDeepEqual(actual, expected, message) { - if (_deepEqual(actual, expected)) { - fail(actual, expected, message, 'notDeepEqual', assert.notDeepEqual); - } -}; - -// 9. The strict equality assertion tests strict equality, as determined by ===. -// assert.strictEqual(actual, expected, message_opt); - -assert.strictEqual = function strictEqual(actual, expected, message) { - if (actual !== expected) { - fail(actual, expected, message, '===', assert.strictEqual); - } -}; - -// 10. The strict non-equality assertion tests for strict inequality, as -// determined by !==. assert.notStrictEqual(actual, expected, message_opt); - -assert.notStrictEqual = function notStrictEqual(actual, expected, message) { - if (actual === expected) { - fail(actual, expected, message, '!==', assert.notStrictEqual); - } -}; - -function expectedException(actual, expected) { - if (!actual || !expected) { - return false; - } - - if (Object.prototype.toString.call(expected) == '[object RegExp]') { - return expected.test(actual); - } else if (actual instanceof expected) { - return true; - } else if (expected.call({}, actual) === true) { - return true; - } - - return false; -} - -function _throws(shouldThrow, block, expected, message) { - var actual; - - if (util.isString(expected)) { - message = expected; - expected = null; - } - - try { - block(); - } catch (e) { - actual = e; - } - - message = (expected && expected.name ? ' (' + expected.name + ').' : '.') + - (message ? ' ' + message : '.'); - - if (shouldThrow && !actual) { - fail(actual, expected, 'Missing expected exception' + message); - } - - if (!shouldThrow && expectedException(actual, expected)) { - fail(actual, expected, 'Got unwanted exception' + message); - } - - if ((shouldThrow && actual && expected && - !expectedException(actual, expected)) || (!shouldThrow && actual)) { - throw actual; - } -} - -// 11. Expected to throw an error: -// assert.throws(block, Error_opt, message_opt); - -assert.throws = function(block, /*optional*/error, /*optional*/message) { - _throws.apply(this, [true].concat(pSlice.call(arguments))); -}; - -// EXTENSION! This is annoying to write outside this module. -assert.doesNotThrow = function(block, /*optional*/message) { - _throws.apply(this, [false].concat(pSlice.call(arguments))); -}; - -assert.ifError = function(err) { if (err) {throw err;}}; - -var objectKeys = Object.keys || function (obj) { - var keys = []; - for (var key in obj) { - if (hasOwn.call(obj, key)) keys.push(key); - } - return keys; -}; - -},{"util/":28}],10:[function(require,module,exports){ -'use strict'; -module.exports = balanced; -function balanced(a, b, str) { - if (a instanceof RegExp) a = maybeMatch(a, str); - if (b instanceof RegExp) b = maybeMatch(b, str); - - var r = range(a, b, str); - - return r && { - start: r[0], - end: r[1], - pre: str.slice(0, r[0]), - body: str.slice(r[0] + a.length, r[1]), - post: str.slice(r[1] + b.length) - }; -} - -function maybeMatch(reg, str) { - var m = str.match(reg); - return m ? m[0] : null; -} - -balanced.range = range; -function range(a, b, str) { - var begs, beg, left, right, result; - var ai = str.indexOf(a); - var bi = str.indexOf(b, ai + 1); - var i = ai; - - if (ai >= 0 && bi > 0) { - begs = []; - left = str.length; - - while (i >= 0 && !result) { - if (i == ai) { - begs.push(i); - ai = str.indexOf(a, i + 1); - } else if (begs.length == 1) { - result = [ begs.pop(), bi ]; - } else { - beg = begs.pop(); - if (beg < left) { - left = beg; - right = bi; - } - - bi = str.indexOf(b, i + 1); - } - - i = ai < bi && ai >= 0 ? ai : bi; - } - - if (begs.length) { - result = [ left, right ]; - } - } - - return result; -} - -},{}],11:[function(require,module,exports){ -var concatMap = require('concat-map'); -var balanced = require('balanced-match'); - -module.exports = expandTop; - -var escSlash = '\0SLASH'+Math.random()+'\0'; -var escOpen = '\0OPEN'+Math.random()+'\0'; -var escClose = '\0CLOSE'+Math.random()+'\0'; -var escComma = '\0COMMA'+Math.random()+'\0'; -var escPeriod = '\0PERIOD'+Math.random()+'\0'; - -function numeric(str) { - return parseInt(str, 10) == str - ? parseInt(str, 10) - : str.charCodeAt(0); -} - -function escapeBraces(str) { - return str.split('\\\\').join(escSlash) - .split('\\{').join(escOpen) - .split('\\}').join(escClose) - .split('\\,').join(escComma) - .split('\\.').join(escPeriod); -} - -function unescapeBraces(str) { - return str.split(escSlash).join('\\') - .split(escOpen).join('{') - .split(escClose).join('}') - .split(escComma).join(',') - .split(escPeriod).join('.'); -} - - -// Basically just str.split(","), but handling cases -// where we have nested braced sections, which should be -// treated as individual members, like {a,{b,c},d} -function parseCommaParts(str) { - if (!str) - return ['']; - - var parts = []; - var m = balanced('{', '}', str); - - if (!m) - return str.split(','); - - var pre = m.pre; - var body = m.body; - var post = m.post; - var p = pre.split(','); - - p[p.length-1] += '{' + body + '}'; - var postParts = parseCommaParts(post); - if (post.length) { - p[p.length-1] += postParts.shift(); - p.push.apply(p, postParts); - } - - parts.push.apply(parts, p); - - return parts; -} - -function expandTop(str) { - if (!str) - return []; - - // I don't know why Bash 4.3 does this, but it does. - // Anything starting with {} will have the first two bytes preserved - // but *only* at the top level, so {},a}b will not expand to anything, - // but a{},b}c will be expanded to [a}c,abc]. - // One could argue that this is a bug in Bash, but since the goal of - // this module is to match Bash's rules, we escape a leading {} - if (str.substr(0, 2) === '{}') { - str = '\\{\\}' + str.substr(2); - } - - return expand(escapeBraces(str), true).map(unescapeBraces); -} - -function identity(e) { - return e; -} - -function embrace(str) { - return '{' + str + '}'; -} -function isPadded(el) { - return /^-?0\d/.test(el); -} - -function lte(i, y) { - return i <= y; -} -function gte(i, y) { - return i >= y; -} - -function expand(str, isTop) { - var expansions = []; - - var m = balanced('{', '}', str); - if (!m || /\$$/.test(m.pre)) return [str]; - - var isNumericSequence = /^-?\d+\.\.-?\d+(?:\.\.-?\d+)?$/.test(m.body); - var isAlphaSequence = /^[a-zA-Z]\.\.[a-zA-Z](?:\.\.-?\d+)?$/.test(m.body); - var isSequence = isNumericSequence || isAlphaSequence; - var isOptions = m.body.indexOf(',') >= 0; - if (!isSequence && !isOptions) { - // {a},b} - if (m.post.match(/,.*\}/)) { - str = m.pre + '{' + m.body + escClose + m.post; - return expand(str); - } - return [str]; - } - - var n; - if (isSequence) { - n = m.body.split(/\.\./); - } else { - n = parseCommaParts(m.body); - if (n.length === 1) { - // x{{a,b}}y ==> x{a}y x{b}y - n = expand(n[0], false).map(embrace); - if (n.length === 1) { - var post = m.post.length - ? expand(m.post, false) - : ['']; - return post.map(function(p) { - return m.pre + n[0] + p; - }); - } - } - } - - // at this point, n is the parts, and we know it's not a comma set - // with a single entry. - - // no need to expand pre, since it is guaranteed to be free of brace-sets - var pre = m.pre; - var post = m.post.length - ? expand(m.post, false) - : ['']; - - var N; - - if (isSequence) { - var x = numeric(n[0]); - var y = numeric(n[1]); - var width = Math.max(n[0].length, n[1].length) - var incr = n.length == 3 - ? Math.abs(numeric(n[2])) - : 1; - var test = lte; - var reverse = y < x; - if (reverse) { - incr *= -1; - test = gte; - } - var pad = n.some(isPadded); - - N = []; - - for (var i = x; test(i, y); i += incr) { - var c; - if (isAlphaSequence) { - c = String.fromCharCode(i); - if (c === '\\') - c = ''; - } else { - c = String(i); - if (pad) { - var need = width - c.length; - if (need > 0) { - var z = new Array(need + 1).join('0'); - if (i < 0) - c = '-' + z + c.slice(1); - else - c = z + c; - } - } - } - N.push(c); - } - } else { - N = concatMap(n, function(el) { return expand(el, false) }); - } - - for (var j = 0; j < N.length; j++) { - for (var k = 0; k < post.length; k++) { - var expansion = pre + N[j] + post[k]; - if (!isTop || isSequence || expansion) - expansions.push(expansion); - } - } - - return expansions; -} - - -},{"balanced-match":10,"concat-map":13}],12:[function(require,module,exports){ - -},{}],13:[function(require,module,exports){ -module.exports = function (xs, fn) { - var res = []; - for (var i = 0; i < xs.length; i++) { - var x = fn(xs[i], i); - if (isArray(x)) res.push.apply(res, x); - else res.push(x); - } - return res; -}; - -var isArray = Array.isArray || function (xs) { - return Object.prototype.toString.call(xs) === '[object Array]'; -}; - -},{}],14:[function(require,module,exports){ -// Copyright Joyent, Inc. and other Node contributors. -// -// Permission is hereby granted, free of charge, to any person obtaining a -// copy of this software and associated documentation files (the -// "Software"), to deal in the Software without restriction, including -// without limitation the rights to use, copy, modify, merge, publish, -// distribute, sublicense, and/or sell copies of the Software, and to permit -// persons to whom the Software is furnished to do so, subject to the -// following conditions: -// -// The above copyright notice and this permission notice shall be included -// in all copies or substantial portions of the Software. -// -// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS -// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN -// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, -// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR -// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE -// USE OR OTHER DEALINGS IN THE SOFTWARE. - -function EventEmitter() { - this._events = this._events || {}; - this._maxListeners = this._maxListeners || undefined; -} -module.exports = EventEmitter; - -// Backwards-compat with node 0.10.x -EventEmitter.EventEmitter = EventEmitter; - -EventEmitter.prototype._events = undefined; -EventEmitter.prototype._maxListeners = undefined; - -// By default EventEmitters will print a warning if more than 10 listeners are -// added to it. This is a useful default which helps finding memory leaks. -EventEmitter.defaultMaxListeners = 10; - -// Obviously not all Emitters should be limited to 10. This function allows -// that to be increased. Set to zero for unlimited. -EventEmitter.prototype.setMaxListeners = function(n) { - if (!isNumber(n) || n < 0 || isNaN(n)) - throw TypeError('n must be a positive number'); - this._maxListeners = n; - return this; -}; - -EventEmitter.prototype.emit = function(type) { - var er, handler, len, args, i, listeners; - - if (!this._events) - this._events = {}; - - // If there is no 'error' event listener then throw. - if (type === 'error') { - if (!this._events.error || - (isObject(this._events.error) && !this._events.error.length)) { - er = arguments[1]; - if (er instanceof Error) { - throw er; // Unhandled 'error' event - } - throw TypeError('Uncaught, unspecified "error" event.'); - } - } - - handler = this._events[type]; - - if (isUndefined(handler)) - return false; - - if (isFunction(handler)) { - switch (arguments.length) { - // fast cases - case 1: - handler.call(this); - break; - case 2: - handler.call(this, arguments[1]); - break; - case 3: - handler.call(this, arguments[1], arguments[2]); - break; - // slower - default: - len = arguments.length; - args = new Array(len - 1); - for (i = 1; i < len; i++) - args[i - 1] = arguments[i]; - handler.apply(this, args); - } - } else if (isObject(handler)) { - len = arguments.length; - args = new Array(len - 1); - for (i = 1; i < len; i++) - args[i - 1] = arguments[i]; - - listeners = handler.slice(); - len = listeners.length; - for (i = 0; i < len; i++) - listeners[i].apply(this, args); - } - - return true; -}; - -EventEmitter.prototype.addListener = function(type, listener) { - var m; - - if (!isFunction(listener)) - throw TypeError('listener must be a function'); - - if (!this._events) - this._events = {}; - - // To avoid recursion in the case that type === "newListener"! Before - // adding it to the listeners, first emit "newListener". - if (this._events.newListener) - this.emit('newListener', type, - isFunction(listener.listener) ? - listener.listener : listener); - - if (!this._events[type]) - // Optimize the case of one listener. Don't need the extra array object. - this._events[type] = listener; - else if (isObject(this._events[type])) - // If we've already got an array, just append. - this._events[type].push(listener); - else - // Adding the second element, need to change to array. - this._events[type] = [this._events[type], listener]; - - // Check for listener leak - if (isObject(this._events[type]) && !this._events[type].warned) { - var m; - if (!isUndefined(this._maxListeners)) { - m = this._maxListeners; - } else { - m = EventEmitter.defaultMaxListeners; - } - - if (m && m > 0 && this._events[type].length > m) { - this._events[type].warned = true; - console.error('(node) warning: possible EventEmitter memory ' + - 'leak detected. %d listeners added. ' + - 'Use emitter.setMaxListeners() to increase limit.', - this._events[type].length); - if (typeof console.trace === 'function') { - // not supported in IE 10 - console.trace(); - } - } - } - - return this; -}; - -EventEmitter.prototype.on = EventEmitter.prototype.addListener; - -EventEmitter.prototype.once = function(type, listener) { - if (!isFunction(listener)) - throw TypeError('listener must be a function'); - - var fired = false; - - function g() { - this.removeListener(type, g); - - if (!fired) { - fired = true; - listener.apply(this, arguments); - } - } - - g.listener = listener; - this.on(type, g); - - return this; -}; - -// emits a 'removeListener' event iff the listener was removed -EventEmitter.prototype.removeListener = function(type, listener) { - var list, position, length, i; - - if (!isFunction(listener)) - throw TypeError('listener must be a function'); - - if (!this._events || !this._events[type]) - return this; - - list = this._events[type]; - length = list.length; - position = -1; - - if (list === listener || - (isFunction(list.listener) && list.listener === listener)) { - delete this._events[type]; - if (this._events.removeListener) - this.emit('removeListener', type, listener); - - } else if (isObject(list)) { - for (i = length; i-- > 0;) { - if (list[i] === listener || - (list[i].listener && list[i].listener === listener)) { - position = i; - break; - } - } - - if (position < 0) - return this; - - if (list.length === 1) { - list.length = 0; - delete this._events[type]; - } else { - list.splice(position, 1); - } - - if (this._events.removeListener) - this.emit('removeListener', type, listener); - } - - return this; -}; - -EventEmitter.prototype.removeAllListeners = function(type) { - var key, listeners; - - if (!this._events) - return this; - - // not listening for removeListener, no need to emit - if (!this._events.removeListener) { - if (arguments.length === 0) - this._events = {}; - else if (this._events[type]) - delete this._events[type]; - return this; - } - - // emit removeListener for all listeners on all events - if (arguments.length === 0) { - for (key in this._events) { - if (key === 'removeListener') continue; - this.removeAllListeners(key); - } - this.removeAllListeners('removeListener'); - this._events = {}; - return this; - } - - listeners = this._events[type]; - - if (isFunction(listeners)) { - this.removeListener(type, listeners); - } else { - // LIFO order - while (listeners.length) - this.removeListener(type, listeners[listeners.length - 1]); - } - delete this._events[type]; - - return this; -}; - -EventEmitter.prototype.listeners = function(type) { - var ret; - if (!this._events || !this._events[type]) - ret = []; - else if (isFunction(this._events[type])) - ret = [this._events[type]]; - else - ret = this._events[type].slice(); - return ret; -}; - -EventEmitter.listenerCount = function(emitter, type) { - var ret; - if (!emitter._events || !emitter._events[type]) - ret = 0; - else if (isFunction(emitter._events[type])) - ret = 1; - else - ret = emitter._events[type].length; - return ret; -}; - -function isFunction(arg) { - return typeof arg === 'function'; -} - -function isNumber(arg) { - return typeof arg === 'number'; -} - -function isObject(arg) { - return typeof arg === 'object' && arg !== null; -} - -function isUndefined(arg) { - return arg === void 0; -} - -},{}],15:[function(require,module,exports){ -(function (process){ -exports.alphasort = alphasort -exports.alphasorti = alphasorti -exports.setopts = setopts -exports.ownProp = ownProp -exports.makeAbs = makeAbs -exports.finish = finish -exports.mark = mark -exports.isIgnored = isIgnored -exports.childrenIgnored = childrenIgnored - -function ownProp (obj, field) { - return Object.prototype.hasOwnProperty.call(obj, field) -} - -var path = require("path") -var minimatch = require("minimatch") -var isAbsolute = require("path-is-absolute") -var Minimatch = minimatch.Minimatch - -function alphasorti (a, b) { - return a.toLowerCase().localeCompare(b.toLowerCase()) -} - -function alphasort (a, b) { - return a.localeCompare(b) -} - -function setupIgnores (self, options) { - self.ignore = options.ignore || [] - - if (!Array.isArray(self.ignore)) - self.ignore = [self.ignore] - - if (self.ignore.length) { - self.ignore = self.ignore.map(ignoreMap) - } -} - -function ignoreMap (pattern) { - var gmatcher = null - if (pattern.slice(-3) === '/**') { - var gpattern = pattern.replace(/(\/\*\*)+$/, '') - gmatcher = new Minimatch(gpattern) - } - - return { - matcher: new Minimatch(pattern), - gmatcher: gmatcher - } -} - -function setopts (self, pattern, options) { - if (!options) - options = {} - - // base-matching: just use globstar for that. - if (options.matchBase && -1 === pattern.indexOf("/")) { - if (options.noglobstar) { - throw new Error("base matching requires globstar") - } - pattern = "**/" + pattern - } - - self.silent = !!options.silent - self.pattern = pattern - self.strict = options.strict !== false - self.realpath = !!options.realpath - self.realpathCache = options.realpathCache || Object.create(null) - self.follow = !!options.follow - self.dot = !!options.dot - self.mark = !!options.mark - self.nodir = !!options.nodir - if (self.nodir) - self.mark = true - self.sync = !!options.sync - self.nounique = !!options.nounique - self.nonull = !!options.nonull - self.nosort = !!options.nosort - self.nocase = !!options.nocase - self.stat = !!options.stat - self.noprocess = !!options.noprocess - - self.maxLength = options.maxLength || Infinity - self.cache = options.cache || Object.create(null) - self.statCache = options.statCache || Object.create(null) - self.symlinks = options.symlinks || Object.create(null) - - setupIgnores(self, options) - - self.changedCwd = false - var cwd = process.cwd() - if (!ownProp(options, "cwd")) - self.cwd = cwd - else { - self.cwd = options.cwd - self.changedCwd = path.resolve(options.cwd) !== cwd - } - - self.root = options.root || path.resolve(self.cwd, "/") - self.root = path.resolve(self.root) - if (process.platform === "win32") - self.root = self.root.replace(/\\/g, "/") - - self.nomount = !!options.nomount - - // disable comments and negation unless the user explicitly - // passes in false as the option. - options.nonegate = options.nonegate === false ? false : true - options.nocomment = options.nocomment === false ? false : true - deprecationWarning(options) - - self.minimatch = new Minimatch(pattern, options) - self.options = self.minimatch.options -} - -// TODO(isaacs): remove entirely in v6 -// exported to reset in tests -exports.deprecationWarned -function deprecationWarning(options) { - if (!options.nonegate || !options.nocomment) { - if (process.noDeprecation !== true && !exports.deprecationWarned) { - var msg = 'glob WARNING: comments and negation will be disabled in v6' - if (process.throwDeprecation) - throw new Error(msg) - else if (process.traceDeprecation) - console.trace(msg) - else - console.error(msg) - - exports.deprecationWarned = true - } - } -} - -function finish (self) { - var nou = self.nounique - var all = nou ? [] : Object.create(null) - - for (var i = 0, l = self.matches.length; i < l; i ++) { - var matches = self.matches[i] - if (!matches || Object.keys(matches).length === 0) { - if (self.nonull) { - // do like the shell, and spit out the literal glob - var literal = self.minimatch.globSet[i] - if (nou) - all.push(literal) - else - all[literal] = true - } - } else { - // had matches - var m = Object.keys(matches) - if (nou) - all.push.apply(all, m) - else - m.forEach(function (m) { - all[m] = true - }) - } - } - - if (!nou) - all = Object.keys(all) - - if (!self.nosort) - all = all.sort(self.nocase ? alphasorti : alphasort) - - // at *some* point we statted all of these - if (self.mark) { - for (var i = 0; i < all.length; i++) { - all[i] = self._mark(all[i]) - } - if (self.nodir) { - all = all.filter(function (e) { - return !(/\/$/.test(e)) - }) - } - } - - if (self.ignore.length) - all = all.filter(function(m) { - return !isIgnored(self, m) - }) - - self.found = all -} - -function mark (self, p) { - var abs = makeAbs(self, p) - var c = self.cache[abs] - var m = p - if (c) { - var isDir = c === 'DIR' || Array.isArray(c) - var slash = p.slice(-1) === '/' - - if (isDir && !slash) - m += '/' - else if (!isDir && slash) - m = m.slice(0, -1) - - if (m !== p) { - var mabs = makeAbs(self, m) - self.statCache[mabs] = self.statCache[abs] - self.cache[mabs] = self.cache[abs] - } - } - - return m -} - -// lotta situps... -function makeAbs (self, f) { - var abs = f - if (f.charAt(0) === '/') { - abs = path.join(self.root, f) - } else if (isAbsolute(f) || f === '') { - abs = f - } else if (self.changedCwd) { - abs = path.resolve(self.cwd, f) - } else { - abs = path.resolve(f) - } - return abs -} - - -// Return true, if pattern ends with globstar '**', for the accompanying parent directory. -// Ex:- If node_modules/** is the pattern, add 'node_modules' to ignore list along with it's contents -function isIgnored (self, path) { - if (!self.ignore.length) - return false - - return self.ignore.some(function(item) { - return item.matcher.match(path) || !!(item.gmatcher && item.gmatcher.match(path)) - }) -} - -function childrenIgnored (self, path) { - if (!self.ignore.length) - return false - - return self.ignore.some(function(item) { - return !!(item.gmatcher && item.gmatcher.match(path)) - }) -} - -}).call(this,require('_process')) -},{"_process":24,"minimatch":20,"path":22,"path-is-absolute":23}],16:[function(require,module,exports){ -(function (process){ -// Approach: -// -// 1. Get the minimatch set -// 2. For each pattern in the set, PROCESS(pattern, false) -// 3. Store matches per-set, then uniq them -// -// PROCESS(pattern, inGlobStar) -// Get the first [n] items from pattern that are all strings -// Join these together. This is PREFIX. -// If there is no more remaining, then stat(PREFIX) and -// add to matches if it succeeds. END. -// -// If inGlobStar and PREFIX is symlink and points to dir -// set ENTRIES = [] -// else readdir(PREFIX) as ENTRIES -// If fail, END -// -// with ENTRIES -// If pattern[n] is GLOBSTAR -// // handle the case where the globstar match is empty -// // by pruning it out, and testing the resulting pattern -// PROCESS(pattern[0..n] + pattern[n+1 .. $], false) -// // handle other cases. -// for ENTRY in ENTRIES (not dotfiles) -// // attach globstar + tail onto the entry -// // Mark that this entry is a globstar match -// PROCESS(pattern[0..n] + ENTRY + pattern[n .. $], true) -// -// else // not globstar -// for ENTRY in ENTRIES (not dotfiles, unless pattern[n] is dot) -// Test ENTRY against pattern[n] -// If fails, continue -// If passes, PROCESS(pattern[0..n] + item + pattern[n+1 .. $]) -// -// Caveat: -// Cache all stats and readdirs results to minimize syscall. Since all -// we ever care about is existence and directory-ness, we can just keep -// `true` for files, and [children,...] for directories, or `false` for -// things that don't exist. - -module.exports = glob - -var fs = require('fs') -var minimatch = require('minimatch') -var Minimatch = minimatch.Minimatch -var inherits = require('inherits') -var EE = require('events').EventEmitter -var path = require('path') -var assert = require('assert') -var isAbsolute = require('path-is-absolute') -var globSync = require('./sync.js') -var common = require('./common.js') -var alphasort = common.alphasort -var alphasorti = common.alphasorti -var setopts = common.setopts -var ownProp = common.ownProp -var inflight = require('inflight') -var util = require('util') -var childrenIgnored = common.childrenIgnored -var isIgnored = common.isIgnored - -var once = require('once') - -function glob (pattern, options, cb) { - if (typeof options === 'function') cb = options, options = {} - if (!options) options = {} - - if (options.sync) { - if (cb) - throw new TypeError('callback provided to sync glob') - return globSync(pattern, options) - } - - return new Glob(pattern, options, cb) -} - -glob.sync = globSync -var GlobSync = glob.GlobSync = globSync.GlobSync - -// old api surface -glob.glob = glob - -glob.hasMagic = function (pattern, options_) { - var options = util._extend({}, options_) - options.noprocess = true - - var g = new Glob(pattern, options) - var set = g.minimatch.set - if (set.length > 1) - return true - - for (var j = 0; j < set[0].length; j++) { - if (typeof set[0][j] !== 'string') - return true - } - - return false -} - -glob.Glob = Glob -inherits(Glob, EE) -function Glob (pattern, options, cb) { - if (typeof options === 'function') { - cb = options - options = null - } - - if (options && options.sync) { - if (cb) - throw new TypeError('callback provided to sync glob') - return new GlobSync(pattern, options) - } - - if (!(this instanceof Glob)) - return new Glob(pattern, options, cb) - - setopts(this, pattern, options) - this._didRealPath = false - - // process each pattern in the minimatch set - var n = this.minimatch.set.length - - // The matches are stored as {: true,...} so that - // duplicates are automagically pruned. - // Later, we do an Object.keys() on these. - // Keep them as a list so we can fill in when nonull is set. - this.matches = new Array(n) - - if (typeof cb === 'function') { - cb = once(cb) - this.on('error', cb) - this.on('end', function (matches) { - cb(null, matches) - }) - } - - var self = this - var n = this.minimatch.set.length - this._processing = 0 - this.matches = new Array(n) - - this._emitQueue = [] - this._processQueue = [] - this.paused = false - - if (this.noprocess) - return this - - if (n === 0) - return done() - - for (var i = 0; i < n; i ++) { - this._process(this.minimatch.set[i], i, false, done) - } - - function done () { - --self._processing - if (self._processing <= 0) - self._finish() - } -} - -Glob.prototype._finish = function () { - assert(this instanceof Glob) - if (this.aborted) - return - - if (this.realpath && !this._didRealpath) - return this._realpath() - - common.finish(this) - this.emit('end', this.found) -} - -Glob.prototype._realpath = function () { - if (this._didRealpath) - return - - this._didRealpath = true - - var n = this.matches.length - if (n === 0) - return this._finish() - - var self = this - for (var i = 0; i < this.matches.length; i++) - this._realpathSet(i, next) - - function next () { - if (--n === 0) - self._finish() - } -} - -Glob.prototype._realpathSet = function (index, cb) { - var matchset = this.matches[index] - if (!matchset) - return cb() - - var found = Object.keys(matchset) - var self = this - var n = found.length - - if (n === 0) - return cb() - - var set = this.matches[index] = Object.create(null) - found.forEach(function (p, i) { - // If there's a problem with the stat, then it means that - // one or more of the links in the realpath couldn't be - // resolved. just return the abs value in that case. - p = self._makeAbs(p) - fs.realpath(p, self.realpathCache, function (er, real) { - if (!er) - set[real] = true - else if (er.syscall === 'stat') - set[p] = true - else - self.emit('error', er) // srsly wtf right here - - if (--n === 0) { - self.matches[index] = set - cb() - } - }) - }) -} - -Glob.prototype._mark = function (p) { - return common.mark(this, p) -} - -Glob.prototype._makeAbs = function (f) { - return common.makeAbs(this, f) -} - -Glob.prototype.abort = function () { - this.aborted = true - this.emit('abort') -} - -Glob.prototype.pause = function () { - if (!this.paused) { - this.paused = true - this.emit('pause') - } -} - -Glob.prototype.resume = function () { - if (this.paused) { - this.emit('resume') - this.paused = false - if (this._emitQueue.length) { - var eq = this._emitQueue.slice(0) - this._emitQueue.length = 0 - for (var i = 0; i < eq.length; i ++) { - var e = eq[i] - this._emitMatch(e[0], e[1]) - } - } - if (this._processQueue.length) { - var pq = this._processQueue.slice(0) - this._processQueue.length = 0 - for (var i = 0; i < pq.length; i ++) { - var p = pq[i] - this._processing-- - this._process(p[0], p[1], p[2], p[3]) - } - } - } -} - -Glob.prototype._process = function (pattern, index, inGlobStar, cb) { - assert(this instanceof Glob) - assert(typeof cb === 'function') - - if (this.aborted) - return - - this._processing++ - if (this.paused) { - this._processQueue.push([pattern, index, inGlobStar, cb]) - return - } - - //console.error('PROCESS %d', this._processing, pattern) - - // Get the first [n] parts of pattern that are all strings. - var n = 0 - while (typeof pattern[n] === 'string') { - n ++ - } - // now n is the index of the first one that is *not* a string. - - // see if there's anything else - var prefix - switch (n) { - // if not, then this is rather simple - case pattern.length: - this._processSimple(pattern.join('/'), index, cb) - return - - case 0: - // pattern *starts* with some non-trivial item. - // going to readdir(cwd), but not include the prefix in matches. - prefix = null - break - - default: - // pattern has some string bits in the front. - // whatever it starts with, whether that's 'absolute' like /foo/bar, - // or 'relative' like '../baz' - prefix = pattern.slice(0, n).join('/') - break - } - - var remain = pattern.slice(n) - - // get the list of entries. - var read - if (prefix === null) - read = '.' - else if (isAbsolute(prefix) || isAbsolute(pattern.join('/'))) { - if (!prefix || !isAbsolute(prefix)) - prefix = '/' + prefix - read = prefix - } else - read = prefix - - var abs = this._makeAbs(read) - - //if ignored, skip _processing - if (childrenIgnored(this, read)) - return cb() - - var isGlobStar = remain[0] === minimatch.GLOBSTAR - if (isGlobStar) - this._processGlobStar(prefix, read, abs, remain, index, inGlobStar, cb) - else - this._processReaddir(prefix, read, abs, remain, index, inGlobStar, cb) -} - -Glob.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar, cb) { - var self = this - this._readdir(abs, inGlobStar, function (er, entries) { - return self._processReaddir2(prefix, read, abs, remain, index, inGlobStar, entries, cb) - }) -} - -Glob.prototype._processReaddir2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) { - - // if the abs isn't a dir, then nothing can match! - if (!entries) - return cb() - - // It will only match dot entries if it starts with a dot, or if - // dot is set. Stuff like @(.foo|.bar) isn't allowed. - var pn = remain[0] - var negate = !!this.minimatch.negate - var rawGlob = pn._glob - var dotOk = this.dot || rawGlob.charAt(0) === '.' - - var matchedEntries = [] - for (var i = 0; i < entries.length; i++) { - var e = entries[i] - if (e.charAt(0) !== '.' || dotOk) { - var m - if (negate && !prefix) { - m = !e.match(pn) - } else { - m = e.match(pn) - } - if (m) - matchedEntries.push(e) - } - } - - //console.error('prd2', prefix, entries, remain[0]._glob, matchedEntries) - - var len = matchedEntries.length - // If there are no matched entries, then nothing matches. - if (len === 0) - return cb() - - // if this is the last remaining pattern bit, then no need for - // an additional stat *unless* the user has specified mark or - // stat explicitly. We know they exist, since readdir returned - // them. - - if (remain.length === 1 && !this.mark && !this.stat) { - if (!this.matches[index]) - this.matches[index] = Object.create(null) - - for (var i = 0; i < len; i ++) { - var e = matchedEntries[i] - if (prefix) { - if (prefix !== '/') - e = prefix + '/' + e - else - e = prefix + e - } - - if (e.charAt(0) === '/' && !this.nomount) { - e = path.join(this.root, e) - } - this._emitMatch(index, e) - } - // This was the last one, and no stats were needed - return cb() - } - - // now test all matched entries as stand-ins for that part - // of the pattern. - remain.shift() - for (var i = 0; i < len; i ++) { - var e = matchedEntries[i] - var newPattern - if (prefix) { - if (prefix !== '/') - e = prefix + '/' + e - else - e = prefix + e - } - this._process([e].concat(remain), index, inGlobStar, cb) - } - cb() -} - -Glob.prototype._emitMatch = function (index, e) { - if (this.aborted) - return - - if (this.matches[index][e]) - return - - if (isIgnored(this, e)) - return - - if (this.paused) { - this._emitQueue.push([index, e]) - return - } - - var abs = this._makeAbs(e) - - if (this.nodir) { - var c = this.cache[abs] - if (c === 'DIR' || Array.isArray(c)) - return - } - - if (this.mark) - e = this._mark(e) - - this.matches[index][e] = true - - var st = this.statCache[abs] - if (st) - this.emit('stat', e, st) - - this.emit('match', e) -} - -Glob.prototype._readdirInGlobStar = function (abs, cb) { - if (this.aborted) - return - - // follow all symlinked directories forever - // just proceed as if this is a non-globstar situation - if (this.follow) - return this._readdir(abs, false, cb) - - var lstatkey = 'lstat\0' + abs - var self = this - var lstatcb = inflight(lstatkey, lstatcb_) - - if (lstatcb) - fs.lstat(abs, lstatcb) - - function lstatcb_ (er, lstat) { - if (er) - return cb() - - var isSym = lstat.isSymbolicLink() - self.symlinks[abs] = isSym - - // If it's not a symlink or a dir, then it's definitely a regular file. - // don't bother doing a readdir in that case. - if (!isSym && !lstat.isDirectory()) { - self.cache[abs] = 'FILE' - cb() - } else - self._readdir(abs, false, cb) - } -} - -Glob.prototype._readdir = function (abs, inGlobStar, cb) { - if (this.aborted) - return - - cb = inflight('readdir\0'+abs+'\0'+inGlobStar, cb) - if (!cb) - return - - //console.error('RD %j %j', +inGlobStar, abs) - if (inGlobStar && !ownProp(this.symlinks, abs)) - return this._readdirInGlobStar(abs, cb) - - if (ownProp(this.cache, abs)) { - var c = this.cache[abs] - if (!c || c === 'FILE') - return cb() - - if (Array.isArray(c)) - return cb(null, c) - } - - var self = this - fs.readdir(abs, readdirCb(this, abs, cb)) -} - -function readdirCb (self, abs, cb) { - return function (er, entries) { - if (er) - self._readdirError(abs, er, cb) - else - self._readdirEntries(abs, entries, cb) - } -} - -Glob.prototype._readdirEntries = function (abs, entries, cb) { - if (this.aborted) - return - - // if we haven't asked to stat everything, then just - // assume that everything in there exists, so we can avoid - // having to stat it a second time. - if (!this.mark && !this.stat) { - for (var i = 0; i < entries.length; i ++) { - var e = entries[i] - if (abs === '/') - e = abs + e - else - e = abs + '/' + e - this.cache[e] = true - } - } - - this.cache[abs] = entries - return cb(null, entries) -} - -Glob.prototype._readdirError = function (f, er, cb) { - if (this.aborted) - return - - // handle errors, and cache the information - switch (er.code) { - case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205 - case 'ENOTDIR': // totally normal. means it *does* exist. - this.cache[this._makeAbs(f)] = 'FILE' - break - - case 'ENOENT': // not terribly unusual - case 'ELOOP': - case 'ENAMETOOLONG': - case 'UNKNOWN': - this.cache[this._makeAbs(f)] = false - break - - default: // some unusual error. Treat as failure. - this.cache[this._makeAbs(f)] = false - if (this.strict) { - this.emit('error', er) - // If the error is handled, then we abort - // if not, we threw out of here - this.abort() - } - if (!this.silent) - console.error('glob error', er) - break - } - - return cb() -} - -Glob.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar, cb) { - var self = this - this._readdir(abs, inGlobStar, function (er, entries) { - self._processGlobStar2(prefix, read, abs, remain, index, inGlobStar, entries, cb) - }) -} - - -Glob.prototype._processGlobStar2 = function (prefix, read, abs, remain, index, inGlobStar, entries, cb) { - //console.error('pgs2', prefix, remain[0], entries) - - // no entries means not a dir, so it can never have matches - // foo.txt/** doesn't match foo.txt - if (!entries) - return cb() - - // test without the globstar, and with every child both below - // and replacing the globstar. - var remainWithoutGlobStar = remain.slice(1) - var gspref = prefix ? [ prefix ] : [] - var noGlobStar = gspref.concat(remainWithoutGlobStar) - - // the noGlobStar pattern exits the inGlobStar state - this._process(noGlobStar, index, false, cb) - - var isSym = this.symlinks[abs] - var len = entries.length - - // If it's a symlink, and we're in a globstar, then stop - if (isSym && inGlobStar) - return cb() - - for (var i = 0; i < len; i++) { - var e = entries[i] - if (e.charAt(0) === '.' && !this.dot) - continue - - // these two cases enter the inGlobStar state - var instead = gspref.concat(entries[i], remainWithoutGlobStar) - this._process(instead, index, true, cb) - - var below = gspref.concat(entries[i], remain) - this._process(below, index, true, cb) - } - - cb() -} - -Glob.prototype._processSimple = function (prefix, index, cb) { - // XXX review this. Shouldn't it be doing the mounting etc - // before doing stat? kinda weird? - var self = this - this._stat(prefix, function (er, exists) { - self._processSimple2(prefix, index, er, exists, cb) - }) -} -Glob.prototype._processSimple2 = function (prefix, index, er, exists, cb) { - - //console.error('ps2', prefix, exists) - - if (!this.matches[index]) - this.matches[index] = Object.create(null) - - // If it doesn't exist, then just mark the lack of results - if (!exists) - return cb() - - if (prefix && isAbsolute(prefix) && !this.nomount) { - var trail = /[\/\\]$/.test(prefix) - if (prefix.charAt(0) === '/') { - prefix = path.join(this.root, prefix) - } else { - prefix = path.resolve(this.root, prefix) - if (trail) - prefix += '/' - } - } - - if (process.platform === 'win32') - prefix = prefix.replace(/\\/g, '/') - - // Mark this as a match - this._emitMatch(index, prefix) - cb() -} - -// Returns either 'DIR', 'FILE', or false -Glob.prototype._stat = function (f, cb) { - var abs = this._makeAbs(f) - var needDir = f.slice(-1) === '/' - - if (f.length > this.maxLength) - return cb() - - if (!this.stat && ownProp(this.cache, abs)) { - var c = this.cache[abs] - - if (Array.isArray(c)) - c = 'DIR' - - // It exists, but maybe not how we need it - if (!needDir || c === 'DIR') - return cb(null, c) - - if (needDir && c === 'FILE') - return cb() - - // otherwise we have to stat, because maybe c=true - // if we know it exists, but not what it is. - } - - var exists - var stat = this.statCache[abs] - if (stat !== undefined) { - if (stat === false) - return cb(null, stat) - else { - var type = stat.isDirectory() ? 'DIR' : 'FILE' - if (needDir && type === 'FILE') - return cb() - else - return cb(null, type, stat) - } - } - - var self = this - var statcb = inflight('stat\0' + abs, lstatcb_) - if (statcb) - fs.lstat(abs, statcb) - - function lstatcb_ (er, lstat) { - if (lstat && lstat.isSymbolicLink()) { - // If it's a symlink, then treat it as the target, unless - // the target does not exist, then treat it as a file. - return fs.stat(abs, function (er, stat) { - if (er) - self._stat2(f, abs, null, lstat, cb) - else - self._stat2(f, abs, er, stat, cb) - }) - } else { - self._stat2(f, abs, er, lstat, cb) - } - } -} - -Glob.prototype._stat2 = function (f, abs, er, stat, cb) { - if (er) { - this.statCache[abs] = false - return cb() - } - - var needDir = f.slice(-1) === '/' - this.statCache[abs] = stat - - if (abs.slice(-1) === '/' && !stat.isDirectory()) - return cb(null, false, stat) - - var c = stat.isDirectory() ? 'DIR' : 'FILE' - this.cache[abs] = this.cache[abs] || c - - if (needDir && c !== 'DIR') - return cb() - - return cb(null, c, stat) -} - -}).call(this,require('_process')) -},{"./common.js":15,"./sync.js":17,"_process":24,"assert":9,"events":14,"fs":12,"inflight":18,"inherits":19,"minimatch":20,"once":21,"path":22,"path-is-absolute":23,"util":28}],17:[function(require,module,exports){ -(function (process){ -module.exports = globSync -globSync.GlobSync = GlobSync - -var fs = require('fs') -var minimatch = require('minimatch') -var Minimatch = minimatch.Minimatch -var Glob = require('./glob.js').Glob -var util = require('util') -var path = require('path') -var assert = require('assert') -var isAbsolute = require('path-is-absolute') -var common = require('./common.js') -var alphasort = common.alphasort -var alphasorti = common.alphasorti -var setopts = common.setopts -var ownProp = common.ownProp -var childrenIgnored = common.childrenIgnored - -function globSync (pattern, options) { - if (typeof options === 'function' || arguments.length === 3) - throw new TypeError('callback provided to sync glob\n'+ - 'See: https://github.com/isaacs/node-glob/issues/167') - - return new GlobSync(pattern, options).found -} - -function GlobSync (pattern, options) { - if (!pattern) - throw new Error('must provide pattern') - - if (typeof options === 'function' || arguments.length === 3) - throw new TypeError('callback provided to sync glob\n'+ - 'See: https://github.com/isaacs/node-glob/issues/167') - - if (!(this instanceof GlobSync)) - return new GlobSync(pattern, options) - - setopts(this, pattern, options) - - if (this.noprocess) - return this - - var n = this.minimatch.set.length - this.matches = new Array(n) - for (var i = 0; i < n; i ++) { - this._process(this.minimatch.set[i], i, false) - } - this._finish() -} - -GlobSync.prototype._finish = function () { - assert(this instanceof GlobSync) - if (this.realpath) { - var self = this - this.matches.forEach(function (matchset, index) { - var set = self.matches[index] = Object.create(null) - for (var p in matchset) { - try { - p = self._makeAbs(p) - var real = fs.realpathSync(p, self.realpathCache) - set[real] = true - } catch (er) { - if (er.syscall === 'stat') - set[self._makeAbs(p)] = true - else - throw er - } - } - }) - } - common.finish(this) -} - - -GlobSync.prototype._process = function (pattern, index, inGlobStar) { - assert(this instanceof GlobSync) - - // Get the first [n] parts of pattern that are all strings. - var n = 0 - while (typeof pattern[n] === 'string') { - n ++ - } - // now n is the index of the first one that is *not* a string. - - // See if there's anything else - var prefix - switch (n) { - // if not, then this is rather simple - case pattern.length: - this._processSimple(pattern.join('/'), index) - return - - case 0: - // pattern *starts* with some non-trivial item. - // going to readdir(cwd), but not include the prefix in matches. - prefix = null - break - - default: - // pattern has some string bits in the front. - // whatever it starts with, whether that's 'absolute' like /foo/bar, - // or 'relative' like '../baz' - prefix = pattern.slice(0, n).join('/') - break - } - - var remain = pattern.slice(n) - - // get the list of entries. - var read - if (prefix === null) - read = '.' - else if (isAbsolute(prefix) || isAbsolute(pattern.join('/'))) { - if (!prefix || !isAbsolute(prefix)) - prefix = '/' + prefix - read = prefix - } else - read = prefix - - var abs = this._makeAbs(read) - - //if ignored, skip processing - if (childrenIgnored(this, read)) - return - - var isGlobStar = remain[0] === minimatch.GLOBSTAR - if (isGlobStar) - this._processGlobStar(prefix, read, abs, remain, index, inGlobStar) - else - this._processReaddir(prefix, read, abs, remain, index, inGlobStar) -} - - -GlobSync.prototype._processReaddir = function (prefix, read, abs, remain, index, inGlobStar) { - var entries = this._readdir(abs, inGlobStar) - - // if the abs isn't a dir, then nothing can match! - if (!entries) - return - - // It will only match dot entries if it starts with a dot, or if - // dot is set. Stuff like @(.foo|.bar) isn't allowed. - var pn = remain[0] - var negate = !!this.minimatch.negate - var rawGlob = pn._glob - var dotOk = this.dot || rawGlob.charAt(0) === '.' - - var matchedEntries = [] - for (var i = 0; i < entries.length; i++) { - var e = entries[i] - if (e.charAt(0) !== '.' || dotOk) { - var m - if (negate && !prefix) { - m = !e.match(pn) - } else { - m = e.match(pn) - } - if (m) - matchedEntries.push(e) - } - } - - var len = matchedEntries.length - // If there are no matched entries, then nothing matches. - if (len === 0) - return - - // if this is the last remaining pattern bit, then no need for - // an additional stat *unless* the user has specified mark or - // stat explicitly. We know they exist, since readdir returned - // them. - - if (remain.length === 1 && !this.mark && !this.stat) { - if (!this.matches[index]) - this.matches[index] = Object.create(null) - - for (var i = 0; i < len; i ++) { - var e = matchedEntries[i] - if (prefix) { - if (prefix.slice(-1) !== '/') - e = prefix + '/' + e - else - e = prefix + e - } - - if (e.charAt(0) === '/' && !this.nomount) { - e = path.join(this.root, e) - } - this.matches[index][e] = true - } - // This was the last one, and no stats were needed - return - } - - // now test all matched entries as stand-ins for that part - // of the pattern. - remain.shift() - for (var i = 0; i < len; i ++) { - var e = matchedEntries[i] - var newPattern - if (prefix) - newPattern = [prefix, e] - else - newPattern = [e] - this._process(newPattern.concat(remain), index, inGlobStar) - } -} - - -GlobSync.prototype._emitMatch = function (index, e) { - var abs = this._makeAbs(e) - if (this.mark) - e = this._mark(e) - - if (this.matches[index][e]) - return - - if (this.nodir) { - var c = this.cache[this._makeAbs(e)] - if (c === 'DIR' || Array.isArray(c)) - return - } - - this.matches[index][e] = true - if (this.stat) - this._stat(e) -} - - -GlobSync.prototype._readdirInGlobStar = function (abs) { - // follow all symlinked directories forever - // just proceed as if this is a non-globstar situation - if (this.follow) - return this._readdir(abs, false) - - var entries - var lstat - var stat - try { - lstat = fs.lstatSync(abs) - } catch (er) { - // lstat failed, doesn't exist - return null - } - - var isSym = lstat.isSymbolicLink() - this.symlinks[abs] = isSym - - // If it's not a symlink or a dir, then it's definitely a regular file. - // don't bother doing a readdir in that case. - if (!isSym && !lstat.isDirectory()) - this.cache[abs] = 'FILE' - else - entries = this._readdir(abs, false) - - return entries -} - -GlobSync.prototype._readdir = function (abs, inGlobStar) { - var entries - - if (inGlobStar && !ownProp(this.symlinks, abs)) - return this._readdirInGlobStar(abs) - - if (ownProp(this.cache, abs)) { - var c = this.cache[abs] - if (!c || c === 'FILE') - return null - - if (Array.isArray(c)) - return c - } - - try { - return this._readdirEntries(abs, fs.readdirSync(abs)) - } catch (er) { - this._readdirError(abs, er) - return null - } -} - -GlobSync.prototype._readdirEntries = function (abs, entries) { - // if we haven't asked to stat everything, then just - // assume that everything in there exists, so we can avoid - // having to stat it a second time. - if (!this.mark && !this.stat) { - for (var i = 0; i < entries.length; i ++) { - var e = entries[i] - if (abs === '/') - e = abs + e - else - e = abs + '/' + e - this.cache[e] = true - } - } - - this.cache[abs] = entries - - // mark and cache dir-ness - return entries -} - -GlobSync.prototype._readdirError = function (f, er) { - // handle errors, and cache the information - switch (er.code) { - case 'ENOTSUP': // https://github.com/isaacs/node-glob/issues/205 - case 'ENOTDIR': // totally normal. means it *does* exist. - this.cache[this._makeAbs(f)] = 'FILE' - break - - case 'ENOENT': // not terribly unusual - case 'ELOOP': - case 'ENAMETOOLONG': - case 'UNKNOWN': - this.cache[this._makeAbs(f)] = false - break - - default: // some unusual error. Treat as failure. - this.cache[this._makeAbs(f)] = false - if (this.strict) - throw er - if (!this.silent) - console.error('glob error', er) - break - } -} - -GlobSync.prototype._processGlobStar = function (prefix, read, abs, remain, index, inGlobStar) { - - var entries = this._readdir(abs, inGlobStar) - - // no entries means not a dir, so it can never have matches - // foo.txt/** doesn't match foo.txt - if (!entries) - return - - // test without the globstar, and with every child both below - // and replacing the globstar. - var remainWithoutGlobStar = remain.slice(1) - var gspref = prefix ? [ prefix ] : [] - var noGlobStar = gspref.concat(remainWithoutGlobStar) - - // the noGlobStar pattern exits the inGlobStar state - this._process(noGlobStar, index, false) - - var len = entries.length - var isSym = this.symlinks[abs] - - // If it's a symlink, and we're in a globstar, then stop - if (isSym && inGlobStar) - return - - for (var i = 0; i < len; i++) { - var e = entries[i] - if (e.charAt(0) === '.' && !this.dot) - continue - - // these two cases enter the inGlobStar state - var instead = gspref.concat(entries[i], remainWithoutGlobStar) - this._process(instead, index, true) - - var below = gspref.concat(entries[i], remain) - this._process(below, index, true) - } -} - -GlobSync.prototype._processSimple = function (prefix, index) { - // XXX review this. Shouldn't it be doing the mounting etc - // before doing stat? kinda weird? - var exists = this._stat(prefix) - - if (!this.matches[index]) - this.matches[index] = Object.create(null) - - // If it doesn't exist, then just mark the lack of results - if (!exists) - return - - if (prefix && isAbsolute(prefix) && !this.nomount) { - var trail = /[\/\\]$/.test(prefix) - if (prefix.charAt(0) === '/') { - prefix = path.join(this.root, prefix) - } else { - prefix = path.resolve(this.root, prefix) - if (trail) - prefix += '/' - } - } - - if (process.platform === 'win32') - prefix = prefix.replace(/\\/g, '/') - - // Mark this as a match - this.matches[index][prefix] = true -} - -// Returns either 'DIR', 'FILE', or false -GlobSync.prototype._stat = function (f) { - var abs = this._makeAbs(f) - var needDir = f.slice(-1) === '/' - - if (f.length > this.maxLength) - return false - - if (!this.stat && ownProp(this.cache, abs)) { - var c = this.cache[abs] - - if (Array.isArray(c)) - c = 'DIR' - - // It exists, but maybe not how we need it - if (!needDir || c === 'DIR') - return c - - if (needDir && c === 'FILE') - return false - - // otherwise we have to stat, because maybe c=true - // if we know it exists, but not what it is. - } - - var exists - var stat = this.statCache[abs] - if (!stat) { - var lstat - try { - lstat = fs.lstatSync(abs) - } catch (er) { - return false - } - - if (lstat.isSymbolicLink()) { - try { - stat = fs.statSync(abs) - } catch (er) { - stat = lstat - } - } else { - stat = lstat - } - } - - this.statCache[abs] = stat - - var c = stat.isDirectory() ? 'DIR' : 'FILE' - this.cache[abs] = this.cache[abs] || c - - if (needDir && c !== 'DIR') - return false - - return c -} - -GlobSync.prototype._mark = function (p) { - return common.mark(this, p) -} - -GlobSync.prototype._makeAbs = function (f) { - return common.makeAbs(this, f) -} - -}).call(this,require('_process')) -},{"./common.js":15,"./glob.js":16,"_process":24,"assert":9,"fs":12,"minimatch":20,"path":22,"path-is-absolute":23,"util":28}],18:[function(require,module,exports){ -(function (process){ -var wrappy = require('wrappy') -var reqs = Object.create(null) -var once = require('once') - -module.exports = wrappy(inflight) - -function inflight (key, cb) { - if (reqs[key]) { - reqs[key].push(cb) - return null - } else { - reqs[key] = [cb] - return makeres(key) - } -} - -function makeres (key) { - return once(function RES () { - var cbs = reqs[key] - var len = cbs.length - var args = slice(arguments) - - // XXX It's somewhat ambiguous whether a new callback added in this - // pass should be queued for later execution if something in the - // list of callbacks throws, or if it should just be discarded. - // However, it's such an edge case that it hardly matters, and either - // choice is likely as surprising as the other. - // As it happens, we do go ahead and schedule it for later execution. - try { - for (var i = 0; i < len; i++) { - cbs[i].apply(null, args) - } - } finally { - if (cbs.length > len) { - // added more in the interim. - // de-zalgo, just in case, but don't call again. - cbs.splice(0, len) - process.nextTick(function () { - RES.apply(null, args) - }) - } else { - delete reqs[key] - } - } - }) -} - -function slice (args) { - var length = args.length - var array = [] - - for (var i = 0; i < length; i++) array[i] = args[i] - return array -} - -}).call(this,require('_process')) -},{"_process":24,"once":21,"wrappy":29}],19:[function(require,module,exports){ -if (typeof Object.create === 'function') { - // implementation from standard node.js 'util' module - module.exports = function inherits(ctor, superCtor) { - ctor.super_ = superCtor - ctor.prototype = Object.create(superCtor.prototype, { - constructor: { - value: ctor, - enumerable: false, - writable: true, - configurable: true - } - }); - }; -} else { - // old school shim for old browsers - module.exports = function inherits(ctor, superCtor) { - ctor.super_ = superCtor - var TempCtor = function () {} - TempCtor.prototype = superCtor.prototype - ctor.prototype = new TempCtor() - ctor.prototype.constructor = ctor - } -} - -},{}],20:[function(require,module,exports){ -module.exports = minimatch -minimatch.Minimatch = Minimatch - -var path = { sep: '/' } -try { - path = require('path') -} catch (er) {} - -var GLOBSTAR = minimatch.GLOBSTAR = Minimatch.GLOBSTAR = {} -var expand = require('brace-expansion') - -var plTypes = { - '!': { open: '(?:(?!(?:', close: '))[^/]*?)'}, - '?': { open: '(?:', close: ')?' }, - '+': { open: '(?:', close: ')+' }, - '*': { open: '(?:', close: ')*' }, - '@': { open: '(?:', close: ')' } -} - -// any single thing other than / -// don't need to escape / when using new RegExp() -var qmark = '[^/]' - -// * => any number of characters -var star = qmark + '*?' - -// ** when dots are allowed. Anything goes, except .. and . -// not (^ or / followed by one or two dots followed by $ or /), -// followed by anything, any number of times. -var twoStarDot = '(?:(?!(?:\\\/|^)(?:\\.{1,2})($|\\\/)).)*?' - -// not a ^ or / followed by a dot, -// followed by anything, any number of times. -var twoStarNoDot = '(?:(?!(?:\\\/|^)\\.).)*?' - -// characters that need to be escaped in RegExp. -var reSpecials = charSet('().*{}+?[]^$\\!') - -// "abc" -> { a:true, b:true, c:true } -function charSet (s) { - return s.split('').reduce(function (set, c) { - set[c] = true - return set - }, {}) -} - -// normalizes slashes. -var slashSplit = /\/+/ - -minimatch.filter = filter -function filter (pattern, options) { - options = options || {} - return function (p, i, list) { - return minimatch(p, pattern, options) - } -} - -function ext (a, b) { - a = a || {} - b = b || {} - var t = {} - Object.keys(b).forEach(function (k) { - t[k] = b[k] - }) - Object.keys(a).forEach(function (k) { - t[k] = a[k] - }) - return t -} - -minimatch.defaults = function (def) { - if (!def || !Object.keys(def).length) return minimatch - - var orig = minimatch - - var m = function minimatch (p, pattern, options) { - return orig.minimatch(p, pattern, ext(def, options)) - } - - m.Minimatch = function Minimatch (pattern, options) { - return new orig.Minimatch(pattern, ext(def, options)) - } - - return m -} - -Minimatch.defaults = function (def) { - if (!def || !Object.keys(def).length) return Minimatch - return minimatch.defaults(def).Minimatch -} - -function minimatch (p, pattern, options) { - if (typeof pattern !== 'string') { - throw new TypeError('glob pattern string required') - } - - if (!options) options = {} - - // shortcut: comments match nothing. - if (!options.nocomment && pattern.charAt(0) === '#') { - return false - } - - // "" only matches "" - if (pattern.trim() === '') return p === '' - - return new Minimatch(pattern, options).match(p) -} - -function Minimatch (pattern, options) { - if (!(this instanceof Minimatch)) { - return new Minimatch(pattern, options) - } - - if (typeof pattern !== 'string') { - throw new TypeError('glob pattern string required') - } - - if (!options) options = {} - pattern = pattern.trim() - - // windows support: need to use /, not \ - if (path.sep !== '/') { - pattern = pattern.split(path.sep).join('/') - } - - this.options = options - this.set = [] - this.pattern = pattern - this.regexp = null - this.negate = false - this.comment = false - this.empty = false - - // make the set of regexps etc. - this.make() -} - -Minimatch.prototype.debug = function () {} - -Minimatch.prototype.make = make -function make () { - // don't do it more than once. - if (this._made) return - - var pattern = this.pattern - var options = this.options - - // empty patterns and comments match nothing. - if (!options.nocomment && pattern.charAt(0) === '#') { - this.comment = true - return - } - if (!pattern) { - this.empty = true - return - } - - // step 1: figure out negation, etc. - this.parseNegate() - - // step 2: expand braces - var set = this.globSet = this.braceExpand() - - if (options.debug) this.debug = console.error - - this.debug(this.pattern, set) - - // step 3: now we have a set, so turn each one into a series of path-portion - // matching patterns. - // These will be regexps, except in the case of "**", which is - // set to the GLOBSTAR object for globstar behavior, - // and will not contain any / characters - set = this.globParts = set.map(function (s) { - return s.split(slashSplit) - }) - - this.debug(this.pattern, set) - - // glob --> regexps - set = set.map(function (s, si, set) { - return s.map(this.parse, this) - }, this) - - this.debug(this.pattern, set) - - // filter out everything that didn't compile properly. - set = set.filter(function (s) { - return s.indexOf(false) === -1 - }) - - this.debug(this.pattern, set) - - this.set = set -} - -Minimatch.prototype.parseNegate = parseNegate -function parseNegate () { - var pattern = this.pattern - var negate = false - var options = this.options - var negateOffset = 0 - - if (options.nonegate) return - - for (var i = 0, l = pattern.length - ; i < l && pattern.charAt(i) === '!' - ; i++) { - negate = !negate - negateOffset++ - } - - if (negateOffset) this.pattern = pattern.substr(negateOffset) - this.negate = negate -} - -// Brace expansion: -// a{b,c}d -> abd acd -// a{b,}c -> abc ac -// a{0..3}d -> a0d a1d a2d a3d -// a{b,c{d,e}f}g -> abg acdfg acefg -// a{b,c}d{e,f}g -> abdeg acdeg abdeg abdfg -// -// Invalid sets are not expanded. -// a{2..}b -> a{2..}b -// a{b}c -> a{b}c -minimatch.braceExpand = function (pattern, options) { - return braceExpand(pattern, options) -} - -Minimatch.prototype.braceExpand = braceExpand - -function braceExpand (pattern, options) { - if (!options) { - if (this instanceof Minimatch) { - options = this.options - } else { - options = {} - } - } - - pattern = typeof pattern === 'undefined' - ? this.pattern : pattern - - if (typeof pattern === 'undefined') { - throw new TypeError('undefined pattern') - } - - if (options.nobrace || - !pattern.match(/\{.*\}/)) { - // shortcut. no need to expand. - return [pattern] - } - - return expand(pattern) -} - -// parse a component of the expanded set. -// At this point, no pattern may contain "/" in it -// so we're going to return a 2d array, where each entry is the full -// pattern, split on '/', and then turned into a regular expression. -// A regexp is made at the end which joins each array with an -// escaped /, and another full one which joins each regexp with |. -// -// Following the lead of Bash 4.1, note that "**" only has special meaning -// when it is the *only* thing in a path portion. Otherwise, any series -// of * is equivalent to a single *. Globstar behavior is enabled by -// default, and can be disabled by setting options.noglobstar. -Minimatch.prototype.parse = parse -var SUBPARSE = {} -function parse (pattern, isSub) { - if (pattern.length > 1024 * 64) { - throw new TypeError('pattern is too long') - } - - var options = this.options - - // shortcuts - if (!options.noglobstar && pattern === '**') return GLOBSTAR - if (pattern === '') return '' - - var re = '' - var hasMagic = !!options.nocase - var escaping = false - // ? => one single character - var patternListStack = [] - var negativeLists = [] - var stateChar - var inClass = false - var reClassStart = -1 - var classStart = -1 - // . and .. never match anything that doesn't start with ., - // even when options.dot is set. - var patternStart = pattern.charAt(0) === '.' ? '' // anything - // not (start or / followed by . or .. followed by / or end) - : options.dot ? '(?!(?:^|\\\/)\\.{1,2}(?:$|\\\/))' - : '(?!\\.)' - var self = this - - function clearStateChar () { - if (stateChar) { - // we had some state-tracking character - // that wasn't consumed by this pass. - switch (stateChar) { - case '*': - re += star - hasMagic = true - break - case '?': - re += qmark - hasMagic = true - break - default: - re += '\\' + stateChar - break - } - self.debug('clearStateChar %j %j', stateChar, re) - stateChar = false - } - } - - for (var i = 0, len = pattern.length, c - ; (i < len) && (c = pattern.charAt(i)) - ; i++) { - this.debug('%s\t%s %s %j', pattern, i, re, c) - - // skip over any that are escaped. - if (escaping && reSpecials[c]) { - re += '\\' + c - escaping = false - continue - } - - switch (c) { - case '/': - // completely not allowed, even escaped. - // Should already be path-split by now. - return false - - case '\\': - clearStateChar() - escaping = true - continue - - // the various stateChar values - // for the "extglob" stuff. - case '?': - case '*': - case '+': - case '@': - case '!': - this.debug('%s\t%s %s %j <-- stateChar', pattern, i, re, c) - - // all of those are literals inside a class, except that - // the glob [!a] means [^a] in regexp - if (inClass) { - this.debug(' in class') - if (c === '!' && i === classStart + 1) c = '^' - re += c - continue - } - - // if we already have a stateChar, then it means - // that there was something like ** or +? in there. - // Handle the stateChar, then proceed with this one. - self.debug('call clearStateChar %j', stateChar) - clearStateChar() - stateChar = c - // if extglob is disabled, then +(asdf|foo) isn't a thing. - // just clear the statechar *now*, rather than even diving into - // the patternList stuff. - if (options.noext) clearStateChar() - continue - - case '(': - if (inClass) { - re += '(' - continue - } - - if (!stateChar) { - re += '\\(' - continue - } - - patternListStack.push({ - type: stateChar, - start: i - 1, - reStart: re.length, - open: plTypes[stateChar].open, - close: plTypes[stateChar].close - }) - // negation is (?:(?!js)[^/]*) - re += stateChar === '!' ? '(?:(?!(?:' : '(?:' - this.debug('plType %j %j', stateChar, re) - stateChar = false - continue - - case ')': - if (inClass || !patternListStack.length) { - re += '\\)' - continue - } - - clearStateChar() - hasMagic = true - var pl = patternListStack.pop() - // negation is (?:(?!js)[^/]*) - // The others are (?:) - re += pl.close - if (pl.type === '!') { - negativeLists.push(pl) - } - pl.reEnd = re.length - continue - - case '|': - if (inClass || !patternListStack.length || escaping) { - re += '\\|' - escaping = false - continue - } - - clearStateChar() - re += '|' - continue - - // these are mostly the same in regexp and glob - case '[': - // swallow any state-tracking char before the [ - clearStateChar() - - if (inClass) { - re += '\\' + c - continue - } - - inClass = true - classStart = i - reClassStart = re.length - re += c - continue - - case ']': - // a right bracket shall lose its special - // meaning and represent itself in - // a bracket expression if it occurs - // first in the list. -- POSIX.2 2.8.3.2 - if (i === classStart + 1 || !inClass) { - re += '\\' + c - escaping = false - continue - } - - // handle the case where we left a class open. - // "[z-a]" is valid, equivalent to "\[z-a\]" - if (inClass) { - // split where the last [ was, make sure we don't have - // an invalid re. if so, re-walk the contents of the - // would-be class to re-translate any characters that - // were passed through as-is - // TODO: It would probably be faster to determine this - // without a try/catch and a new RegExp, but it's tricky - // to do safely. For now, this is safe and works. - var cs = pattern.substring(classStart + 1, i) - try { - RegExp('[' + cs + ']') - } catch (er) { - // not a valid class! - var sp = this.parse(cs, SUBPARSE) - re = re.substr(0, reClassStart) + '\\[' + sp[0] + '\\]' - hasMagic = hasMagic || sp[1] - inClass = false - continue - } - } - - // finish up the class. - hasMagic = true - inClass = false - re += c - continue - - default: - // swallow any state char that wasn't consumed - clearStateChar() - - if (escaping) { - // no need - escaping = false - } else if (reSpecials[c] - && !(c === '^' && inClass)) { - re += '\\' - } - - re += c - - } // switch - } // for - - // handle the case where we left a class open. - // "[abc" is valid, equivalent to "\[abc" - if (inClass) { - // split where the last [ was, and escape it - // this is a huge pita. We now have to re-walk - // the contents of the would-be class to re-translate - // any characters that were passed through as-is - cs = pattern.substr(classStart + 1) - sp = this.parse(cs, SUBPARSE) - re = re.substr(0, reClassStart) + '\\[' + sp[0] - hasMagic = hasMagic || sp[1] - } - - // handle the case where we had a +( thing at the *end* - // of the pattern. - // each pattern list stack adds 3 chars, and we need to go through - // and escape any | chars that were passed through as-is for the regexp. - // Go through and escape them, taking care not to double-escape any - // | chars that were already escaped. - for (pl = patternListStack.pop(); pl; pl = patternListStack.pop()) { - var tail = re.slice(pl.reStart + pl.open.length) - this.debug('setting tail', re, pl) - // maybe some even number of \, then maybe 1 \, followed by a | - tail = tail.replace(/((?:\\{2}){0,64})(\\?)\|/g, function (_, $1, $2) { - if (!$2) { - // the | isn't already escaped, so escape it. - $2 = '\\' - } - - // need to escape all those slashes *again*, without escaping the - // one that we need for escaping the | character. As it works out, - // escaping an even number of slashes can be done by simply repeating - // it exactly after itself. That's why this trick works. - // - // I am sorry that you have to see this. - return $1 + $1 + $2 + '|' - }) - - this.debug('tail=%j\n %s', tail, tail, pl, re) - var t = pl.type === '*' ? star - : pl.type === '?' ? qmark - : '\\' + pl.type - - hasMagic = true - re = re.slice(0, pl.reStart) + t + '\\(' + tail - } - - // handle trailing things that only matter at the very end. - clearStateChar() - if (escaping) { - // trailing \\ - re += '\\\\' - } - - // only need to apply the nodot start if the re starts with - // something that could conceivably capture a dot - var addPatternStart = false - switch (re.charAt(0)) { - case '.': - case '[': - case '(': addPatternStart = true - } - - // Hack to work around lack of negative lookbehind in JS - // A pattern like: *.!(x).!(y|z) needs to ensure that a name - // like 'a.xyz.yz' doesn't match. So, the first negative - // lookahead, has to look ALL the way ahead, to the end of - // the pattern. - for (var n = negativeLists.length - 1; n > -1; n--) { - var nl = negativeLists[n] - - var nlBefore = re.slice(0, nl.reStart) - var nlFirst = re.slice(nl.reStart, nl.reEnd - 8) - var nlLast = re.slice(nl.reEnd - 8, nl.reEnd) - var nlAfter = re.slice(nl.reEnd) - - nlLast += nlAfter - - // Handle nested stuff like *(*.js|!(*.json)), where open parens - // mean that we should *not* include the ) in the bit that is considered - // "after" the negated section. - var openParensBefore = nlBefore.split('(').length - 1 - var cleanAfter = nlAfter - for (i = 0; i < openParensBefore; i++) { - cleanAfter = cleanAfter.replace(/\)[+*?]?/, '') - } - nlAfter = cleanAfter - - var dollar = '' - if (nlAfter === '' && isSub !== SUBPARSE) { - dollar = '$' - } - var newRe = nlBefore + nlFirst + nlAfter + dollar + nlLast - re = newRe - } - - // if the re is not "" at this point, then we need to make sure - // it doesn't match against an empty path part. - // Otherwise a/* will match a/, which it should not. - if (re !== '' && hasMagic) { - re = '(?=.)' + re - } - - if (addPatternStart) { - re = patternStart + re - } - - // parsing just a piece of a larger pattern. - if (isSub === SUBPARSE) { - return [re, hasMagic] - } - - // skip the regexp for non-magical patterns - // unescape anything in it, though, so that it'll be - // an exact match against a file etc. - if (!hasMagic) { - return globUnescape(pattern) - } - - var flags = options.nocase ? 'i' : '' - try { - var regExp = new RegExp('^' + re + '$', flags) - } catch (er) { - // If it was an invalid regular expression, then it can't match - // anything. This trick looks for a character after the end of - // the string, which is of course impossible, except in multi-line - // mode, but it's not a /m regex. - return new RegExp('$.') - } - - regExp._glob = pattern - regExp._src = re - - return regExp -} - -minimatch.makeRe = function (pattern, options) { - return new Minimatch(pattern, options || {}).makeRe() -} - -Minimatch.prototype.makeRe = makeRe -function makeRe () { - if (this.regexp || this.regexp === false) return this.regexp - - // at this point, this.set is a 2d array of partial - // pattern strings, or "**". - // - // It's better to use .match(). This function shouldn't - // be used, really, but it's pretty convenient sometimes, - // when you just want to work with a regex. - var set = this.set - - if (!set.length) { - this.regexp = false - return this.regexp - } - var options = this.options - - var twoStar = options.noglobstar ? star - : options.dot ? twoStarDot - : twoStarNoDot - var flags = options.nocase ? 'i' : '' - - var re = set.map(function (pattern) { - return pattern.map(function (p) { - return (p === GLOBSTAR) ? twoStar - : (typeof p === 'string') ? regExpEscape(p) - : p._src - }).join('\\\/') - }).join('|') - - // must match entire pattern - // ending in a * or ** will make it less strict. - re = '^(?:' + re + ')$' - - // can match anything, as long as it's not this. - if (this.negate) re = '^(?!' + re + ').*$' - - try { - this.regexp = new RegExp(re, flags) - } catch (ex) { - this.regexp = false - } - return this.regexp -} - -minimatch.match = function (list, pattern, options) { - options = options || {} - var mm = new Minimatch(pattern, options) - list = list.filter(function (f) { - return mm.match(f) - }) - if (mm.options.nonull && !list.length) { - list.push(pattern) - } - return list -} - -Minimatch.prototype.match = match -function match (f, partial) { - this.debug('match', f, this.pattern) - // short-circuit in the case of busted things. - // comments, etc. - if (this.comment) return false - if (this.empty) return f === '' - - if (f === '/' && partial) return true - - var options = this.options - - // windows: need to use /, not \ - if (path.sep !== '/') { - f = f.split(path.sep).join('/') - } - - // treat the test path as a set of pathparts. - f = f.split(slashSplit) - this.debug(this.pattern, 'split', f) - - // just ONE of the pattern sets in this.set needs to match - // in order for it to be valid. If negating, then just one - // match means that we have failed. - // Either way, return on the first hit. - - var set = this.set - this.debug(this.pattern, 'set', set) - - // Find the basename of the path by looking for the last non-empty segment - var filename - var i - for (i = f.length - 1; i >= 0; i--) { - filename = f[i] - if (filename) break - } - - for (i = 0; i < set.length; i++) { - var pattern = set[i] - var file = f - if (options.matchBase && pattern.length === 1) { - file = [filename] - } - var hit = this.matchOne(file, pattern, partial) - if (hit) { - if (options.flipNegate) return true - return !this.negate - } - } - - // didn't get any hits. this is success if it's a negative - // pattern, failure otherwise. - if (options.flipNegate) return false - return this.negate -} - -// set partial to true to test if, for example, -// "/a/b" matches the start of "/*/b/*/d" -// Partial means, if you run out of file before you run -// out of pattern, then that's fine, as long as all -// the parts match. -Minimatch.prototype.matchOne = function (file, pattern, partial) { - var options = this.options - - this.debug('matchOne', - { 'this': this, file: file, pattern: pattern }) - - this.debug('matchOne', file.length, pattern.length) - - for (var fi = 0, - pi = 0, - fl = file.length, - pl = pattern.length - ; (fi < fl) && (pi < pl) - ; fi++, pi++) { - this.debug('matchOne loop') - var p = pattern[pi] - var f = file[fi] - - this.debug(pattern, p, f) - - // should be impossible. - // some invalid regexp stuff in the set. - if (p === false) return false - - if (p === GLOBSTAR) { - this.debug('GLOBSTAR', [pattern, p, f]) - - // "**" - // a/**/b/**/c would match the following: - // a/b/x/y/z/c - // a/x/y/z/b/c - // a/b/x/b/x/c - // a/b/c - // To do this, take the rest of the pattern after - // the **, and see if it would match the file remainder. - // If so, return success. - // If not, the ** "swallows" a segment, and try again. - // This is recursively awful. - // - // a/**/b/**/c matching a/b/x/y/z/c - // - a matches a - // - doublestar - // - matchOne(b/x/y/z/c, b/**/c) - // - b matches b - // - doublestar - // - matchOne(x/y/z/c, c) -> no - // - matchOne(y/z/c, c) -> no - // - matchOne(z/c, c) -> no - // - matchOne(c, c) yes, hit - var fr = fi - var pr = pi + 1 - if (pr === pl) { - this.debug('** at the end') - // a ** at the end will just swallow the rest. - // We have found a match. - // however, it will not swallow /.x, unless - // options.dot is set. - // . and .. are *never* matched by **, for explosively - // exponential reasons. - for (; fi < fl; fi++) { - if (file[fi] === '.' || file[fi] === '..' || - (!options.dot && file[fi].charAt(0) === '.')) return false - } - return true - } - - // ok, let's see if we can swallow whatever we can. - while (fr < fl) { - var swallowee = file[fr] - - this.debug('\nglobstar while', file, fr, pattern, pr, swallowee) - - // XXX remove this slice. Just pass the start index. - if (this.matchOne(file.slice(fr), pattern.slice(pr), partial)) { - this.debug('globstar found match!', fr, fl, swallowee) - // found a match. - return true - } else { - // can't swallow "." or ".." ever. - // can only swallow ".foo" when explicitly asked. - if (swallowee === '.' || swallowee === '..' || - (!options.dot && swallowee.charAt(0) === '.')) { - this.debug('dot detected!', file, fr, pattern, pr) - break - } - - // ** swallows a segment, and continue. - this.debug('globstar swallow a segment, and continue') - fr++ - } - } - - // no match was found. - // However, in partial mode, we can't say this is necessarily over. - // If there's more *pattern* left, then - if (partial) { - // ran out of file - this.debug('\n>>> no match, partial?', file, fr, pattern, pr) - if (fr === fl) return true - } - return false - } - - // something other than ** - // non-magic patterns just have to match exactly - // patterns with magic have been turned into regexps. - var hit - if (typeof p === 'string') { - if (options.nocase) { - hit = f.toLowerCase() === p.toLowerCase() - } else { - hit = f === p - } - this.debug('string match', p, f, hit) - } else { - hit = f.match(p) - this.debug('pattern match', p, f, hit) - } - - if (!hit) return false - } - - // Note: ending in / means that we'll get a final "" - // at the end of the pattern. This can only match a - // corresponding "" at the end of the file. - // If the file ends in /, then it can only match a - // a pattern that ends in /, unless the pattern just - // doesn't have any more for it. But, a/b/ should *not* - // match "a/b/*", even though "" matches against the - // [^/]*? pattern, except in partial mode, where it might - // simply not be reached yet. - // However, a/b/ should still satisfy a/* - - // now either we fell off the end of the pattern, or we're done. - if (fi === fl && pi === pl) { - // ran out of pattern and filename at the same time. - // an exact hit! - return true - } else if (fi === fl) { - // ran out of file, but still had pattern left. - // this is ok if we're doing the match as part of - // a glob fs traversal. - return partial - } else if (pi === pl) { - // ran out of pattern, still have file left. - // this is only acceptable if we're on the very last - // empty segment of a file with a trailing slash. - // a/* should match a/b/ - var emptyFileEnd = (fi === fl - 1) && (file[fi] === '') - return emptyFileEnd - } - - // should be unreachable. - throw new Error('wtf?') -} - -// replace stuff like \* with * -function globUnescape (s) { - return s.replace(/\\(.)/g, '$1') -} - -function regExpEscape (s) { - return s.replace(/[-[\]{}()*+?.,\\^$|#\s]/g, '\\$&') -} - -},{"brace-expansion":11,"path":22}],21:[function(require,module,exports){ -var wrappy = require('wrappy') -module.exports = wrappy(once) -module.exports.strict = wrappy(onceStrict) - -once.proto = once(function () { - Object.defineProperty(Function.prototype, 'once', { - value: function () { - return once(this) - }, - configurable: true - }) - - Object.defineProperty(Function.prototype, 'onceStrict', { - value: function () { - return onceStrict(this) - }, - configurable: true - }) -}) - -function once (fn) { - var f = function () { - if (f.called) return f.value - f.called = true - return f.value = fn.apply(this, arguments) - } - f.called = false - return f -} - -function onceStrict (fn) { - var f = function () { - if (f.called) - throw new Error(f.onceError) - f.called = true - return f.value = fn.apply(this, arguments) - } - var name = fn.name || 'Function wrapped with `once`' - f.onceError = name + " shouldn't be called more than once" - f.called = false - return f -} - -},{"wrappy":29}],22:[function(require,module,exports){ -(function (process){ -// Copyright Joyent, Inc. and other Node contributors. -// -// Permission is hereby granted, free of charge, to any person obtaining a -// copy of this software and associated documentation files (the -// "Software"), to deal in the Software without restriction, including -// without limitation the rights to use, copy, modify, merge, publish, -// distribute, sublicense, and/or sell copies of the Software, and to permit -// persons to whom the Software is furnished to do so, subject to the -// following conditions: -// -// The above copyright notice and this permission notice shall be included -// in all copies or substantial portions of the Software. -// -// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS -// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN -// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, -// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR -// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE -// USE OR OTHER DEALINGS IN THE SOFTWARE. - -// resolves . and .. elements in a path array with directory names there -// must be no slashes, empty elements, or device names (c:\) in the array -// (so also no leading and trailing slashes - it does not distinguish -// relative and absolute paths) -function normalizeArray(parts, allowAboveRoot) { - // if the path tries to go above the root, `up` ends up > 0 - var up = 0; - for (var i = parts.length - 1; i >= 0; i--) { - var last = parts[i]; - if (last === '.') { - parts.splice(i, 1); - } else if (last === '..') { - parts.splice(i, 1); - up++; - } else if (up) { - parts.splice(i, 1); - up--; - } - } - - // if the path is allowed to go above the root, restore leading ..s - if (allowAboveRoot) { - for (; up--; up) { - parts.unshift('..'); - } - } - - return parts; -} - -// Split a filename into [root, dir, basename, ext], unix version -// 'root' is just a slash, or nothing. -var splitPathRe = - /^(\/?|)([\s\S]*?)((?:\.{1,2}|[^\/]+?|)(\.[^.\/]*|))(?:[\/]*)$/; -var splitPath = function(filename) { - return splitPathRe.exec(filename).slice(1); -}; - -// path.resolve([from ...], to) -// posix version -exports.resolve = function() { - var resolvedPath = '', - resolvedAbsolute = false; - - for (var i = arguments.length - 1; i >= -1 && !resolvedAbsolute; i--) { - var path = (i >= 0) ? arguments[i] : process.cwd(); - - // Skip empty and invalid entries - if (typeof path !== 'string') { - throw new TypeError('Arguments to path.resolve must be strings'); - } else if (!path) { - continue; - } - - resolvedPath = path + '/' + resolvedPath; - resolvedAbsolute = path.charAt(0) === '/'; - } - - // At this point the path should be resolved to a full absolute path, but - // handle relative paths to be safe (might happen when process.cwd() fails) - - // Normalize the path - resolvedPath = normalizeArray(filter(resolvedPath.split('/'), function(p) { - return !!p; - }), !resolvedAbsolute).join('/'); - - return ((resolvedAbsolute ? '/' : '') + resolvedPath) || '.'; -}; - -// path.normalize(path) -// posix version -exports.normalize = function(path) { - var isAbsolute = exports.isAbsolute(path), - trailingSlash = substr(path, -1) === '/'; - - // Normalize the path - path = normalizeArray(filter(path.split('/'), function(p) { - return !!p; - }), !isAbsolute).join('/'); - - if (!path && !isAbsolute) { - path = '.'; - } - if (path && trailingSlash) { - path += '/'; - } - - return (isAbsolute ? '/' : '') + path; -}; - -// posix version -exports.isAbsolute = function(path) { - return path.charAt(0) === '/'; -}; - -// posix version -exports.join = function() { - var paths = Array.prototype.slice.call(arguments, 0); - return exports.normalize(filter(paths, function(p, index) { - if (typeof p !== 'string') { - throw new TypeError('Arguments to path.join must be strings'); - } - return p; - }).join('/')); -}; - - -// path.relative(from, to) -// posix version -exports.relative = function(from, to) { - from = exports.resolve(from).substr(1); - to = exports.resolve(to).substr(1); - - function trim(arr) { - var start = 0; - for (; start < arr.length; start++) { - if (arr[start] !== '') break; - } - - var end = arr.length - 1; - for (; end >= 0; end--) { - if (arr[end] !== '') break; - } - - if (start > end) return []; - return arr.slice(start, end - start + 1); - } - - var fromParts = trim(from.split('/')); - var toParts = trim(to.split('/')); - - var length = Math.min(fromParts.length, toParts.length); - var samePartsLength = length; - for (var i = 0; i < length; i++) { - if (fromParts[i] !== toParts[i]) { - samePartsLength = i; - break; - } - } - - var outputParts = []; - for (var i = samePartsLength; i < fromParts.length; i++) { - outputParts.push('..'); - } - - outputParts = outputParts.concat(toParts.slice(samePartsLength)); - - return outputParts.join('/'); -}; - -exports.sep = '/'; -exports.delimiter = ':'; - -exports.dirname = function(path) { - var result = splitPath(path), - root = result[0], - dir = result[1]; - - if (!root && !dir) { - // No dirname whatsoever - return '.'; - } - - if (dir) { - // It has a dirname, strip trailing slash - dir = dir.substr(0, dir.length - 1); - } - - return root + dir; -}; - - -exports.basename = function(path, ext) { - var f = splitPath(path)[2]; - // TODO: make this comparison case-insensitive on windows? - if (ext && f.substr(-1 * ext.length) === ext) { - f = f.substr(0, f.length - ext.length); - } - return f; -}; - - -exports.extname = function(path) { - return splitPath(path)[3]; -}; - -function filter (xs, f) { - if (xs.filter) return xs.filter(f); - var res = []; - for (var i = 0; i < xs.length; i++) { - if (f(xs[i], i, xs)) res.push(xs[i]); - } - return res; -} - -// String.prototype.substr - negative index don't work in IE8 -var substr = 'ab'.substr(-1) === 'b' - ? function (str, start, len) { return str.substr(start, len) } - : function (str, start, len) { - if (start < 0) start = str.length + start; - return str.substr(start, len); - } -; - -}).call(this,require('_process')) -},{"_process":24}],23:[function(require,module,exports){ -(function (process){ -'use strict'; - -function posix(path) { - return path.charAt(0) === '/'; -} - -function win32(path) { - // https://github.com/nodejs/node/blob/b3fcc245fb25539909ef1d5eaa01dbf92e168633/lib/path.js#L56 - var splitDeviceRe = /^([a-zA-Z]:|[\\\/]{2}[^\\\/]+[\\\/]+[^\\\/]+)?([\\\/])?([\s\S]*?)$/; - var result = splitDeviceRe.exec(path); - var device = result[1] || ''; - var isUnc = Boolean(device && device.charAt(1) !== ':'); - - // UNC paths are always absolute - return Boolean(result[2] || isUnc); -} - -module.exports = process.platform === 'win32' ? win32 : posix; -module.exports.posix = posix; -module.exports.win32 = win32; - -}).call(this,require('_process')) -},{"_process":24}],24:[function(require,module,exports){ -// shim for using process in browser -var process = module.exports = {}; - -// cached from whatever global is present so that test runners that stub it -// don't break things. But we need to wrap it in a try catch in case it is -// wrapped in strict mode code which doesn't define any globals. It's inside a -// function because try/catches deoptimize in certain engines. - -var cachedSetTimeout; -var cachedClearTimeout; - -function defaultSetTimout() { - throw new Error('setTimeout has not been defined'); -} -function defaultClearTimeout () { - throw new Error('clearTimeout has not been defined'); -} -(function () { - try { - if (typeof setTimeout === 'function') { - cachedSetTimeout = setTimeout; - } else { - cachedSetTimeout = defaultSetTimout; - } - } catch (e) { - cachedSetTimeout = defaultSetTimout; - } - try { - if (typeof clearTimeout === 'function') { - cachedClearTimeout = clearTimeout; - } else { - cachedClearTimeout = defaultClearTimeout; - } - } catch (e) { - cachedClearTimeout = defaultClearTimeout; - } -} ()) -function runTimeout(fun) { - if (cachedSetTimeout === setTimeout) { - //normal enviroments in sane situations - return setTimeout(fun, 0); - } - // if setTimeout wasn't available but was latter defined - if ((cachedSetTimeout === defaultSetTimout || !cachedSetTimeout) && setTimeout) { - cachedSetTimeout = setTimeout; - return setTimeout(fun, 0); - } - try { - // when when somebody has screwed with setTimeout but no I.E. maddness - return cachedSetTimeout(fun, 0); - } catch(e){ - try { - // When we are in I.E. but the script has been evaled so I.E. doesn't trust the global object when called normally - return cachedSetTimeout.call(null, fun, 0); - } catch(e){ - // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error - return cachedSetTimeout.call(this, fun, 0); - } - } - - -} -function runClearTimeout(marker) { - if (cachedClearTimeout === clearTimeout) { - //normal enviroments in sane situations - return clearTimeout(marker); - } - // if clearTimeout wasn't available but was latter defined - if ((cachedClearTimeout === defaultClearTimeout || !cachedClearTimeout) && clearTimeout) { - cachedClearTimeout = clearTimeout; - return clearTimeout(marker); - } - try { - // when when somebody has screwed with setTimeout but no I.E. maddness - return cachedClearTimeout(marker); - } catch (e){ - try { - // When we are in I.E. but the script has been evaled so I.E. doesn't trust the global object when called normally - return cachedClearTimeout.call(null, marker); - } catch (e){ - // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error. - // Some versions of I.E. have different rules for clearTimeout vs setTimeout - return cachedClearTimeout.call(this, marker); - } - } - - - -} -var queue = []; -var draining = false; -var currentQueue; -var queueIndex = -1; - -function cleanUpNextTick() { - if (!draining || !currentQueue) { - return; - } - draining = false; - if (currentQueue.length) { - queue = currentQueue.concat(queue); - } else { - queueIndex = -1; - } - if (queue.length) { - drainQueue(); - } -} - -function drainQueue() { - if (draining) { - return; - } - var timeout = runTimeout(cleanUpNextTick); - draining = true; - - var len = queue.length; - while(len) { - currentQueue = queue; - queue = []; - while (++queueIndex < len) { - if (currentQueue) { - currentQueue[queueIndex].run(); - } - } - queueIndex = -1; - len = queue.length; - } - currentQueue = null; - draining = false; - runClearTimeout(timeout); -} - -process.nextTick = function (fun) { - var args = new Array(arguments.length - 1); - if (arguments.length > 1) { - for (var i = 1; i < arguments.length; i++) { - args[i - 1] = arguments[i]; - } - } - queue.push(new Item(fun, args)); - if (queue.length === 1 && !draining) { - runTimeout(drainQueue); - } -}; - -// v8 likes predictible objects -function Item(fun, array) { - this.fun = fun; - this.array = array; -} -Item.prototype.run = function () { - this.fun.apply(null, this.array); -}; -process.title = 'browser'; -process.browser = true; -process.env = {}; -process.argv = []; -process.version = ''; // empty string to avoid regexp issues -process.versions = {}; - -function noop() {} - -process.on = noop; -process.addListener = noop; -process.once = noop; -process.off = noop; -process.removeListener = noop; -process.removeAllListeners = noop; -process.emit = noop; -process.prependListener = noop; -process.prependOnceListener = noop; - -process.listeners = function (name) { return [] } - -process.binding = function (name) { - throw new Error('process.binding is not supported'); -}; - -process.cwd = function () { return '/' }; -process.chdir = function (dir) { - throw new Error('process.chdir is not supported'); -}; -process.umask = function() { return 0; }; - -},{}],25:[function(require,module,exports){ -// Underscore.js 1.8.3 -// http://underscorejs.org -// (c) 2009-2015 Jeremy Ashkenas, DocumentCloud and Investigative Reporters & Editors -// Underscore may be freely distributed under the MIT license. - -(function() { - - // Baseline setup - // -------------- - - // Establish the root object, `window` in the browser, or `exports` on the server. - var root = this; - - // Save the previous value of the `_` variable. - var previousUnderscore = root._; - - // Save bytes in the minified (but not gzipped) version: - var ArrayProto = Array.prototype, ObjProto = Object.prototype, FuncProto = Function.prototype; - - // Create quick reference variables for speed access to core prototypes. - var - push = ArrayProto.push, - slice = ArrayProto.slice, - toString = ObjProto.toString, - hasOwnProperty = ObjProto.hasOwnProperty; - - // All **ECMAScript 5** native function implementations that we hope to use - // are declared here. - var - nativeIsArray = Array.isArray, - nativeKeys = Object.keys, - nativeBind = FuncProto.bind, - nativeCreate = Object.create; - - // Naked function reference for surrogate-prototype-swapping. - var Ctor = function(){}; - - // Create a safe reference to the Underscore object for use below. - var _ = function(obj) { - if (obj instanceof _) return obj; - if (!(this instanceof _)) return new _(obj); - this._wrapped = obj; - }; - - // Export the Underscore object for **Node.js**, with - // backwards-compatibility for the old `require()` API. If we're in - // the browser, add `_` as a global object. - if (typeof exports !== 'undefined') { - if (typeof module !== 'undefined' && module.exports) { - exports = module.exports = _; - } - exports._ = _; - } else { - root._ = _; - } - - // Current version. - _.VERSION = '1.8.3'; - - // Internal function that returns an efficient (for current engines) version - // of the passed-in callback, to be repeatedly applied in other Underscore - // functions. - var optimizeCb = function(func, context, argCount) { - if (context === void 0) return func; - switch (argCount == null ? 3 : argCount) { - case 1: return function(value) { - return func.call(context, value); - }; - case 2: return function(value, other) { - return func.call(context, value, other); - }; - case 3: return function(value, index, collection) { - return func.call(context, value, index, collection); - }; - case 4: return function(accumulator, value, index, collection) { - return func.call(context, accumulator, value, index, collection); - }; - } - return function() { - return func.apply(context, arguments); - }; - }; - - // A mostly-internal function to generate callbacks that can be applied - // to each element in a collection, returning the desired result — either - // identity, an arbitrary callback, a property matcher, or a property accessor. - var cb = function(value, context, argCount) { - if (value == null) return _.identity; - if (_.isFunction(value)) return optimizeCb(value, context, argCount); - if (_.isObject(value)) return _.matcher(value); - return _.property(value); - }; - _.iteratee = function(value, context) { - return cb(value, context, Infinity); - }; - - // An internal function for creating assigner functions. - var createAssigner = function(keysFunc, undefinedOnly) { - return function(obj) { - var length = arguments.length; - if (length < 2 || obj == null) return obj; - for (var index = 1; index < length; index++) { - var source = arguments[index], - keys = keysFunc(source), - l = keys.length; - for (var i = 0; i < l; i++) { - var key = keys[i]; - if (!undefinedOnly || obj[key] === void 0) obj[key] = source[key]; - } - } - return obj; - }; - }; - - // An internal function for creating a new object that inherits from another. - var baseCreate = function(prototype) { - if (!_.isObject(prototype)) return {}; - if (nativeCreate) return nativeCreate(prototype); - Ctor.prototype = prototype; - var result = new Ctor; - Ctor.prototype = null; - return result; - }; - - var property = function(key) { - return function(obj) { - return obj == null ? void 0 : obj[key]; - }; - }; - - // Helper for collection methods to determine whether a collection - // should be iterated as an array or as an object - // Related: http://people.mozilla.org/~jorendorff/es6-draft.html#sec-tolength - // Avoids a very nasty iOS 8 JIT bug on ARM-64. #2094 - var MAX_ARRAY_INDEX = Math.pow(2, 53) - 1; - var getLength = property('length'); - var isArrayLike = function(collection) { - var length = getLength(collection); - return typeof length == 'number' && length >= 0 && length <= MAX_ARRAY_INDEX; - }; - - // Collection Functions - // -------------------- - - // The cornerstone, an `each` implementation, aka `forEach`. - // Handles raw objects in addition to array-likes. Treats all - // sparse array-likes as if they were dense. - _.each = _.forEach = function(obj, iteratee, context) { - iteratee = optimizeCb(iteratee, context); - var i, length; - if (isArrayLike(obj)) { - for (i = 0, length = obj.length; i < length; i++) { - iteratee(obj[i], i, obj); - } - } else { - var keys = _.keys(obj); - for (i = 0, length = keys.length; i < length; i++) { - iteratee(obj[keys[i]], keys[i], obj); - } - } - return obj; - }; - - // Return the results of applying the iteratee to each element. - _.map = _.collect = function(obj, iteratee, context) { - iteratee = cb(iteratee, context); - var keys = !isArrayLike(obj) && _.keys(obj), - length = (keys || obj).length, - results = Array(length); - for (var index = 0; index < length; index++) { - var currentKey = keys ? keys[index] : index; - results[index] = iteratee(obj[currentKey], currentKey, obj); - } - return results; - }; - - // Create a reducing function iterating left or right. - function createReduce(dir) { - // Optimized iterator function as using arguments.length - // in the main function will deoptimize the, see #1991. - function iterator(obj, iteratee, memo, keys, index, length) { - for (; index >= 0 && index < length; index += dir) { - var currentKey = keys ? keys[index] : index; - memo = iteratee(memo, obj[currentKey], currentKey, obj); - } - return memo; - } - - return function(obj, iteratee, memo, context) { - iteratee = optimizeCb(iteratee, context, 4); - var keys = !isArrayLike(obj) && _.keys(obj), - length = (keys || obj).length, - index = dir > 0 ? 0 : length - 1; - // Determine the initial value if none is provided. - if (arguments.length < 3) { - memo = obj[keys ? keys[index] : index]; - index += dir; - } - return iterator(obj, iteratee, memo, keys, index, length); - }; - } - - // **Reduce** builds up a single result from a list of values, aka `inject`, - // or `foldl`. - _.reduce = _.foldl = _.inject = createReduce(1); - - // The right-associative version of reduce, also known as `foldr`. - _.reduceRight = _.foldr = createReduce(-1); - - // Return the first value which passes a truth test. Aliased as `detect`. - _.find = _.detect = function(obj, predicate, context) { - var key; - if (isArrayLike(obj)) { - key = _.findIndex(obj, predicate, context); - } else { - key = _.findKey(obj, predicate, context); - } - if (key !== void 0 && key !== -1) return obj[key]; - }; - - // Return all the elements that pass a truth test. - // Aliased as `select`. - _.filter = _.select = function(obj, predicate, context) { - var results = []; - predicate = cb(predicate, context); - _.each(obj, function(value, index, list) { - if (predicate(value, index, list)) results.push(value); - }); - return results; - }; - - // Return all the elements for which a truth test fails. - _.reject = function(obj, predicate, context) { - return _.filter(obj, _.negate(cb(predicate)), context); - }; - - // Determine whether all of the elements match a truth test. - // Aliased as `all`. - _.every = _.all = function(obj, predicate, context) { - predicate = cb(predicate, context); - var keys = !isArrayLike(obj) && _.keys(obj), - length = (keys || obj).length; - for (var index = 0; index < length; index++) { - var currentKey = keys ? keys[index] : index; - if (!predicate(obj[currentKey], currentKey, obj)) return false; - } - return true; - }; - - // Determine if at least one element in the object matches a truth test. - // Aliased as `any`. - _.some = _.any = function(obj, predicate, context) { - predicate = cb(predicate, context); - var keys = !isArrayLike(obj) && _.keys(obj), - length = (keys || obj).length; - for (var index = 0; index < length; index++) { - var currentKey = keys ? keys[index] : index; - if (predicate(obj[currentKey], currentKey, obj)) return true; - } - return false; - }; - - // Determine if the array or object contains a given item (using `===`). - // Aliased as `includes` and `include`. - _.contains = _.includes = _.include = function(obj, item, fromIndex, guard) { - if (!isArrayLike(obj)) obj = _.values(obj); - if (typeof fromIndex != 'number' || guard) fromIndex = 0; - return _.indexOf(obj, item, fromIndex) >= 0; - }; - - // Invoke a method (with arguments) on every item in a collection. - _.invoke = function(obj, method) { - var args = slice.call(arguments, 2); - var isFunc = _.isFunction(method); - return _.map(obj, function(value) { - var func = isFunc ? method : value[method]; - return func == null ? func : func.apply(value, args); - }); - }; - - // Convenience version of a common use case of `map`: fetching a property. - _.pluck = function(obj, key) { - return _.map(obj, _.property(key)); - }; - - // Convenience version of a common use case of `filter`: selecting only objects - // containing specific `key:value` pairs. - _.where = function(obj, attrs) { - return _.filter(obj, _.matcher(attrs)); - }; - - // Convenience version of a common use case of `find`: getting the first object - // containing specific `key:value` pairs. - _.findWhere = function(obj, attrs) { - return _.find(obj, _.matcher(attrs)); - }; - - // Return the maximum element (or element-based computation). - _.max = function(obj, iteratee, context) { - var result = -Infinity, lastComputed = -Infinity, - value, computed; - if (iteratee == null && obj != null) { - obj = isArrayLike(obj) ? obj : _.values(obj); - for (var i = 0, length = obj.length; i < length; i++) { - value = obj[i]; - if (value > result) { - result = value; - } - } - } else { - iteratee = cb(iteratee, context); - _.each(obj, function(value, index, list) { - computed = iteratee(value, index, list); - if (computed > lastComputed || computed === -Infinity && result === -Infinity) { - result = value; - lastComputed = computed; - } - }); - } - return result; - }; - - // Return the minimum element (or element-based computation). - _.min = function(obj, iteratee, context) { - var result = Infinity, lastComputed = Infinity, - value, computed; - if (iteratee == null && obj != null) { - obj = isArrayLike(obj) ? obj : _.values(obj); - for (var i = 0, length = obj.length; i < length; i++) { - value = obj[i]; - if (value < result) { - result = value; - } - } - } else { - iteratee = cb(iteratee, context); - _.each(obj, function(value, index, list) { - computed = iteratee(value, index, list); - if (computed < lastComputed || computed === Infinity && result === Infinity) { - result = value; - lastComputed = computed; - } - }); - } - return result; - }; - - // Shuffle a collection, using the modern version of the - // [Fisher-Yates shuffle](http://en.wikipedia.org/wiki/Fisher–Yates_shuffle). - _.shuffle = function(obj) { - var set = isArrayLike(obj) ? obj : _.values(obj); - var length = set.length; - var shuffled = Array(length); - for (var index = 0, rand; index < length; index++) { - rand = _.random(0, index); - if (rand !== index) shuffled[index] = shuffled[rand]; - shuffled[rand] = set[index]; - } - return shuffled; - }; - - // Sample **n** random values from a collection. - // If **n** is not specified, returns a single random element. - // The internal `guard` argument allows it to work with `map`. - _.sample = function(obj, n, guard) { - if (n == null || guard) { - if (!isArrayLike(obj)) obj = _.values(obj); - return obj[_.random(obj.length - 1)]; - } - return _.shuffle(obj).slice(0, Math.max(0, n)); - }; - - // Sort the object's values by a criterion produced by an iteratee. - _.sortBy = function(obj, iteratee, context) { - iteratee = cb(iteratee, context); - return _.pluck(_.map(obj, function(value, index, list) { - return { - value: value, - index: index, - criteria: iteratee(value, index, list) - }; - }).sort(function(left, right) { - var a = left.criteria; - var b = right.criteria; - if (a !== b) { - if (a > b || a === void 0) return 1; - if (a < b || b === void 0) return -1; - } - return left.index - right.index; - }), 'value'); - }; - - // An internal function used for aggregate "group by" operations. - var group = function(behavior) { - return function(obj, iteratee, context) { - var result = {}; - iteratee = cb(iteratee, context); - _.each(obj, function(value, index) { - var key = iteratee(value, index, obj); - behavior(result, value, key); - }); - return result; - }; - }; - - // Groups the object's values by a criterion. Pass either a string attribute - // to group by, or a function that returns the criterion. - _.groupBy = group(function(result, value, key) { - if (_.has(result, key)) result[key].push(value); else result[key] = [value]; - }); - - // Indexes the object's values by a criterion, similar to `groupBy`, but for - // when you know that your index values will be unique. - _.indexBy = group(function(result, value, key) { - result[key] = value; - }); - - // Counts instances of an object that group by a certain criterion. Pass - // either a string attribute to count by, or a function that returns the - // criterion. - _.countBy = group(function(result, value, key) { - if (_.has(result, key)) result[key]++; else result[key] = 1; - }); - - // Safely create a real, live array from anything iterable. - _.toArray = function(obj) { - if (!obj) return []; - if (_.isArray(obj)) return slice.call(obj); - if (isArrayLike(obj)) return _.map(obj, _.identity); - return _.values(obj); - }; - - // Return the number of elements in an object. - _.size = function(obj) { - if (obj == null) return 0; - return isArrayLike(obj) ? obj.length : _.keys(obj).length; - }; - - // Split a collection into two arrays: one whose elements all satisfy the given - // predicate, and one whose elements all do not satisfy the predicate. - _.partition = function(obj, predicate, context) { - predicate = cb(predicate, context); - var pass = [], fail = []; - _.each(obj, function(value, key, obj) { - (predicate(value, key, obj) ? pass : fail).push(value); - }); - return [pass, fail]; - }; - - // Array Functions - // --------------- - - // Get the first element of an array. Passing **n** will return the first N - // values in the array. Aliased as `head` and `take`. The **guard** check - // allows it to work with `_.map`. - _.first = _.head = _.take = function(array, n, guard) { - if (array == null) return void 0; - if (n == null || guard) return array[0]; - return _.initial(array, array.length - n); - }; - - // Returns everything but the last entry of the array. Especially useful on - // the arguments object. Passing **n** will return all the values in - // the array, excluding the last N. - _.initial = function(array, n, guard) { - return slice.call(array, 0, Math.max(0, array.length - (n == null || guard ? 1 : n))); - }; - - // Get the last element of an array. Passing **n** will return the last N - // values in the array. - _.last = function(array, n, guard) { - if (array == null) return void 0; - if (n == null || guard) return array[array.length - 1]; - return _.rest(array, Math.max(0, array.length - n)); - }; - - // Returns everything but the first entry of the array. Aliased as `tail` and `drop`. - // Especially useful on the arguments object. Passing an **n** will return - // the rest N values in the array. - _.rest = _.tail = _.drop = function(array, n, guard) { - return slice.call(array, n == null || guard ? 1 : n); - }; - - // Trim out all falsy values from an array. - _.compact = function(array) { - return _.filter(array, _.identity); - }; - - // Internal implementation of a recursive `flatten` function. - var flatten = function(input, shallow, strict, startIndex) { - var output = [], idx = 0; - for (var i = startIndex || 0, length = getLength(input); i < length; i++) { - var value = input[i]; - if (isArrayLike(value) && (_.isArray(value) || _.isArguments(value))) { - //flatten current level of array or arguments object - if (!shallow) value = flatten(value, shallow, strict); - var j = 0, len = value.length; - output.length += len; - while (j < len) { - output[idx++] = value[j++]; - } - } else if (!strict) { - output[idx++] = value; - } - } - return output; - }; - - // Flatten out an array, either recursively (by default), or just one level. - _.flatten = function(array, shallow) { - return flatten(array, shallow, false); - }; - - // Return a version of the array that does not contain the specified value(s). - _.without = function(array) { - return _.difference(array, slice.call(arguments, 1)); - }; - - // Produce a duplicate-free version of the array. If the array has already - // been sorted, you have the option of using a faster algorithm. - // Aliased as `unique`. - _.uniq = _.unique = function(array, isSorted, iteratee, context) { - if (!_.isBoolean(isSorted)) { - context = iteratee; - iteratee = isSorted; - isSorted = false; - } - if (iteratee != null) iteratee = cb(iteratee, context); - var result = []; - var seen = []; - for (var i = 0, length = getLength(array); i < length; i++) { - var value = array[i], - computed = iteratee ? iteratee(value, i, array) : value; - if (isSorted) { - if (!i || seen !== computed) result.push(value); - seen = computed; - } else if (iteratee) { - if (!_.contains(seen, computed)) { - seen.push(computed); - result.push(value); - } - } else if (!_.contains(result, value)) { - result.push(value); - } - } - return result; - }; - - // Produce an array that contains the union: each distinct element from all of - // the passed-in arrays. - _.union = function() { - return _.uniq(flatten(arguments, true, true)); - }; - - // Produce an array that contains every item shared between all the - // passed-in arrays. - _.intersection = function(array) { - var result = []; - var argsLength = arguments.length; - for (var i = 0, length = getLength(array); i < length; i++) { - var item = array[i]; - if (_.contains(result, item)) continue; - for (var j = 1; j < argsLength; j++) { - if (!_.contains(arguments[j], item)) break; - } - if (j === argsLength) result.push(item); - } - return result; - }; - - // Take the difference between one array and a number of other arrays. - // Only the elements present in just the first array will remain. - _.difference = function(array) { - var rest = flatten(arguments, true, true, 1); - return _.filter(array, function(value){ - return !_.contains(rest, value); - }); - }; - - // Zip together multiple lists into a single array -- elements that share - // an index go together. - _.zip = function() { - return _.unzip(arguments); - }; - - // Complement of _.zip. Unzip accepts an array of arrays and groups - // each array's elements on shared indices - _.unzip = function(array) { - var length = array && _.max(array, getLength).length || 0; - var result = Array(length); - - for (var index = 0; index < length; index++) { - result[index] = _.pluck(array, index); - } - return result; - }; - - // Converts lists into objects. Pass either a single array of `[key, value]` - // pairs, or two parallel arrays of the same length -- one of keys, and one of - // the corresponding values. - _.object = function(list, values) { - var result = {}; - for (var i = 0, length = getLength(list); i < length; i++) { - if (values) { - result[list[i]] = values[i]; - } else { - result[list[i][0]] = list[i][1]; - } - } - return result; - }; - - // Generator function to create the findIndex and findLastIndex functions - function createPredicateIndexFinder(dir) { - return function(array, predicate, context) { - predicate = cb(predicate, context); - var length = getLength(array); - var index = dir > 0 ? 0 : length - 1; - for (; index >= 0 && index < length; index += dir) { - if (predicate(array[index], index, array)) return index; - } - return -1; - }; - } - - // Returns the first index on an array-like that passes a predicate test - _.findIndex = createPredicateIndexFinder(1); - _.findLastIndex = createPredicateIndexFinder(-1); - - // Use a comparator function to figure out the smallest index at which - // an object should be inserted so as to maintain order. Uses binary search. - _.sortedIndex = function(array, obj, iteratee, context) { - iteratee = cb(iteratee, context, 1); - var value = iteratee(obj); - var low = 0, high = getLength(array); - while (low < high) { - var mid = Math.floor((low + high) / 2); - if (iteratee(array[mid]) < value) low = mid + 1; else high = mid; - } - return low; - }; - - // Generator function to create the indexOf and lastIndexOf functions - function createIndexFinder(dir, predicateFind, sortedIndex) { - return function(array, item, idx) { - var i = 0, length = getLength(array); - if (typeof idx == 'number') { - if (dir > 0) { - i = idx >= 0 ? idx : Math.max(idx + length, i); - } else { - length = idx >= 0 ? Math.min(idx + 1, length) : idx + length + 1; - } - } else if (sortedIndex && idx && length) { - idx = sortedIndex(array, item); - return array[idx] === item ? idx : -1; - } - if (item !== item) { - idx = predicateFind(slice.call(array, i, length), _.isNaN); - return idx >= 0 ? idx + i : -1; - } - for (idx = dir > 0 ? i : length - 1; idx >= 0 && idx < length; idx += dir) { - if (array[idx] === item) return idx; - } - return -1; - }; - } - - // Return the position of the first occurrence of an item in an array, - // or -1 if the item is not included in the array. - // If the array is large and already in sort order, pass `true` - // for **isSorted** to use binary search. - _.indexOf = createIndexFinder(1, _.findIndex, _.sortedIndex); - _.lastIndexOf = createIndexFinder(-1, _.findLastIndex); - - // Generate an integer Array containing an arithmetic progression. A port of - // the native Python `range()` function. See - // [the Python documentation](http://docs.python.org/library/functions.html#range). - _.range = function(start, stop, step) { - if (stop == null) { - stop = start || 0; - start = 0; - } - step = step || 1; - - var length = Math.max(Math.ceil((stop - start) / step), 0); - var range = Array(length); - - for (var idx = 0; idx < length; idx++, start += step) { - range[idx] = start; - } - - return range; - }; - - // Function (ahem) Functions - // ------------------ - - // Determines whether to execute a function as a constructor - // or a normal function with the provided arguments - var executeBound = function(sourceFunc, boundFunc, context, callingContext, args) { - if (!(callingContext instanceof boundFunc)) return sourceFunc.apply(context, args); - var self = baseCreate(sourceFunc.prototype); - var result = sourceFunc.apply(self, args); - if (_.isObject(result)) return result; - return self; - }; - - // Create a function bound to a given object (assigning `this`, and arguments, - // optionally). Delegates to **ECMAScript 5**'s native `Function.bind` if - // available. - _.bind = function(func, context) { - if (nativeBind && func.bind === nativeBind) return nativeBind.apply(func, slice.call(arguments, 1)); - if (!_.isFunction(func)) throw new TypeError('Bind must be called on a function'); - var args = slice.call(arguments, 2); - var bound = function() { - return executeBound(func, bound, context, this, args.concat(slice.call(arguments))); - }; - return bound; - }; - - // Partially apply a function by creating a version that has had some of its - // arguments pre-filled, without changing its dynamic `this` context. _ acts - // as a placeholder, allowing any combination of arguments to be pre-filled. - _.partial = function(func) { - var boundArgs = slice.call(arguments, 1); - var bound = function() { - var position = 0, length = boundArgs.length; - var args = Array(length); - for (var i = 0; i < length; i++) { - args[i] = boundArgs[i] === _ ? arguments[position++] : boundArgs[i]; - } - while (position < arguments.length) args.push(arguments[position++]); - return executeBound(func, bound, this, this, args); - }; - return bound; - }; - - // Bind a number of an object's methods to that object. Remaining arguments - // are the method names to be bound. Useful for ensuring that all callbacks - // defined on an object belong to it. - _.bindAll = function(obj) { - var i, length = arguments.length, key; - if (length <= 1) throw new Error('bindAll must be passed function names'); - for (i = 1; i < length; i++) { - key = arguments[i]; - obj[key] = _.bind(obj[key], obj); - } - return obj; - }; - - // Memoize an expensive function by storing its results. - _.memoize = function(func, hasher) { - var memoize = function(key) { - var cache = memoize.cache; - var address = '' + (hasher ? hasher.apply(this, arguments) : key); - if (!_.has(cache, address)) cache[address] = func.apply(this, arguments); - return cache[address]; - }; - memoize.cache = {}; - return memoize; - }; - - // Delays a function for the given number of milliseconds, and then calls - // it with the arguments supplied. - _.delay = function(func, wait) { - var args = slice.call(arguments, 2); - return setTimeout(function(){ - return func.apply(null, args); - }, wait); - }; - - // Defers a function, scheduling it to run after the current call stack has - // cleared. - _.defer = _.partial(_.delay, _, 1); - - // Returns a function, that, when invoked, will only be triggered at most once - // during a given window of time. Normally, the throttled function will run - // as much as it can, without ever going more than once per `wait` duration; - // but if you'd like to disable the execution on the leading edge, pass - // `{leading: false}`. To disable execution on the trailing edge, ditto. - _.throttle = function(func, wait, options) { - var context, args, result; - var timeout = null; - var previous = 0; - if (!options) options = {}; - var later = function() { - previous = options.leading === false ? 0 : _.now(); - timeout = null; - result = func.apply(context, args); - if (!timeout) context = args = null; - }; - return function() { - var now = _.now(); - if (!previous && options.leading === false) previous = now; - var remaining = wait - (now - previous); - context = this; - args = arguments; - if (remaining <= 0 || remaining > wait) { - if (timeout) { - clearTimeout(timeout); - timeout = null; - } - previous = now; - result = func.apply(context, args); - if (!timeout) context = args = null; - } else if (!timeout && options.trailing !== false) { - timeout = setTimeout(later, remaining); - } - return result; - }; - }; - - // Returns a function, that, as long as it continues to be invoked, will not - // be triggered. The function will be called after it stops being called for - // N milliseconds. If `immediate` is passed, trigger the function on the - // leading edge, instead of the trailing. - _.debounce = function(func, wait, immediate) { - var timeout, args, context, timestamp, result; - - var later = function() { - var last = _.now() - timestamp; - - if (last < wait && last >= 0) { - timeout = setTimeout(later, wait - last); - } else { - timeout = null; - if (!immediate) { - result = func.apply(context, args); - if (!timeout) context = args = null; - } - } - }; - - return function() { - context = this; - args = arguments; - timestamp = _.now(); - var callNow = immediate && !timeout; - if (!timeout) timeout = setTimeout(later, wait); - if (callNow) { - result = func.apply(context, args); - context = args = null; - } - - return result; - }; - }; - - // Returns the first function passed as an argument to the second, - // allowing you to adjust arguments, run code before and after, and - // conditionally execute the original function. - _.wrap = function(func, wrapper) { - return _.partial(wrapper, func); - }; - - // Returns a negated version of the passed-in predicate. - _.negate = function(predicate) { - return function() { - return !predicate.apply(this, arguments); - }; - }; - - // Returns a function that is the composition of a list of functions, each - // consuming the return value of the function that follows. - _.compose = function() { - var args = arguments; - var start = args.length - 1; - return function() { - var i = start; - var result = args[start].apply(this, arguments); - while (i--) result = args[i].call(this, result); - return result; - }; - }; - - // Returns a function that will only be executed on and after the Nth call. - _.after = function(times, func) { - return function() { - if (--times < 1) { - return func.apply(this, arguments); - } - }; - }; - - // Returns a function that will only be executed up to (but not including) the Nth call. - _.before = function(times, func) { - var memo; - return function() { - if (--times > 0) { - memo = func.apply(this, arguments); - } - if (times <= 1) func = null; - return memo; - }; - }; - - // Returns a function that will be executed at most one time, no matter how - // often you call it. Useful for lazy initialization. - _.once = _.partial(_.before, 2); - - // Object Functions - // ---------------- - - // Keys in IE < 9 that won't be iterated by `for key in ...` and thus missed. - var hasEnumBug = !{toString: null}.propertyIsEnumerable('toString'); - var nonEnumerableProps = ['valueOf', 'isPrototypeOf', 'toString', - 'propertyIsEnumerable', 'hasOwnProperty', 'toLocaleString']; - - function collectNonEnumProps(obj, keys) { - var nonEnumIdx = nonEnumerableProps.length; - var constructor = obj.constructor; - var proto = (_.isFunction(constructor) && constructor.prototype) || ObjProto; - - // Constructor is a special case. - var prop = 'constructor'; - if (_.has(obj, prop) && !_.contains(keys, prop)) keys.push(prop); - - while (nonEnumIdx--) { - prop = nonEnumerableProps[nonEnumIdx]; - if (prop in obj && obj[prop] !== proto[prop] && !_.contains(keys, prop)) { - keys.push(prop); - } - } - } - - // Retrieve the names of an object's own properties. - // Delegates to **ECMAScript 5**'s native `Object.keys` - _.keys = function(obj) { - if (!_.isObject(obj)) return []; - if (nativeKeys) return nativeKeys(obj); - var keys = []; - for (var key in obj) if (_.has(obj, key)) keys.push(key); - // Ahem, IE < 9. - if (hasEnumBug) collectNonEnumProps(obj, keys); - return keys; - }; - - // Retrieve all the property names of an object. - _.allKeys = function(obj) { - if (!_.isObject(obj)) return []; - var keys = []; - for (var key in obj) keys.push(key); - // Ahem, IE < 9. - if (hasEnumBug) collectNonEnumProps(obj, keys); - return keys; - }; - - // Retrieve the values of an object's properties. - _.values = function(obj) { - var keys = _.keys(obj); - var length = keys.length; - var values = Array(length); - for (var i = 0; i < length; i++) { - values[i] = obj[keys[i]]; - } - return values; - }; - - // Returns the results of applying the iteratee to each element of the object - // In contrast to _.map it returns an object - _.mapObject = function(obj, iteratee, context) { - iteratee = cb(iteratee, context); - var keys = _.keys(obj), - length = keys.length, - results = {}, - currentKey; - for (var index = 0; index < length; index++) { - currentKey = keys[index]; - results[currentKey] = iteratee(obj[currentKey], currentKey, obj); - } - return results; - }; - - // Convert an object into a list of `[key, value]` pairs. - _.pairs = function(obj) { - var keys = _.keys(obj); - var length = keys.length; - var pairs = Array(length); - for (var i = 0; i < length; i++) { - pairs[i] = [keys[i], obj[keys[i]]]; - } - return pairs; - }; - - // Invert the keys and values of an object. The values must be serializable. - _.invert = function(obj) { - var result = {}; - var keys = _.keys(obj); - for (var i = 0, length = keys.length; i < length; i++) { - result[obj[keys[i]]] = keys[i]; - } - return result; - }; - - // Return a sorted list of the function names available on the object. - // Aliased as `methods` - _.functions = _.methods = function(obj) { - var names = []; - for (var key in obj) { - if (_.isFunction(obj[key])) names.push(key); - } - return names.sort(); - }; - - // Extend a given object with all the properties in passed-in object(s). - _.extend = createAssigner(_.allKeys); - - // Assigns a given object with all the own properties in the passed-in object(s) - // (https://developer.mozilla.org/docs/Web/JavaScript/Reference/Global_Objects/Object/assign) - _.extendOwn = _.assign = createAssigner(_.keys); - - // Returns the first key on an object that passes a predicate test - _.findKey = function(obj, predicate, context) { - predicate = cb(predicate, context); - var keys = _.keys(obj), key; - for (var i = 0, length = keys.length; i < length; i++) { - key = keys[i]; - if (predicate(obj[key], key, obj)) return key; - } - }; - - // Return a copy of the object only containing the whitelisted properties. - _.pick = function(object, oiteratee, context) { - var result = {}, obj = object, iteratee, keys; - if (obj == null) return result; - if (_.isFunction(oiteratee)) { - keys = _.allKeys(obj); - iteratee = optimizeCb(oiteratee, context); - } else { - keys = flatten(arguments, false, false, 1); - iteratee = function(value, key, obj) { return key in obj; }; - obj = Object(obj); - } - for (var i = 0, length = keys.length; i < length; i++) { - var key = keys[i]; - var value = obj[key]; - if (iteratee(value, key, obj)) result[key] = value; - } - return result; - }; - - // Return a copy of the object without the blacklisted properties. - _.omit = function(obj, iteratee, context) { - if (_.isFunction(iteratee)) { - iteratee = _.negate(iteratee); - } else { - var keys = _.map(flatten(arguments, false, false, 1), String); - iteratee = function(value, key) { - return !_.contains(keys, key); - }; - } - return _.pick(obj, iteratee, context); - }; - - // Fill in a given object with default properties. - _.defaults = createAssigner(_.allKeys, true); - - // Creates an object that inherits from the given prototype object. - // If additional properties are provided then they will be added to the - // created object. - _.create = function(prototype, props) { - var result = baseCreate(prototype); - if (props) _.extendOwn(result, props); - return result; - }; - - // Create a (shallow-cloned) duplicate of an object. - _.clone = function(obj) { - if (!_.isObject(obj)) return obj; - return _.isArray(obj) ? obj.slice() : _.extend({}, obj); - }; - - // Invokes interceptor with the obj, and then returns obj. - // The primary purpose of this method is to "tap into" a method chain, in - // order to perform operations on intermediate results within the chain. - _.tap = function(obj, interceptor) { - interceptor(obj); - return obj; - }; - - // Returns whether an object has a given set of `key:value` pairs. - _.isMatch = function(object, attrs) { - var keys = _.keys(attrs), length = keys.length; - if (object == null) return !length; - var obj = Object(object); - for (var i = 0; i < length; i++) { - var key = keys[i]; - if (attrs[key] !== obj[key] || !(key in obj)) return false; - } - return true; - }; - - - // Internal recursive comparison function for `isEqual`. - var eq = function(a, b, aStack, bStack) { - // Identical objects are equal. `0 === -0`, but they aren't identical. - // See the [Harmony `egal` proposal](http://wiki.ecmascript.org/doku.php?id=harmony:egal). - if (a === b) return a !== 0 || 1 / a === 1 / b; - // A strict comparison is necessary because `null == undefined`. - if (a == null || b == null) return a === b; - // Unwrap any wrapped objects. - if (a instanceof _) a = a._wrapped; - if (b instanceof _) b = b._wrapped; - // Compare `[[Class]]` names. - var className = toString.call(a); - if (className !== toString.call(b)) return false; - switch (className) { - // Strings, numbers, regular expressions, dates, and booleans are compared by value. - case '[object RegExp]': - // RegExps are coerced to strings for comparison (Note: '' + /a/i === '/a/i') - case '[object String]': - // Primitives and their corresponding object wrappers are equivalent; thus, `"5"` is - // equivalent to `new String("5")`. - return '' + a === '' + b; - case '[object Number]': - // `NaN`s are equivalent, but non-reflexive. - // Object(NaN) is equivalent to NaN - if (+a !== +a) return +b !== +b; - // An `egal` comparison is performed for other numeric values. - return +a === 0 ? 1 / +a === 1 / b : +a === +b; - case '[object Date]': - case '[object Boolean]': - // Coerce dates and booleans to numeric primitive values. Dates are compared by their - // millisecond representations. Note that invalid dates with millisecond representations - // of `NaN` are not equivalent. - return +a === +b; - } - - var areArrays = className === '[object Array]'; - if (!areArrays) { - if (typeof a != 'object' || typeof b != 'object') return false; - - // Objects with different constructors are not equivalent, but `Object`s or `Array`s - // from different frames are. - var aCtor = a.constructor, bCtor = b.constructor; - if (aCtor !== bCtor && !(_.isFunction(aCtor) && aCtor instanceof aCtor && - _.isFunction(bCtor) && bCtor instanceof bCtor) - && ('constructor' in a && 'constructor' in b)) { - return false; - } - } - // Assume equality for cyclic structures. The algorithm for detecting cyclic - // structures is adapted from ES 5.1 section 15.12.3, abstract operation `JO`. - - // Initializing stack of traversed objects. - // It's done here since we only need them for objects and arrays comparison. - aStack = aStack || []; - bStack = bStack || []; - var length = aStack.length; - while (length--) { - // Linear search. Performance is inversely proportional to the number of - // unique nested structures. - if (aStack[length] === a) return bStack[length] === b; - } - - // Add the first object to the stack of traversed objects. - aStack.push(a); - bStack.push(b); - - // Recursively compare objects and arrays. - if (areArrays) { - // Compare array lengths to determine if a deep comparison is necessary. - length = a.length; - if (length !== b.length) return false; - // Deep compare the contents, ignoring non-numeric properties. - while (length--) { - if (!eq(a[length], b[length], aStack, bStack)) return false; - } - } else { - // Deep compare objects. - var keys = _.keys(a), key; - length = keys.length; - // Ensure that both objects contain the same number of properties before comparing deep equality. - if (_.keys(b).length !== length) return false; - while (length--) { - // Deep compare each member - key = keys[length]; - if (!(_.has(b, key) && eq(a[key], b[key], aStack, bStack))) return false; - } - } - // Remove the first object from the stack of traversed objects. - aStack.pop(); - bStack.pop(); - return true; - }; - - // Perform a deep comparison to check if two objects are equal. - _.isEqual = function(a, b) { - return eq(a, b); - }; - - // Is a given array, string, or object empty? - // An "empty" object has no enumerable own-properties. - _.isEmpty = function(obj) { - if (obj == null) return true; - if (isArrayLike(obj) && (_.isArray(obj) || _.isString(obj) || _.isArguments(obj))) return obj.length === 0; - return _.keys(obj).length === 0; - }; - - // Is a given value a DOM element? - _.isElement = function(obj) { - return !!(obj && obj.nodeType === 1); - }; - - // Is a given value an array? - // Delegates to ECMA5's native Array.isArray - _.isArray = nativeIsArray || function(obj) { - return toString.call(obj) === '[object Array]'; - }; - - // Is a given variable an object? - _.isObject = function(obj) { - var type = typeof obj; - return type === 'function' || type === 'object' && !!obj; - }; - - // Add some isType methods: isArguments, isFunction, isString, isNumber, isDate, isRegExp, isError. - _.each(['Arguments', 'Function', 'String', 'Number', 'Date', 'RegExp', 'Error'], function(name) { - _['is' + name] = function(obj) { - return toString.call(obj) === '[object ' + name + ']'; - }; - }); - - // Define a fallback version of the method in browsers (ahem, IE < 9), where - // there isn't any inspectable "Arguments" type. - if (!_.isArguments(arguments)) { - _.isArguments = function(obj) { - return _.has(obj, 'callee'); - }; - } - - // Optimize `isFunction` if appropriate. Work around some typeof bugs in old v8, - // IE 11 (#1621), and in Safari 8 (#1929). - if (typeof /./ != 'function' && typeof Int8Array != 'object') { - _.isFunction = function(obj) { - return typeof obj == 'function' || false; - }; - } - - // Is a given object a finite number? - _.isFinite = function(obj) { - return isFinite(obj) && !isNaN(parseFloat(obj)); - }; - - // Is the given value `NaN`? (NaN is the only number which does not equal itself). - _.isNaN = function(obj) { - return _.isNumber(obj) && obj !== +obj; - }; - - // Is a given value a boolean? - _.isBoolean = function(obj) { - return obj === true || obj === false || toString.call(obj) === '[object Boolean]'; - }; - - // Is a given value equal to null? - _.isNull = function(obj) { - return obj === null; - }; - - // Is a given variable undefined? - _.isUndefined = function(obj) { - return obj === void 0; - }; - - // Shortcut function for checking if an object has a given property directly - // on itself (in other words, not on a prototype). - _.has = function(obj, key) { - return obj != null && hasOwnProperty.call(obj, key); - }; - - // Utility Functions - // ----------------- - - // Run Underscore.js in *noConflict* mode, returning the `_` variable to its - // previous owner. Returns a reference to the Underscore object. - _.noConflict = function() { - root._ = previousUnderscore; - return this; - }; - - // Keep the identity function around for default iteratees. - _.identity = function(value) { - return value; - }; - - // Predicate-generating functions. Often useful outside of Underscore. - _.constant = function(value) { - return function() { - return value; - }; - }; - - _.noop = function(){}; - - _.property = property; - - // Generates a function for a given object that returns a given property. - _.propertyOf = function(obj) { - return obj == null ? function(){} : function(key) { - return obj[key]; - }; - }; - - // Returns a predicate for checking whether an object has a given set of - // `key:value` pairs. - _.matcher = _.matches = function(attrs) { - attrs = _.extendOwn({}, attrs); - return function(obj) { - return _.isMatch(obj, attrs); - }; - }; - - // Run a function **n** times. - _.times = function(n, iteratee, context) { - var accum = Array(Math.max(0, n)); - iteratee = optimizeCb(iteratee, context, 1); - for (var i = 0; i < n; i++) accum[i] = iteratee(i); - return accum; - }; - - // Return a random integer between min and max (inclusive). - _.random = function(min, max) { - if (max == null) { - max = min; - min = 0; - } - return min + Math.floor(Math.random() * (max - min + 1)); - }; - - // A (possibly faster) way to get the current timestamp as an integer. - _.now = Date.now || function() { - return new Date().getTime(); - }; - - // List of HTML entities for escaping. - var escapeMap = { - '&': '&', - '<': '<', - '>': '>', - '"': '"', - "'": ''', - '`': '`' - }; - var unescapeMap = _.invert(escapeMap); - - // Functions for escaping and unescaping strings to/from HTML interpolation. - var createEscaper = function(map) { - var escaper = function(match) { - return map[match]; - }; - // Regexes for identifying a key that needs to be escaped - var source = '(?:' + _.keys(map).join('|') + ')'; - var testRegexp = RegExp(source); - var replaceRegexp = RegExp(source, 'g'); - return function(string) { - string = string == null ? '' : '' + string; - return testRegexp.test(string) ? string.replace(replaceRegexp, escaper) : string; - }; - }; - _.escape = createEscaper(escapeMap); - _.unescape = createEscaper(unescapeMap); - - // If the value of the named `property` is a function then invoke it with the - // `object` as context; otherwise, return it. - _.result = function(object, property, fallback) { - var value = object == null ? void 0 : object[property]; - if (value === void 0) { - value = fallback; - } - return _.isFunction(value) ? value.call(object) : value; - }; - - // Generate a unique integer id (unique within the entire client session). - // Useful for temporary DOM ids. - var idCounter = 0; - _.uniqueId = function(prefix) { - var id = ++idCounter + ''; - return prefix ? prefix + id : id; - }; - - // By default, Underscore uses ERB-style template delimiters, change the - // following template settings to use alternative delimiters. - _.templateSettings = { - evaluate : /<%([\s\S]+?)%>/g, - interpolate : /<%=([\s\S]+?)%>/g, - escape : /<%-([\s\S]+?)%>/g - }; - - // When customizing `templateSettings`, if you don't want to define an - // interpolation, evaluation or escaping regex, we need one that is - // guaranteed not to match. - var noMatch = /(.)^/; - - // Certain characters need to be escaped so that they can be put into a - // string literal. - var escapes = { - "'": "'", - '\\': '\\', - '\r': 'r', - '\n': 'n', - '\u2028': 'u2028', - '\u2029': 'u2029' - }; - - var escaper = /\\|'|\r|\n|\u2028|\u2029/g; - - var escapeChar = function(match) { - return '\\' + escapes[match]; - }; - - // JavaScript micro-templating, similar to John Resig's implementation. - // Underscore templating handles arbitrary delimiters, preserves whitespace, - // and correctly escapes quotes within interpolated code. - // NB: `oldSettings` only exists for backwards compatibility. - _.template = function(text, settings, oldSettings) { - if (!settings && oldSettings) settings = oldSettings; - settings = _.defaults({}, settings, _.templateSettings); - - // Combine delimiters into one regular expression via alternation. - var matcher = RegExp([ - (settings.escape || noMatch).source, - (settings.interpolate || noMatch).source, - (settings.evaluate || noMatch).source - ].join('|') + '|$', 'g'); - - // Compile the template source, escaping string literals appropriately. - var index = 0; - var source = "__p+='"; - text.replace(matcher, function(match, escape, interpolate, evaluate, offset) { - source += text.slice(index, offset).replace(escaper, escapeChar); - index = offset + match.length; - - if (escape) { - source += "'+\n((__t=(" + escape + "))==null?'':_.escape(__t))+\n'"; - } else if (interpolate) { - source += "'+\n((__t=(" + interpolate + "))==null?'':__t)+\n'"; - } else if (evaluate) { - source += "';\n" + evaluate + "\n__p+='"; - } - - // Adobe VMs need the match returned to produce the correct offest. - return match; - }); - source += "';\n"; - - // If a variable is not specified, place data values in local scope. - if (!settings.variable) source = 'with(obj||{}){\n' + source + '}\n'; - - source = "var __t,__p='',__j=Array.prototype.join," + - "print=function(){__p+=__j.call(arguments,'');};\n" + - source + 'return __p;\n'; - - try { - var render = new Function(settings.variable || 'obj', '_', source); - } catch (e) { - e.source = source; - throw e; - } - - var template = function(data) { - return render.call(this, data, _); - }; - - // Provide the compiled source as a convenience for precompilation. - var argument = settings.variable || 'obj'; - template.source = 'function(' + argument + '){\n' + source + '}'; - - return template; - }; - - // Add a "chain" function. Start chaining a wrapped Underscore object. - _.chain = function(obj) { - var instance = _(obj); - instance._chain = true; - return instance; - }; - - // OOP - // --------------- - // If Underscore is called as a function, it returns a wrapped object that - // can be used OO-style. This wrapper holds altered versions of all the - // underscore functions. Wrapped objects may be chained. - - // Helper function to continue chaining intermediate results. - var result = function(instance, obj) { - return instance._chain ? _(obj).chain() : obj; - }; - - // Add your own custom functions to the Underscore object. - _.mixin = function(obj) { - _.each(_.functions(obj), function(name) { - var func = _[name] = obj[name]; - _.prototype[name] = function() { - var args = [this._wrapped]; - push.apply(args, arguments); - return result(this, func.apply(_, args)); - }; - }); - }; - - // Add all of the Underscore functions to the wrapper object. - _.mixin(_); - - // Add all mutator Array functions to the wrapper. - _.each(['pop', 'push', 'reverse', 'shift', 'sort', 'splice', 'unshift'], function(name) { - var method = ArrayProto[name]; - _.prototype[name] = function() { - var obj = this._wrapped; - method.apply(obj, arguments); - if ((name === 'shift' || name === 'splice') && obj.length === 0) delete obj[0]; - return result(this, obj); - }; - }); - - // Add all accessor Array functions to the wrapper. - _.each(['concat', 'join', 'slice'], function(name) { - var method = ArrayProto[name]; - _.prototype[name] = function() { - return result(this, method.apply(this._wrapped, arguments)); - }; - }); - - // Extracts the result from a wrapped and chained object. - _.prototype.value = function() { - return this._wrapped; - }; - - // Provide unwrapping proxy for some methods used in engine operations - // such as arithmetic and JSON stringification. - _.prototype.valueOf = _.prototype.toJSON = _.prototype.value; - - _.prototype.toString = function() { - return '' + this._wrapped; - }; - - // AMD registration happens at the end for compatibility with AMD loaders - // that may not enforce next-turn semantics on modules. Even though general - // practice for AMD registration is to be anonymous, underscore registers - // as a named module because, like jQuery, it is a base library that is - // popular enough to be bundled in a third party lib, but not be part of - // an AMD load request. Those cases could generate an error when an - // anonymous define() is called outside of a loader request. - if (typeof define === 'function' && define.amd) { - define('underscore', [], function() { - return _; - }); - } -}.call(this)); - -},{}],26:[function(require,module,exports){ -arguments[4][19][0].apply(exports,arguments) -},{"dup":19}],27:[function(require,module,exports){ -module.exports = function isBuffer(arg) { - return arg && typeof arg === 'object' - && typeof arg.copy === 'function' - && typeof arg.fill === 'function' - && typeof arg.readUInt8 === 'function'; -} -},{}],28:[function(require,module,exports){ -(function (process,global){ -// Copyright Joyent, Inc. and other Node contributors. -// -// Permission is hereby granted, free of charge, to any person obtaining a -// copy of this software and associated documentation files (the -// "Software"), to deal in the Software without restriction, including -// without limitation the rights to use, copy, modify, merge, publish, -// distribute, sublicense, and/or sell copies of the Software, and to permit -// persons to whom the Software is furnished to do so, subject to the -// following conditions: -// -// The above copyright notice and this permission notice shall be included -// in all copies or substantial portions of the Software. -// -// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS -// OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF -// MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN -// NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, -// DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR -// OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE -// USE OR OTHER DEALINGS IN THE SOFTWARE. - -var formatRegExp = /%[sdj%]/g; -exports.format = function(f) { - if (!isString(f)) { - var objects = []; - for (var i = 0; i < arguments.length; i++) { - objects.push(inspect(arguments[i])); - } - return objects.join(' '); - } - - var i = 1; - var args = arguments; - var len = args.length; - var str = String(f).replace(formatRegExp, function(x) { - if (x === '%%') return '%'; - if (i >= len) return x; - switch (x) { - case '%s': return String(args[i++]); - case '%d': return Number(args[i++]); - case '%j': - try { - return JSON.stringify(args[i++]); - } catch (_) { - return '[Circular]'; - } - default: - return x; - } - }); - for (var x = args[i]; i < len; x = args[++i]) { - if (isNull(x) || !isObject(x)) { - str += ' ' + x; - } else { - str += ' ' + inspect(x); - } - } - return str; -}; - - -// Mark that a method should not be used. -// Returns a modified function which warns once by default. -// If --no-deprecation is set, then it is a no-op. -exports.deprecate = function(fn, msg) { - // Allow for deprecating things in the process of starting up. - if (isUndefined(global.process)) { - return function() { - return exports.deprecate(fn, msg).apply(this, arguments); - }; - } - - if (process.noDeprecation === true) { - return fn; - } - - var warned = false; - function deprecated() { - if (!warned) { - if (process.throwDeprecation) { - throw new Error(msg); - } else if (process.traceDeprecation) { - console.trace(msg); - } else { - console.error(msg); - } - warned = true; - } - return fn.apply(this, arguments); - } - - return deprecated; -}; - - -var debugs = {}; -var debugEnviron; -exports.debuglog = function(set) { - if (isUndefined(debugEnviron)) - debugEnviron = process.env.NODE_DEBUG || ''; - set = set.toUpperCase(); - if (!debugs[set]) { - if (new RegExp('\\b' + set + '\\b', 'i').test(debugEnviron)) { - var pid = process.pid; - debugs[set] = function() { - var msg = exports.format.apply(exports, arguments); - console.error('%s %d: %s', set, pid, msg); - }; - } else { - debugs[set] = function() {}; - } - } - return debugs[set]; -}; - - -/** - * Echos the value of a value. Trys to print the value out - * in the best way possible given the different types. - * - * @param {Object} obj The object to print out. - * @param {Object} opts Optional options object that alters the output. - */ -/* legacy: obj, showHidden, depth, colors*/ -function inspect(obj, opts) { - // default options - var ctx = { - seen: [], - stylize: stylizeNoColor - }; - // legacy... - if (arguments.length >= 3) ctx.depth = arguments[2]; - if (arguments.length >= 4) ctx.colors = arguments[3]; - if (isBoolean(opts)) { - // legacy... - ctx.showHidden = opts; - } else if (opts) { - // got an "options" object - exports._extend(ctx, opts); - } - // set default options - if (isUndefined(ctx.showHidden)) ctx.showHidden = false; - if (isUndefined(ctx.depth)) ctx.depth = 2; - if (isUndefined(ctx.colors)) ctx.colors = false; - if (isUndefined(ctx.customInspect)) ctx.customInspect = true; - if (ctx.colors) ctx.stylize = stylizeWithColor; - return formatValue(ctx, obj, ctx.depth); -} -exports.inspect = inspect; - - -// http://en.wikipedia.org/wiki/ANSI_escape_code#graphics -inspect.colors = { - 'bold' : [1, 22], - 'italic' : [3, 23], - 'underline' : [4, 24], - 'inverse' : [7, 27], - 'white' : [37, 39], - 'grey' : [90, 39], - 'black' : [30, 39], - 'blue' : [34, 39], - 'cyan' : [36, 39], - 'green' : [32, 39], - 'magenta' : [35, 39], - 'red' : [31, 39], - 'yellow' : [33, 39] -}; - -// Don't use 'blue' not visible on cmd.exe -inspect.styles = { - 'special': 'cyan', - 'number': 'yellow', - 'boolean': 'yellow', - 'undefined': 'grey', - 'null': 'bold', - 'string': 'green', - 'date': 'magenta', - // "name": intentionally not styling - 'regexp': 'red' -}; - - -function stylizeWithColor(str, styleType) { - var style = inspect.styles[styleType]; - - if (style) { - return '\u001b[' + inspect.colors[style][0] + 'm' + str + - '\u001b[' + inspect.colors[style][1] + 'm'; - } else { - return str; - } -} - - -function stylizeNoColor(str, styleType) { - return str; -} - - -function arrayToHash(array) { - var hash = {}; - - array.forEach(function(val, idx) { - hash[val] = true; - }); - - return hash; -} - - -function formatValue(ctx, value, recurseTimes) { - // Provide a hook for user-specified inspect functions. - // Check that value is an object with an inspect function on it - if (ctx.customInspect && - value && - isFunction(value.inspect) && - // Filter out the util module, it's inspect function is special - value.inspect !== exports.inspect && - // Also filter out any prototype objects using the circular check. - !(value.constructor && value.constructor.prototype === value)) { - var ret = value.inspect(recurseTimes, ctx); - if (!isString(ret)) { - ret = formatValue(ctx, ret, recurseTimes); - } - return ret; - } - - // Primitive types cannot have properties - var primitive = formatPrimitive(ctx, value); - if (primitive) { - return primitive; - } - - // Look up the keys of the object. - var keys = Object.keys(value); - var visibleKeys = arrayToHash(keys); - - if (ctx.showHidden) { - keys = Object.getOwnPropertyNames(value); - } - - // IE doesn't make error fields non-enumerable - // http://msdn.microsoft.com/en-us/library/ie/dww52sbt(v=vs.94).aspx - if (isError(value) - && (keys.indexOf('message') >= 0 || keys.indexOf('description') >= 0)) { - return formatError(value); - } - - // Some type of object without properties can be shortcutted. - if (keys.length === 0) { - if (isFunction(value)) { - var name = value.name ? ': ' + value.name : ''; - return ctx.stylize('[Function' + name + ']', 'special'); - } - if (isRegExp(value)) { - return ctx.stylize(RegExp.prototype.toString.call(value), 'regexp'); - } - if (isDate(value)) { - return ctx.stylize(Date.prototype.toString.call(value), 'date'); - } - if (isError(value)) { - return formatError(value); - } - } - - var base = '', array = false, braces = ['{', '}']; - - // Make Array say that they are Array - if (isArray(value)) { - array = true; - braces = ['[', ']']; - } - - // Make functions say that they are functions - if (isFunction(value)) { - var n = value.name ? ': ' + value.name : ''; - base = ' [Function' + n + ']'; - } - - // Make RegExps say that they are RegExps - if (isRegExp(value)) { - base = ' ' + RegExp.prototype.toString.call(value); - } - - // Make dates with properties first say the date - if (isDate(value)) { - base = ' ' + Date.prototype.toUTCString.call(value); - } - - // Make error with message first say the error - if (isError(value)) { - base = ' ' + formatError(value); - } - - if (keys.length === 0 && (!array || value.length == 0)) { - return braces[0] + base + braces[1]; - } - - if (recurseTimes < 0) { - if (isRegExp(value)) { - return ctx.stylize(RegExp.prototype.toString.call(value), 'regexp'); - } else { - return ctx.stylize('[Object]', 'special'); - } - } - - ctx.seen.push(value); - - var output; - if (array) { - output = formatArray(ctx, value, recurseTimes, visibleKeys, keys); - } else { - output = keys.map(function(key) { - return formatProperty(ctx, value, recurseTimes, visibleKeys, key, array); - }); - } - - ctx.seen.pop(); - - return reduceToSingleString(output, base, braces); -} - - -function formatPrimitive(ctx, value) { - if (isUndefined(value)) - return ctx.stylize('undefined', 'undefined'); - if (isString(value)) { - var simple = '\'' + JSON.stringify(value).replace(/^"|"$/g, '') - .replace(/'/g, "\\'") - .replace(/\\"/g, '"') + '\''; - return ctx.stylize(simple, 'string'); - } - if (isNumber(value)) - return ctx.stylize('' + value, 'number'); - if (isBoolean(value)) - return ctx.stylize('' + value, 'boolean'); - // For some reason typeof null is "object", so special case here. - if (isNull(value)) - return ctx.stylize('null', 'null'); -} - - -function formatError(value) { - return '[' + Error.prototype.toString.call(value) + ']'; -} - - -function formatArray(ctx, value, recurseTimes, visibleKeys, keys) { - var output = []; - for (var i = 0, l = value.length; i < l; ++i) { - if (hasOwnProperty(value, String(i))) { - output.push(formatProperty(ctx, value, recurseTimes, visibleKeys, - String(i), true)); - } else { - output.push(''); - } - } - keys.forEach(function(key) { - if (!key.match(/^\d+$/)) { - output.push(formatProperty(ctx, value, recurseTimes, visibleKeys, - key, true)); - } - }); - return output; -} - - -function formatProperty(ctx, value, recurseTimes, visibleKeys, key, array) { - var name, str, desc; - desc = Object.getOwnPropertyDescriptor(value, key) || { value: value[key] }; - if (desc.get) { - if (desc.set) { - str = ctx.stylize('[Getter/Setter]', 'special'); - } else { - str = ctx.stylize('[Getter]', 'special'); - } - } else { - if (desc.set) { - str = ctx.stylize('[Setter]', 'special'); - } - } - if (!hasOwnProperty(visibleKeys, key)) { - name = '[' + key + ']'; - } - if (!str) { - if (ctx.seen.indexOf(desc.value) < 0) { - if (isNull(recurseTimes)) { - str = formatValue(ctx, desc.value, null); - } else { - str = formatValue(ctx, desc.value, recurseTimes - 1); - } - if (str.indexOf('\n') > -1) { - if (array) { - str = str.split('\n').map(function(line) { - return ' ' + line; - }).join('\n').substr(2); - } else { - str = '\n' + str.split('\n').map(function(line) { - return ' ' + line; - }).join('\n'); - } - } - } else { - str = ctx.stylize('[Circular]', 'special'); - } - } - if (isUndefined(name)) { - if (array && key.match(/^\d+$/)) { - return str; - } - name = JSON.stringify('' + key); - if (name.match(/^"([a-zA-Z_][a-zA-Z_0-9]*)"$/)) { - name = name.substr(1, name.length - 2); - name = ctx.stylize(name, 'name'); - } else { - name = name.replace(/'/g, "\\'") - .replace(/\\"/g, '"') - .replace(/(^"|"$)/g, "'"); - name = ctx.stylize(name, 'string'); - } - } - - return name + ': ' + str; -} - - -function reduceToSingleString(output, base, braces) { - var numLinesEst = 0; - var length = output.reduce(function(prev, cur) { - numLinesEst++; - if (cur.indexOf('\n') >= 0) numLinesEst++; - return prev + cur.replace(/\u001b\[\d\d?m/g, '').length + 1; - }, 0); - - if (length > 60) { - return braces[0] + - (base === '' ? '' : base + '\n ') + - ' ' + - output.join(',\n ') + - ' ' + - braces[1]; - } - - return braces[0] + base + ' ' + output.join(', ') + ' ' + braces[1]; -} - - -// NOTE: These type checking functions intentionally don't use `instanceof` -// because it is fragile and can be easily faked with `Object.create()`. -function isArray(ar) { - return Array.isArray(ar); -} -exports.isArray = isArray; - -function isBoolean(arg) { - return typeof arg === 'boolean'; -} -exports.isBoolean = isBoolean; - -function isNull(arg) { - return arg === null; -} -exports.isNull = isNull; - -function isNullOrUndefined(arg) { - return arg == null; -} -exports.isNullOrUndefined = isNullOrUndefined; - -function isNumber(arg) { - return typeof arg === 'number'; -} -exports.isNumber = isNumber; - -function isString(arg) { - return typeof arg === 'string'; -} -exports.isString = isString; - -function isSymbol(arg) { - return typeof arg === 'symbol'; -} -exports.isSymbol = isSymbol; - -function isUndefined(arg) { - return arg === void 0; -} -exports.isUndefined = isUndefined; - -function isRegExp(re) { - return isObject(re) && objectToString(re) === '[object RegExp]'; -} -exports.isRegExp = isRegExp; - -function isObject(arg) { - return typeof arg === 'object' && arg !== null; -} -exports.isObject = isObject; - -function isDate(d) { - return isObject(d) && objectToString(d) === '[object Date]'; -} -exports.isDate = isDate; - -function isError(e) { - return isObject(e) && - (objectToString(e) === '[object Error]' || e instanceof Error); -} -exports.isError = isError; - -function isFunction(arg) { - return typeof arg === 'function'; -} -exports.isFunction = isFunction; - -function isPrimitive(arg) { - return arg === null || - typeof arg === 'boolean' || - typeof arg === 'number' || - typeof arg === 'string' || - typeof arg === 'symbol' || // ES6 symbol - typeof arg === 'undefined'; -} -exports.isPrimitive = isPrimitive; - -exports.isBuffer = require('./support/isBuffer'); - -function objectToString(o) { - return Object.prototype.toString.call(o); -} - - -function pad(n) { - return n < 10 ? '0' + n.toString(10) : n.toString(10); -} - - -var months = ['Jan', 'Feb', 'Mar', 'Apr', 'May', 'Jun', 'Jul', 'Aug', 'Sep', - 'Oct', 'Nov', 'Dec']; - -// 26 Feb 16:19:34 -function timestamp() { - var d = new Date(); - var time = [pad(d.getHours()), - pad(d.getMinutes()), - pad(d.getSeconds())].join(':'); - return [d.getDate(), months[d.getMonth()], time].join(' '); -} - - -// log is just a thin wrapper to console.log that prepends a timestamp -exports.log = function() { - console.log('%s - %s', timestamp(), exports.format.apply(exports, arguments)); -}; - - -/** - * Inherit the prototype methods from one constructor into another. - * - * The Function.prototype.inherits from lang.js rewritten as a standalone - * function (not on Function.prototype). NOTE: If this file is to be loaded - * during bootstrapping this function needs to be rewritten using some native - * functions as prototype setup using normal JavaScript does not work as - * expected during bootstrapping (see mirror.js in r114903). - * - * @param {function} ctor Constructor function which needs to inherit the - * prototype. - * @param {function} superCtor Constructor function to inherit prototype from. - */ -exports.inherits = require('inherits'); - -exports._extend = function(origin, add) { - // Don't do anything if add isn't an object - if (!add || !isObject(add)) return origin; - - var keys = Object.keys(add); - var i = keys.length; - while (i--) { - origin[keys[i]] = add[keys[i]]; - } - return origin; -}; - -function hasOwnProperty(obj, prop) { - return Object.prototype.hasOwnProperty.call(obj, prop); -} - -}).call(this,require('_process'),typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : typeof window !== "undefined" ? window : {}) -},{"./support/isBuffer":27,"_process":24,"inherits":26}],29:[function(require,module,exports){ -// Returns a wrapper function that returns a wrapped callback -// The wrapper function should do some stuff, and return a -// presumably different callback function. -// This makes sure that own properties are retained, so that -// decorations and such are not lost along the way. -module.exports = wrappy -function wrappy (fn, cb) { - if (fn && cb) return wrappy(fn)(cb) - - if (typeof fn !== 'function') - throw new TypeError('need wrapper function') - - Object.keys(fn).forEach(function (k) { - wrapper[k] = fn[k] - }) - - return wrapper - - function wrapper() { - var args = new Array(arguments.length) - for (var i = 0; i < args.length; i++) { - args[i] = arguments[i] - } - var ret = fn.apply(this, args) - var cb = args[args.length-1] - if (typeof ret === 'function' && ret !== cb) { - Object.keys(cb).forEach(function (k) { - ret[k] = cb[k] - }) - } - return ret - } -} - -},{}]},{},[7])(7) -}); \ No newline at end of file diff --git a/assets/javascripts/workers/search.b97dbffb.min.js b/assets/javascripts/workers/search.b97dbffb.min.js deleted file mode 100644 index 8201c5e..0000000 --- a/assets/javascripts/workers/search.b97dbffb.min.js +++ /dev/null @@ -1,48 +0,0 @@ -"use strict";(()=>{var ge=Object.create;var W=Object.defineProperty,ye=Object.defineProperties,me=Object.getOwnPropertyDescriptor,ve=Object.getOwnPropertyDescriptors,xe=Object.getOwnPropertyNames,G=Object.getOwnPropertySymbols,Se=Object.getPrototypeOf,X=Object.prototype.hasOwnProperty,Qe=Object.prototype.propertyIsEnumerable;var J=(t,e,r)=>e in t?W(t,e,{enumerable:!0,configurable:!0,writable:!0,value:r}):t[e]=r,M=(t,e)=>{for(var r in e||(e={}))X.call(e,r)&&J(t,r,e[r]);if(G)for(var r of G(e))Qe.call(e,r)&&J(t,r,e[r]);return t},Z=(t,e)=>ye(t,ve(e));var K=(t,e)=>()=>(e||t((e={exports:{}}).exports,e),e.exports);var be=(t,e,r,n)=>{if(e&&typeof e=="object"||typeof e=="function")for(let i of xe(e))!X.call(t,i)&&i!==r&&W(t,i,{get:()=>e[i],enumerable:!(n=me(e,i))||n.enumerable});return t};var H=(t,e,r)=>(r=t!=null?ge(Se(t)):{},be(e||!t||!t.__esModule?W(r,"default",{value:t,enumerable:!0}):r,t));var z=(t,e,r)=>new Promise((n,i)=>{var s=u=>{try{a(r.next(u))}catch(c){i(c)}},o=u=>{try{a(r.throw(u))}catch(c){i(c)}},a=u=>u.done?n(u.value):Promise.resolve(u.value).then(s,o);a((r=r.apply(t,e)).next())});var re=K((ee,te)=>{/** - * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9 - * Copyright (C) 2020 Oliver Nightingale - * @license MIT - */(function(){var t=function(e){var r=new t.Builder;return r.pipeline.add(t.trimmer,t.stopWordFilter,t.stemmer),r.searchPipeline.add(t.stemmer),e.call(r,r),r.build()};t.version="2.3.9";/*! - * lunr.utils - * Copyright (C) 2020 Oliver Nightingale - */t.utils={},t.utils.warn=function(e){return function(r){e.console&&console.warn&&console.warn(r)}}(this),t.utils.asString=function(e){return e==null?"":e.toString()},t.utils.clone=function(e){if(e==null)return e;for(var r=Object.create(null),n=Object.keys(e),i=0;i0){var h=t.utils.clone(r)||{};h.position=[a,c],h.index=s.length,s.push(new t.Token(n.slice(a,o),h))}a=o+1}}return s},t.tokenizer.separator=/[\s\-]+/;/*! - * lunr.Pipeline - * Copyright (C) 2020 Oliver Nightingale - */t.Pipeline=function(){this._stack=[]},t.Pipeline.registeredFunctions=Object.create(null),t.Pipeline.registerFunction=function(e,r){r in this.registeredFunctions&&t.utils.warn("Overwriting existing registered function: "+r),e.label=r,t.Pipeline.registeredFunctions[e.label]=e},t.Pipeline.warnIfFunctionNotRegistered=function(e){var r=e.label&&e.label in this.registeredFunctions;r||t.utils.warn(`Function is not registered with pipeline. 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this.pos1&&(e.backup(),e.emit(t.QueryLexer.TERM)),e.ignore(),e.more())return t.QueryLexer.lexText},t.QueryLexer.lexEditDistance=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(t.QueryLexer.EDIT_DISTANCE),t.QueryLexer.lexText},t.QueryLexer.lexBoost=function(e){return e.ignore(),e.acceptDigitRun(),e.emit(t.QueryLexer.BOOST),t.QueryLexer.lexText},t.QueryLexer.lexEOS=function(e){e.width()>0&&e.emit(t.QueryLexer.TERM)},t.QueryLexer.termSeparator=t.tokenizer.separator,t.QueryLexer.lexText=function(e){for(;;){var r=e.next();if(r==t.QueryLexer.EOS)return t.QueryLexer.lexEOS;if(r.charCodeAt(0)==92){e.escapeCharacter();continue}if(r==":")return t.QueryLexer.lexField;if(r=="~")return e.backup(),e.width()>0&&e.emit(t.QueryLexer.TERM),t.QueryLexer.lexEditDistance;if(r=="^")return e.backup(),e.width()>0&&e.emit(t.QueryLexer.TERM),t.QueryLexer.lexBoost;if(r=="+"&&e.width()===1||r=="-"&&e.width()===1)return e.emit(t.QueryLexer.PRESENCE),t.QueryLexer.lexText;if(r.match(t.QueryLexer.termSeparator))return t.QueryLexer.lexTerm}},t.QueryParser=function(e,r){this.lexer=new t.QueryLexer(e),this.query=r,this.currentClause={},this.lexemeIdx=0},t.QueryParser.prototype.parse=function(){this.lexer.run(),this.lexemes=this.lexer.lexemes;for(var e=t.QueryParser.parseClause;e;)e=e(this);return this.query},t.QueryParser.prototype.peekLexeme=function(){return this.lexemes[this.lexemeIdx]},t.QueryParser.prototype.consumeLexeme=function(){var e=this.peekLexeme();return this.lexemeIdx+=1,e},t.QueryParser.prototype.nextClause=function(){var e=this.currentClause;this.query.clause(e),this.currentClause={}},t.QueryParser.parseClause=function(e){var r=e.peekLexeme();if(r!=null)switch(r.type){case t.QueryLexer.PRESENCE:return t.QueryParser.parsePresence;case t.QueryLexer.FIELD:return t.QueryParser.parseField;case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var n="expected either a field or a term, found "+r.type;throw r.str.length>=1&&(n+=" with value '"+r.str+"'"),new t.QueryParseError(n,r.start,r.end)}},t.QueryParser.parsePresence=function(e){var r=e.consumeLexeme();if(r!=null){switch(r.str){case"-":e.currentClause.presence=t.Query.presence.PROHIBITED;break;case"+":e.currentClause.presence=t.Query.presence.REQUIRED;break;default:var n="unrecognised presence operator'"+r.str+"'";throw new t.QueryParseError(n,r.start,r.end)}var i=e.peekLexeme();if(i==null){var n="expecting term or field, found nothing";throw new t.QueryParseError(n,r.start,r.end)}switch(i.type){case t.QueryLexer.FIELD:return t.QueryParser.parseField;case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var n="expecting term or field, found '"+i.type+"'";throw new t.QueryParseError(n,i.start,i.end)}}},t.QueryParser.parseField=function(e){var r=e.consumeLexeme();if(r!=null){if(e.query.allFields.indexOf(r.str)==-1){var n=e.query.allFields.map(function(o){return"'"+o+"'"}).join(", "),i="unrecognised field '"+r.str+"', possible fields: "+n;throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.fields=[r.str];var s=e.peekLexeme();if(s==null){var i="expecting term, found nothing";throw new t.QueryParseError(i,r.start,r.end)}switch(s.type){case t.QueryLexer.TERM:return t.QueryParser.parseTerm;default:var i="expecting term, found '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},t.QueryParser.parseTerm=function(e){var r=e.consumeLexeme();if(r!=null){e.currentClause.term=r.str.toLowerCase(),r.str.indexOf("*")!=-1&&(e.currentClause.usePipeline=!1);var n=e.peekLexeme();if(n==null){e.nextClause();return}switch(n.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+n.type+"'";throw new t.QueryParseError(i,n.start,n.end)}}},t.QueryParser.parseEditDistance=function(e){var r=e.consumeLexeme();if(r!=null){var n=parseInt(r.str,10);if(isNaN(n)){var i="edit distance must be numeric";throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.editDistance=n;var s=e.peekLexeme();if(s==null){e.nextClause();return}switch(s.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},t.QueryParser.parseBoost=function(e){var r=e.consumeLexeme();if(r!=null){var n=parseInt(r.str,10);if(isNaN(n)){var i="boost must be numeric";throw new t.QueryParseError(i,r.start,r.end)}e.currentClause.boost=n;var s=e.peekLexeme();if(s==null){e.nextClause();return}switch(s.type){case t.QueryLexer.TERM:return e.nextClause(),t.QueryParser.parseTerm;case t.QueryLexer.FIELD:return e.nextClause(),t.QueryParser.parseField;case t.QueryLexer.EDIT_DISTANCE:return t.QueryParser.parseEditDistance;case t.QueryLexer.BOOST:return t.QueryParser.parseBoost;case t.QueryLexer.PRESENCE:return e.nextClause(),t.QueryParser.parsePresence;default:var i="Unexpected lexeme type '"+s.type+"'";throw new t.QueryParseError(i,s.start,s.end)}}},function(e,r){typeof define=="function"&&define.amd?define(r):typeof ee=="object"?te.exports=r():e.lunr=r()}(this,function(){return t})})()});var q=K((Re,ne)=>{"use strict";/*! - * escape-html - * Copyright(c) 2012-2013 TJ Holowaychuk - * Copyright(c) 2015 Andreas Lubbe - * Copyright(c) 2015 Tiancheng "Timothy" Gu - * MIT Licensed - */var Le=/["'&<>]/;ne.exports=we;function we(t){var e=""+t,r=Le.exec(e);if(!r)return e;var n,i="",s=0,o=0;for(s=r.index;s=0;r--){let n=t[r];typeof n!="object"?n=document.createTextNode(n):n.parentNode&&n.parentNode.removeChild(n),r?e.insertBefore(this.previousSibling,n):e.replaceChild(n,this)}}}));var ie=H(q());function se(t){let e=new Map,r=new Set;for(let n of t){let[i,s]=n.location.split("#"),o=n.location,a=n.title,u=n.tags,c=(0,ie.default)(n.text).replace(/\s+(?=[,.:;!?])/g,"").replace(/\s+/g," ");if(s){let h=e.get(i);r.has(h)?e.set(o,{location:o,title:a,text:c,parent:h}):(h.title=n.title,h.text=c,r.add(h))}else e.set(o,M({location:o,title:a,text:c},u&&{tags:u}))}return e}var oe=H(q());function ae(t,e){let r=new RegExp(t.separator,"img"),n=(i,s,o)=>`${s}${o}`;return i=>{i=i.replace(/[\s*+\-:~^]+/g," ").trim();let s=new RegExp(`(^|${t.separator})(${i.replace(/[|\\{}()[\]^$+*?.-]/g,"\\$&").replace(r,"|")})`,"img");return o=>(e?(0,oe.default)(o):o).replace(s,n).replace(/<\/mark>(\s+)]*>/img,"$1")}}function ue(t){let e=new lunr.Query(["title","text"]);return new lunr.QueryParser(t,e).parse(),e.clauses}function ce(t,e){var i;let r=new Set(t),n={};for(let s=0;s!n.has(i)))]}var U=class{constructor({config:e,docs:r,options:n}){this.options=n,this.documents=se(r),this.highlight=ae(e,!1),lunr.tokenizer.separator=new RegExp(e.separator),this.index=lunr(function(){e.lang.length===1&&e.lang[0]!=="en"?this.use(lunr[e.lang[0]]):e.lang.length>1&&this.use(lunr.multiLanguage(...e.lang));let i=Ee(["trimmer","stopWordFilter","stemmer"],n.pipeline);for(let s of e.lang.map(o=>o==="en"?lunr:lunr[o]))for(let o of i)this.pipeline.remove(s[o]),this.searchPipeline.remove(s[o]);this.ref("location"),this.field("title",{boost:1e3}),this.field("text"),this.field("tags",{boost:1e6,extractor:s=>{let{tags:o=[]}=s;return o.reduce((a,u)=>[...a,...lunr.tokenizer(u)],[])}});for(let s of r)this.add(s,{boost:s.boost})})}search(e){if(e)try{let r=this.highlight(e),n=ue(e).filter(o=>o.presence!==lunr.Query.presence.PROHIBITED),i=this.index.search(`${e}*`).reduce((o,{ref:a,score:u,matchData:c})=>{let h=this.documents.get(a);if(typeof h!="undefined"){let{location:y,title:g,text:b,tags:m,parent:Q}=h,p=ce(n,Object.keys(c.metadata)),d=+!Q+ +Object.values(p).every(w=>w);o.push(Z(M({location:y,title:r(g),text:r(b)},m&&{tags:m.map(r)}),{score:u*(1+d),terms:p}))}return o},[]).sort((o,a)=>a.score-o.score).reduce((o,a)=>{let u=this.documents.get(a.location);if(typeof u!="undefined"){let c="parent"in u?u.parent.location:u.location;o.set(c,[...o.get(c)||[],a])}return o},new Map),s;if(this.options.suggestions){let o=this.index.query(a=>{for(let u of n)a.term(u.term,{fields:["title"],presence:lunr.Query.presence.REQUIRED,wildcard:lunr.Query.wildcard.TRAILING})});s=o.length?Object.keys(o[0].matchData.metadata):[]}return M({items:[...i.values()]},typeof s!="undefined"&&{suggestions:s})}catch(r){console.warn(`Invalid query: ${e} \u2013 see https://bit.ly/2s3ChXG`)}return{items:[]}}};var Y;function ke(t){return z(this,null,function*(){let e="../lunr";if(typeof parent!="undefined"&&"IFrameWorker"in parent){let n=document.querySelector("script[src]"),[i]=n.src.split("/worker");e=e.replace("..",i)}let r=[];for(let n of t.lang){switch(n){case"ja":r.push(`${e}/tinyseg.js`);break;case"hi":case"th":r.push(`${e}/wordcut.js`);break}n!=="en"&&r.push(`${e}/min/lunr.${n}.min.js`)}t.lang.length>1&&r.push(`${e}/min/lunr.multi.min.js`),r.length&&(yield importScripts(`${e}/min/lunr.stemmer.support.min.js`,...r))})}function Te(t){return z(this,null,function*(){switch(t.type){case 0:return yield ke(t.data.config),Y=new U(t.data),{type:1};case 2:return{type:3,data:Y?Y.search(t.data):{items:[]}};default:throw new TypeError("Invalid message type")}})}self.lunr=le.default;addEventListener("message",t=>z(void 0,null,function*(){postMessage(yield Te(t.data))}));})(); -//# sourceMappingURL=search.b97dbffb.min.js.map - diff --git a/assets/javascripts/workers/search.b97dbffb.min.js.map b/assets/javascripts/workers/search.b97dbffb.min.js.map deleted file mode 100644 index 5764b1b..0000000 --- a/assets/javascripts/workers/search.b97dbffb.min.js.map +++ /dev/null @@ -1,8 +0,0 @@ -{ - "version": 3, - "sources": ["node_modules/lunr/lunr.js", "node_modules/escape-html/index.js", "src/assets/javascripts/integrations/search/worker/main/index.ts", "src/assets/javascripts/polyfills/index.ts", "src/assets/javascripts/integrations/search/document/index.ts", "src/assets/javascripts/integrations/search/highlighter/index.ts", "src/assets/javascripts/integrations/search/query/_/index.ts", "src/assets/javascripts/integrations/search/_/index.ts"], - "sourceRoot": "../../../..", - "sourcesContent": ["/**\n * lunr - http://lunrjs.com - A bit like Solr, but much smaller and not as bright - 2.3.9\n * Copyright (C) 2020 Oliver Nightingale\n * @license MIT\n */\n\n;(function(){\n\n/**\n * A convenience function for configuring and constructing\n * a new lunr Index.\n *\n * A lunr.Builder instance is created and the pipeline setup\n * with a trimmer, stop word filter and stemmer.\n *\n * This builder object is yielded to the configuration function\n * that is passed as a parameter, allowing the list of fields\n * and other builder parameters to be customised.\n *\n * All documents _must_ be added within the passed config function.\n *\n * @example\n * var idx = lunr(function () {\n * this.field('title')\n * this.field('body')\n * this.ref('id')\n *\n * documents.forEach(function (doc) {\n * this.add(doc)\n * }, this)\n * })\n *\n * @see {@link lunr.Builder}\n * @see {@link lunr.Pipeline}\n * @see {@link lunr.trimmer}\n * @see {@link lunr.stopWordFilter}\n * @see {@link lunr.stemmer}\n * @namespace {function} lunr\n */\nvar lunr = function (config) {\n var builder = new lunr.Builder\n\n builder.pipeline.add(\n lunr.trimmer,\n lunr.stopWordFilter,\n lunr.stemmer\n )\n\n builder.searchPipeline.add(\n lunr.stemmer\n )\n\n config.call(builder, builder)\n return builder.build()\n}\n\nlunr.version = \"2.3.9\"\n/*!\n * lunr.utils\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A namespace containing utils for the rest of the lunr library\n * @namespace lunr.utils\n */\nlunr.utils = {}\n\n/**\n * Print a warning message to the console.\n *\n * @param {String} message The message to be printed.\n * @memberOf lunr.utils\n * @function\n */\nlunr.utils.warn = (function (global) {\n /* eslint-disable no-console */\n return function (message) {\n if (global.console && console.warn) {\n console.warn(message)\n }\n }\n /* eslint-enable no-console */\n})(this)\n\n/**\n * Convert an object to a string.\n *\n * In the case of `null` and `undefined` the function returns\n * the empty string, in all other cases the result of calling\n * `toString` on the passed object is returned.\n *\n * @param {Any} obj The object to convert to a string.\n * @return {String} string representation of the passed object.\n * @memberOf lunr.utils\n */\nlunr.utils.asString = function (obj) {\n if (obj === void 0 || obj === null) {\n return \"\"\n } else {\n return obj.toString()\n }\n}\n\n/**\n * Clones an object.\n *\n * Will create a copy of an existing object such that any mutations\n * on the copy cannot affect the original.\n *\n * Only shallow objects are supported, passing a nested object to this\n * function will cause a TypeError.\n *\n * Objects with primitives, and arrays of primitives are supported.\n *\n * @param {Object} obj The object to clone.\n * @return {Object} a clone of the passed object.\n * @throws {TypeError} when a nested object is passed.\n * @memberOf Utils\n */\nlunr.utils.clone = function (obj) {\n if (obj === null || obj === undefined) {\n return obj\n }\n\n var clone = Object.create(null),\n keys = Object.keys(obj)\n\n for (var i = 0; i < keys.length; i++) {\n var key = keys[i],\n val = obj[key]\n\n if (Array.isArray(val)) {\n clone[key] = val.slice()\n continue\n }\n\n if (typeof val === 'string' ||\n typeof val === 'number' ||\n typeof val === 'boolean') {\n clone[key] = val\n continue\n }\n\n throw new TypeError(\"clone is not deep and does not support nested objects\")\n }\n\n return clone\n}\nlunr.FieldRef = function (docRef, fieldName, stringValue) {\n this.docRef = docRef\n this.fieldName = fieldName\n this._stringValue = stringValue\n}\n\nlunr.FieldRef.joiner = \"/\"\n\nlunr.FieldRef.fromString = function (s) {\n var n = s.indexOf(lunr.FieldRef.joiner)\n\n if (n === -1) {\n throw \"malformed field ref string\"\n }\n\n var fieldRef = s.slice(0, n),\n docRef = s.slice(n + 1)\n\n return new lunr.FieldRef (docRef, fieldRef, s)\n}\n\nlunr.FieldRef.prototype.toString = function () {\n if (this._stringValue == undefined) {\n this._stringValue = this.fieldName + lunr.FieldRef.joiner + this.docRef\n }\n\n return this._stringValue\n}\n/*!\n * lunr.Set\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A lunr set.\n *\n * @constructor\n */\nlunr.Set = function (elements) {\n this.elements = Object.create(null)\n\n if (elements) {\n this.length = elements.length\n\n for (var i = 0; i < this.length; i++) {\n this.elements[elements[i]] = true\n }\n } else {\n this.length = 0\n }\n}\n\n/**\n * A complete set that contains all elements.\n *\n * @static\n * @readonly\n * @type {lunr.Set}\n */\nlunr.Set.complete = {\n intersect: function (other) {\n return other\n },\n\n union: function () {\n return this\n },\n\n contains: function () {\n return true\n }\n}\n\n/**\n * An empty set that contains no elements.\n *\n * @static\n * @readonly\n * @type {lunr.Set}\n */\nlunr.Set.empty = {\n intersect: function () {\n return this\n },\n\n union: function (other) {\n return other\n },\n\n contains: function () {\n return false\n }\n}\n\n/**\n * Returns true if this set contains the specified object.\n *\n * @param {object} object - Object whose presence in this set is to be tested.\n * @returns {boolean} - True if this set contains the specified object.\n */\nlunr.Set.prototype.contains = function (object) {\n return !!this.elements[object]\n}\n\n/**\n * Returns a new set containing only the elements that are present in both\n * this set and the specified set.\n *\n * @param {lunr.Set} other - set to intersect with this set.\n * @returns {lunr.Set} a new set that is the intersection of this and the specified set.\n */\n\nlunr.Set.prototype.intersect = function (other) {\n var a, b, elements, intersection = []\n\n if (other === lunr.Set.complete) {\n return this\n }\n\n if (other === lunr.Set.empty) {\n return other\n }\n\n if (this.length < other.length) {\n a = this\n b = other\n } else {\n a = other\n b = this\n }\n\n elements = Object.keys(a.elements)\n\n for (var i = 0; i < elements.length; i++) {\n var element = elements[i]\n if (element in b.elements) {\n intersection.push(element)\n }\n }\n\n return new lunr.Set (intersection)\n}\n\n/**\n * Returns a new set combining the elements of this and the specified set.\n *\n * @param {lunr.Set} other - set to union with this set.\n * @return {lunr.Set} a new set that is the union of this and the specified set.\n */\n\nlunr.Set.prototype.union = function (other) {\n if (other === lunr.Set.complete) {\n return lunr.Set.complete\n }\n\n if (other === lunr.Set.empty) {\n return this\n }\n\n return new lunr.Set(Object.keys(this.elements).concat(Object.keys(other.elements)))\n}\n/**\n * A function to calculate the inverse document frequency for\n * a posting. This is shared between the builder and the index\n *\n * @private\n * @param {object} posting - The posting for a given term\n * @param {number} documentCount - The total number of documents.\n */\nlunr.idf = function (posting, documentCount) {\n var documentsWithTerm = 0\n\n for (var fieldName in posting) {\n if (fieldName == '_index') continue // Ignore the term index, its not a field\n documentsWithTerm += Object.keys(posting[fieldName]).length\n }\n\n var x = (documentCount - documentsWithTerm + 0.5) / (documentsWithTerm + 0.5)\n\n return Math.log(1 + Math.abs(x))\n}\n\n/**\n * A token wraps a string representation of a token\n * as it is passed through the text processing pipeline.\n *\n * @constructor\n * @param {string} [str=''] - The string token being wrapped.\n * @param {object} [metadata={}] - Metadata associated with this token.\n */\nlunr.Token = function (str, metadata) {\n this.str = str || \"\"\n this.metadata = metadata || {}\n}\n\n/**\n * Returns the token string that is being wrapped by this object.\n *\n * @returns {string}\n */\nlunr.Token.prototype.toString = function () {\n return this.str\n}\n\n/**\n * A token update function is used when updating or optionally\n * when cloning a token.\n *\n * @callback lunr.Token~updateFunction\n * @param {string} str - The string representation of the token.\n * @param {Object} metadata - All metadata associated with this token.\n */\n\n/**\n * Applies the given function to the wrapped string token.\n *\n * @example\n * token.update(function (str, metadata) {\n * return str.toUpperCase()\n * })\n *\n * @param {lunr.Token~updateFunction} fn - A function to apply to the token string.\n * @returns {lunr.Token}\n */\nlunr.Token.prototype.update = function (fn) {\n this.str = fn(this.str, this.metadata)\n return this\n}\n\n/**\n * Creates a clone of this token. Optionally a function can be\n * applied to the cloned token.\n *\n * @param {lunr.Token~updateFunction} [fn] - An optional function to apply to the cloned token.\n * @returns {lunr.Token}\n */\nlunr.Token.prototype.clone = function (fn) {\n fn = fn || function (s) { return s }\n return new lunr.Token (fn(this.str, this.metadata), this.metadata)\n}\n/*!\n * lunr.tokenizer\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A function for splitting a string into tokens ready to be inserted into\n * the search index. Uses `lunr.tokenizer.separator` to split strings, change\n * the value of this property to change how strings are split into tokens.\n *\n * This tokenizer will convert its parameter to a string by calling `toString` and\n * then will split this string on the character in `lunr.tokenizer.separator`.\n * Arrays will have their elements converted to strings and wrapped in a lunr.Token.\n *\n * Optional metadata can be passed to the tokenizer, this metadata will be cloned and\n * added as metadata to every token that is created from the object to be tokenized.\n *\n * @static\n * @param {?(string|object|object[])} obj - The object to convert into tokens\n * @param {?object} metadata - Optional metadata to associate with every token\n * @returns {lunr.Token[]}\n * @see {@link lunr.Pipeline}\n */\nlunr.tokenizer = function (obj, metadata) {\n if (obj == null || obj == undefined) {\n return []\n }\n\n if (Array.isArray(obj)) {\n return obj.map(function (t) {\n return new lunr.Token(\n lunr.utils.asString(t).toLowerCase(),\n lunr.utils.clone(metadata)\n )\n })\n }\n\n var str = obj.toString().toLowerCase(),\n len = str.length,\n tokens = []\n\n for (var sliceEnd = 0, sliceStart = 0; sliceEnd <= len; sliceEnd++) {\n var char = str.charAt(sliceEnd),\n sliceLength = sliceEnd - sliceStart\n\n if ((char.match(lunr.tokenizer.separator) || sliceEnd == len)) {\n\n if (sliceLength > 0) {\n var tokenMetadata = lunr.utils.clone(metadata) || {}\n tokenMetadata[\"position\"] = [sliceStart, sliceLength]\n tokenMetadata[\"index\"] = tokens.length\n\n tokens.push(\n new lunr.Token (\n str.slice(sliceStart, sliceEnd),\n tokenMetadata\n )\n )\n }\n\n sliceStart = sliceEnd + 1\n }\n\n }\n\n return tokens\n}\n\n/**\n * The separator used to split a string into tokens. Override this property to change the behaviour of\n * `lunr.tokenizer` behaviour when tokenizing strings. By default this splits on whitespace and hyphens.\n *\n * @static\n * @see lunr.tokenizer\n */\nlunr.tokenizer.separator = /[\\s\\-]+/\n/*!\n * lunr.Pipeline\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.Pipelines maintain an ordered list of functions to be applied to all\n * tokens in documents entering the search index and queries being ran against\n * the index.\n *\n * An instance of lunr.Index created with the lunr shortcut will contain a\n * pipeline with a stop word filter and an English language stemmer. Extra\n * functions can be added before or after either of these functions or these\n * default functions can be removed.\n *\n * When run the pipeline will call each function in turn, passing a token, the\n * index of that token in the original list of all tokens and finally a list of\n * all the original tokens.\n *\n * The output of functions in the pipeline will be passed to the next function\n * in the pipeline. To exclude a token from entering the index the function\n * should return undefined, the rest of the pipeline will not be called with\n * this token.\n *\n * For serialisation of pipelines to work, all functions used in an instance of\n * a pipeline should be registered with lunr.Pipeline. Registered functions can\n * then be loaded. If trying to load a serialised pipeline that uses functions\n * that are not registered an error will be thrown.\n *\n * If not planning on serialising the pipeline then registering pipeline functions\n * is not necessary.\n *\n * @constructor\n */\nlunr.Pipeline = function () {\n this._stack = []\n}\n\nlunr.Pipeline.registeredFunctions = Object.create(null)\n\n/**\n * A pipeline function maps lunr.Token to lunr.Token. A lunr.Token contains the token\n * string as well as all known metadata. A pipeline function can mutate the token string\n * or mutate (or add) metadata for a given token.\n *\n * A pipeline function can indicate that the passed token should be discarded by returning\n * null, undefined or an empty string. This token will not be passed to any downstream pipeline\n * functions and will not be added to the index.\n *\n * Multiple tokens can be returned by returning an array of tokens. Each token will be passed\n * to any downstream pipeline functions and all will returned tokens will be added to the index.\n *\n * Any number of pipeline functions may be chained together using a lunr.Pipeline.\n *\n * @interface lunr.PipelineFunction\n * @param {lunr.Token} token - A token from the document being processed.\n * @param {number} i - The index of this token in the complete list of tokens for this document/field.\n * @param {lunr.Token[]} tokens - All tokens for this document/field.\n * @returns {(?lunr.Token|lunr.Token[])}\n */\n\n/**\n * Register a function with the pipeline.\n *\n * Functions that are used in the pipeline should be registered if the pipeline\n * needs to be serialised, or a serialised pipeline needs to be loaded.\n *\n * Registering a function does not add it to a pipeline, functions must still be\n * added to instances of the pipeline for them to be used when running a pipeline.\n *\n * @param {lunr.PipelineFunction} fn - The function to check for.\n * @param {String} label - The label to register this function with\n */\nlunr.Pipeline.registerFunction = function (fn, label) {\n if (label in this.registeredFunctions) {\n lunr.utils.warn('Overwriting existing registered function: ' + label)\n }\n\n fn.label = label\n lunr.Pipeline.registeredFunctions[fn.label] = fn\n}\n\n/**\n * Warns if the function is not registered as a Pipeline function.\n *\n * @param {lunr.PipelineFunction} fn - The function to check for.\n * @private\n */\nlunr.Pipeline.warnIfFunctionNotRegistered = function (fn) {\n var isRegistered = fn.label && (fn.label in this.registeredFunctions)\n\n if (!isRegistered) {\n lunr.utils.warn('Function is not registered with pipeline. This may cause problems when serialising the index.\\n', fn)\n }\n}\n\n/**\n * Loads a previously serialised pipeline.\n *\n * All functions to be loaded must already be registered with lunr.Pipeline.\n * If any function from the serialised data has not been registered then an\n * error will be thrown.\n *\n * @param {Object} serialised - The serialised pipeline to load.\n * @returns {lunr.Pipeline}\n */\nlunr.Pipeline.load = function (serialised) {\n var pipeline = new lunr.Pipeline\n\n serialised.forEach(function (fnName) {\n var fn = lunr.Pipeline.registeredFunctions[fnName]\n\n if (fn) {\n pipeline.add(fn)\n } else {\n throw new Error('Cannot load unregistered function: ' + fnName)\n }\n })\n\n return pipeline\n}\n\n/**\n * Adds new functions to the end of the pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction[]} functions - Any number of functions to add to the pipeline.\n */\nlunr.Pipeline.prototype.add = function () {\n var fns = Array.prototype.slice.call(arguments)\n\n fns.forEach(function (fn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(fn)\n this._stack.push(fn)\n }, this)\n}\n\n/**\n * Adds a single function after a function that already exists in the\n * pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.\n * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.\n */\nlunr.Pipeline.prototype.after = function (existingFn, newFn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(newFn)\n\n var pos = this._stack.indexOf(existingFn)\n if (pos == -1) {\n throw new Error('Cannot find existingFn')\n }\n\n pos = pos + 1\n this._stack.splice(pos, 0, newFn)\n}\n\n/**\n * Adds a single function before a function that already exists in the\n * pipeline.\n *\n * Logs a warning if the function has not been registered.\n *\n * @param {lunr.PipelineFunction} existingFn - A function that already exists in the pipeline.\n * @param {lunr.PipelineFunction} newFn - The new function to add to the pipeline.\n */\nlunr.Pipeline.prototype.before = function (existingFn, newFn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(newFn)\n\n var pos = this._stack.indexOf(existingFn)\n if (pos == -1) {\n throw new Error('Cannot find existingFn')\n }\n\n this._stack.splice(pos, 0, newFn)\n}\n\n/**\n * Removes a function from the pipeline.\n *\n * @param {lunr.PipelineFunction} fn The function to remove from the pipeline.\n */\nlunr.Pipeline.prototype.remove = function (fn) {\n var pos = this._stack.indexOf(fn)\n if (pos == -1) {\n return\n }\n\n this._stack.splice(pos, 1)\n}\n\n/**\n * Runs the current list of functions that make up the pipeline against the\n * passed tokens.\n *\n * @param {Array} tokens The tokens to run through the pipeline.\n * @returns {Array}\n */\nlunr.Pipeline.prototype.run = function (tokens) {\n var stackLength = this._stack.length\n\n for (var i = 0; i < stackLength; i++) {\n var fn = this._stack[i]\n var memo = []\n\n for (var j = 0; j < tokens.length; j++) {\n var result = fn(tokens[j], j, tokens)\n\n if (result === null || result === void 0 || result === '') continue\n\n if (Array.isArray(result)) {\n for (var k = 0; k < result.length; k++) {\n memo.push(result[k])\n }\n } else {\n memo.push(result)\n }\n }\n\n tokens = memo\n }\n\n return tokens\n}\n\n/**\n * Convenience method for passing a string through a pipeline and getting\n * strings out. This method takes care of wrapping the passed string in a\n * token and mapping the resulting tokens back to strings.\n *\n * @param {string} str - The string to pass through the pipeline.\n * @param {?object} metadata - Optional metadata to associate with the token\n * passed to the pipeline.\n * @returns {string[]}\n */\nlunr.Pipeline.prototype.runString = function (str, metadata) {\n var token = new lunr.Token (str, metadata)\n\n return this.run([token]).map(function (t) {\n return t.toString()\n })\n}\n\n/**\n * Resets the pipeline by removing any existing processors.\n *\n */\nlunr.Pipeline.prototype.reset = function () {\n this._stack = []\n}\n\n/**\n * Returns a representation of the pipeline ready for serialisation.\n *\n * Logs a warning if the function has not been registered.\n *\n * @returns {Array}\n */\nlunr.Pipeline.prototype.toJSON = function () {\n return this._stack.map(function (fn) {\n lunr.Pipeline.warnIfFunctionNotRegistered(fn)\n\n return fn.label\n })\n}\n/*!\n * lunr.Vector\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A vector is used to construct the vector space of documents and queries. These\n * vectors support operations to determine the similarity between two documents or\n * a document and a query.\n *\n * Normally no parameters are required for initializing a vector, but in the case of\n * loading a previously dumped vector the raw elements can be provided to the constructor.\n *\n * For performance reasons vectors are implemented with a flat array, where an elements\n * index is immediately followed by its value. E.g. [index, value, index, value]. This\n * allows the underlying array to be as sparse as possible and still offer decent\n * performance when being used for vector calculations.\n *\n * @constructor\n * @param {Number[]} [elements] - The flat list of element index and element value pairs.\n */\nlunr.Vector = function (elements) {\n this._magnitude = 0\n this.elements = elements || []\n}\n\n\n/**\n * Calculates the position within the vector to insert a given index.\n *\n * This is used internally by insert and upsert. If there are duplicate indexes then\n * the position is returned as if the value for that index were to be updated, but it\n * is the callers responsibility to check whether there is a duplicate at that index\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @returns {Number}\n */\nlunr.Vector.prototype.positionForIndex = function (index) {\n // For an empty vector the tuple can be inserted at the beginning\n if (this.elements.length == 0) {\n return 0\n }\n\n var start = 0,\n end = this.elements.length / 2,\n sliceLength = end - start,\n pivotPoint = Math.floor(sliceLength / 2),\n pivotIndex = this.elements[pivotPoint * 2]\n\n while (sliceLength > 1) {\n if (pivotIndex < index) {\n start = pivotPoint\n }\n\n if (pivotIndex > index) {\n end = pivotPoint\n }\n\n if (pivotIndex == index) {\n break\n }\n\n sliceLength = end - start\n pivotPoint = start + Math.floor(sliceLength / 2)\n pivotIndex = this.elements[pivotPoint * 2]\n }\n\n if (pivotIndex == index) {\n return pivotPoint * 2\n }\n\n if (pivotIndex > index) {\n return pivotPoint * 2\n }\n\n if (pivotIndex < index) {\n return (pivotPoint + 1) * 2\n }\n}\n\n/**\n * Inserts an element at an index within the vector.\n *\n * Does not allow duplicates, will throw an error if there is already an entry\n * for this index.\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @param {Number} val - The value to be inserted into the vector.\n */\nlunr.Vector.prototype.insert = function (insertIdx, val) {\n this.upsert(insertIdx, val, function () {\n throw \"duplicate index\"\n })\n}\n\n/**\n * Inserts or updates an existing index within the vector.\n *\n * @param {Number} insertIdx - The index at which the element should be inserted.\n * @param {Number} val - The value to be inserted into the vector.\n * @param {function} fn - A function that is called for updates, the existing value and the\n * requested value are passed as arguments\n */\nlunr.Vector.prototype.upsert = function (insertIdx, val, fn) {\n this._magnitude = 0\n var position = this.positionForIndex(insertIdx)\n\n if (this.elements[position] == insertIdx) {\n this.elements[position + 1] = fn(this.elements[position + 1], val)\n } else {\n this.elements.splice(position, 0, insertIdx, val)\n }\n}\n\n/**\n * Calculates the magnitude of this vector.\n *\n * @returns {Number}\n */\nlunr.Vector.prototype.magnitude = function () {\n if (this._magnitude) return this._magnitude\n\n var sumOfSquares = 0,\n elementsLength = this.elements.length\n\n for (var i = 1; i < elementsLength; i += 2) {\n var val = this.elements[i]\n sumOfSquares += val * val\n }\n\n return this._magnitude = Math.sqrt(sumOfSquares)\n}\n\n/**\n * Calculates the dot product of this vector and another vector.\n *\n * @param {lunr.Vector} otherVector - The vector to compute the dot product with.\n * @returns {Number}\n */\nlunr.Vector.prototype.dot = function (otherVector) {\n var dotProduct = 0,\n a = this.elements, b = otherVector.elements,\n aLen = a.length, bLen = b.length,\n aVal = 0, bVal = 0,\n i = 0, j = 0\n\n while (i < aLen && j < bLen) {\n aVal = a[i], bVal = b[j]\n if (aVal < bVal) {\n i += 2\n } else if (aVal > bVal) {\n j += 2\n } else if (aVal == bVal) {\n dotProduct += a[i + 1] * b[j + 1]\n i += 2\n j += 2\n }\n }\n\n return dotProduct\n}\n\n/**\n * Calculates the similarity between this vector and another vector.\n *\n * @param {lunr.Vector} otherVector - The other vector to calculate the\n * similarity with.\n * @returns {Number}\n */\nlunr.Vector.prototype.similarity = function (otherVector) {\n return this.dot(otherVector) / this.magnitude() || 0\n}\n\n/**\n * Converts the vector to an array of the elements within the vector.\n *\n * @returns {Number[]}\n */\nlunr.Vector.prototype.toArray = function () {\n var output = new Array (this.elements.length / 2)\n\n for (var i = 1, j = 0; i < this.elements.length; i += 2, j++) {\n output[j] = this.elements[i]\n }\n\n return output\n}\n\n/**\n * A JSON serializable representation of the vector.\n *\n * @returns {Number[]}\n */\nlunr.Vector.prototype.toJSON = function () {\n return this.elements\n}\n/* eslint-disable */\n/*!\n * lunr.stemmer\n * Copyright (C) 2020 Oliver Nightingale\n * Includes code from - http://tartarus.org/~martin/PorterStemmer/js.txt\n */\n\n/**\n * lunr.stemmer is an english language stemmer, this is a JavaScript\n * implementation of the PorterStemmer taken from http://tartarus.org/~martin\n *\n * @static\n * @implements {lunr.PipelineFunction}\n * @param {lunr.Token} token - The string to stem\n * @returns {lunr.Token}\n * @see {@link lunr.Pipeline}\n * @function\n */\nlunr.stemmer = (function(){\n var step2list = {\n \"ational\" : \"ate\",\n \"tional\" : \"tion\",\n \"enci\" : \"ence\",\n \"anci\" : \"ance\",\n \"izer\" : \"ize\",\n \"bli\" : \"ble\",\n \"alli\" : \"al\",\n \"entli\" : \"ent\",\n \"eli\" : \"e\",\n \"ousli\" : \"ous\",\n \"ization\" : \"ize\",\n \"ation\" : \"ate\",\n \"ator\" : \"ate\",\n \"alism\" : \"al\",\n \"iveness\" : \"ive\",\n \"fulness\" : \"ful\",\n \"ousness\" : \"ous\",\n \"aliti\" : \"al\",\n \"iviti\" : \"ive\",\n \"biliti\" : \"ble\",\n \"logi\" : \"log\"\n },\n\n step3list = {\n \"icate\" : \"ic\",\n \"ative\" : \"\",\n \"alize\" : \"al\",\n \"iciti\" : \"ic\",\n \"ical\" : \"ic\",\n \"ful\" : \"\",\n \"ness\" : \"\"\n },\n\n c = \"[^aeiou]\", // consonant\n v = \"[aeiouy]\", // vowel\n C = c + \"[^aeiouy]*\", // consonant sequence\n V = v + \"[aeiou]*\", // vowel sequence\n\n mgr0 = \"^(\" + C + \")?\" + V + C, // [C]VC... is m>0\n meq1 = \"^(\" + C + \")?\" + V + C + \"(\" + V + \")?$\", // [C]VC[V] is m=1\n mgr1 = \"^(\" + C + \")?\" + V + C + V + C, // [C]VCVC... is m>1\n s_v = \"^(\" + C + \")?\" + v; // vowel in stem\n\n var re_mgr0 = new RegExp(mgr0);\n var re_mgr1 = new RegExp(mgr1);\n var re_meq1 = new RegExp(meq1);\n var re_s_v = new RegExp(s_v);\n\n var re_1a = /^(.+?)(ss|i)es$/;\n var re2_1a = /^(.+?)([^s])s$/;\n var re_1b = /^(.+?)eed$/;\n var re2_1b = /^(.+?)(ed|ing)$/;\n var re_1b_2 = /.$/;\n var re2_1b_2 = /(at|bl|iz)$/;\n var re3_1b_2 = new RegExp(\"([^aeiouylsz])\\\\1$\");\n var re4_1b_2 = new RegExp(\"^\" + C + v + \"[^aeiouwxy]$\");\n\n var re_1c = /^(.+?[^aeiou])y$/;\n var re_2 = /^(.+?)(ational|tional|enci|anci|izer|bli|alli|entli|eli|ousli|ization|ation|ator|alism|iveness|fulness|ousness|aliti|iviti|biliti|logi)$/;\n\n var re_3 = /^(.+?)(icate|ative|alize|iciti|ical|ful|ness)$/;\n\n var re_4 = /^(.+?)(al|ance|ence|er|ic|able|ible|ant|ement|ment|ent|ou|ism|ate|iti|ous|ive|ize)$/;\n var re2_4 = /^(.+?)(s|t)(ion)$/;\n\n var re_5 = /^(.+?)e$/;\n var re_5_1 = /ll$/;\n var re3_5 = new RegExp(\"^\" + C + v + \"[^aeiouwxy]$\");\n\n var porterStemmer = function porterStemmer(w) {\n var stem,\n suffix,\n firstch,\n re,\n re2,\n re3,\n re4;\n\n if (w.length < 3) { return w; }\n\n firstch = w.substr(0,1);\n if (firstch == \"y\") {\n w = firstch.toUpperCase() + w.substr(1);\n }\n\n // Step 1a\n re = re_1a\n re2 = re2_1a;\n\n if (re.test(w)) { w = w.replace(re,\"$1$2\"); }\n else if (re2.test(w)) { w = w.replace(re2,\"$1$2\"); }\n\n // Step 1b\n re = re_1b;\n re2 = re2_1b;\n if (re.test(w)) {\n var fp = re.exec(w);\n re = re_mgr0;\n if (re.test(fp[1])) {\n re = re_1b_2;\n w = w.replace(re,\"\");\n }\n } else if (re2.test(w)) {\n var fp = re2.exec(w);\n stem = fp[1];\n re2 = re_s_v;\n if (re2.test(stem)) {\n w = stem;\n re2 = re2_1b_2;\n re3 = re3_1b_2;\n re4 = re4_1b_2;\n if (re2.test(w)) { w = w + \"e\"; }\n else if (re3.test(w)) { re = re_1b_2; w = w.replace(re,\"\"); }\n else if (re4.test(w)) { w = w + \"e\"; }\n }\n }\n\n // Step 1c - replace suffix y or Y by i if preceded by a non-vowel which is not the first letter of the word (so cry -> cri, by -> by, say -> say)\n re = re_1c;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n w = stem + \"i\";\n }\n\n // Step 2\n re = re_2;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n suffix = fp[2];\n re = re_mgr0;\n if (re.test(stem)) {\n w = stem + step2list[suffix];\n }\n }\n\n // Step 3\n re = re_3;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n suffix = fp[2];\n re = re_mgr0;\n if (re.test(stem)) {\n w = stem + step3list[suffix];\n }\n }\n\n // Step 4\n re = re_4;\n re2 = re2_4;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n re = re_mgr1;\n if (re.test(stem)) {\n w = stem;\n }\n } else if (re2.test(w)) {\n var fp = re2.exec(w);\n stem = fp[1] + fp[2];\n re2 = re_mgr1;\n if (re2.test(stem)) {\n w = stem;\n }\n }\n\n // Step 5\n re = re_5;\n if (re.test(w)) {\n var fp = re.exec(w);\n stem = fp[1];\n re = re_mgr1;\n re2 = re_meq1;\n re3 = re3_5;\n if (re.test(stem) || (re2.test(stem) && !(re3.test(stem)))) {\n w = stem;\n }\n }\n\n re = re_5_1;\n re2 = re_mgr1;\n if (re.test(w) && re2.test(w)) {\n re = re_1b_2;\n w = w.replace(re,\"\");\n }\n\n // and turn initial Y back to y\n\n if (firstch == \"y\") {\n w = firstch.toLowerCase() + w.substr(1);\n }\n\n return w;\n };\n\n return function (token) {\n return token.update(porterStemmer);\n }\n})();\n\nlunr.Pipeline.registerFunction(lunr.stemmer, 'stemmer')\n/*!\n * lunr.stopWordFilter\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.generateStopWordFilter builds a stopWordFilter function from the provided\n * list of stop words.\n *\n * The built in lunr.stopWordFilter is built using this generator and can be used\n * to generate custom stopWordFilters for applications or non English languages.\n *\n * @function\n * @param {Array} token The token to pass through the filter\n * @returns {lunr.PipelineFunction}\n * @see lunr.Pipeline\n * @see lunr.stopWordFilter\n */\nlunr.generateStopWordFilter = function (stopWords) {\n var words = stopWords.reduce(function (memo, stopWord) {\n memo[stopWord] = stopWord\n return memo\n }, {})\n\n return function (token) {\n if (token && words[token.toString()] !== token.toString()) return token\n }\n}\n\n/**\n * lunr.stopWordFilter is an English language stop word list filter, any words\n * contained in the list will not be passed through the filter.\n *\n * This is intended to be used in the Pipeline. If the token does not pass the\n * filter then undefined will be returned.\n *\n * @function\n * @implements {lunr.PipelineFunction}\n * @params {lunr.Token} token - A token to check for being a stop word.\n * @returns {lunr.Token}\n * @see {@link lunr.Pipeline}\n */\nlunr.stopWordFilter = lunr.generateStopWordFilter([\n 'a',\n 'able',\n 'about',\n 'across',\n 'after',\n 'all',\n 'almost',\n 'also',\n 'am',\n 'among',\n 'an',\n 'and',\n 'any',\n 'are',\n 'as',\n 'at',\n 'be',\n 'because',\n 'been',\n 'but',\n 'by',\n 'can',\n 'cannot',\n 'could',\n 'dear',\n 'did',\n 'do',\n 'does',\n 'either',\n 'else',\n 'ever',\n 'every',\n 'for',\n 'from',\n 'get',\n 'got',\n 'had',\n 'has',\n 'have',\n 'he',\n 'her',\n 'hers',\n 'him',\n 'his',\n 'how',\n 'however',\n 'i',\n 'if',\n 'in',\n 'into',\n 'is',\n 'it',\n 'its',\n 'just',\n 'least',\n 'let',\n 'like',\n 'likely',\n 'may',\n 'me',\n 'might',\n 'most',\n 'must',\n 'my',\n 'neither',\n 'no',\n 'nor',\n 'not',\n 'of',\n 'off',\n 'often',\n 'on',\n 'only',\n 'or',\n 'other',\n 'our',\n 'own',\n 'rather',\n 'said',\n 'say',\n 'says',\n 'she',\n 'should',\n 'since',\n 'so',\n 'some',\n 'than',\n 'that',\n 'the',\n 'their',\n 'them',\n 'then',\n 'there',\n 'these',\n 'they',\n 'this',\n 'tis',\n 'to',\n 'too',\n 'twas',\n 'us',\n 'wants',\n 'was',\n 'we',\n 'were',\n 'what',\n 'when',\n 'where',\n 'which',\n 'while',\n 'who',\n 'whom',\n 'why',\n 'will',\n 'with',\n 'would',\n 'yet',\n 'you',\n 'your'\n])\n\nlunr.Pipeline.registerFunction(lunr.stopWordFilter, 'stopWordFilter')\n/*!\n * lunr.trimmer\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.trimmer is a pipeline function for trimming non word\n * characters from the beginning and end of tokens before they\n * enter the index.\n *\n * This implementation may not work correctly for non latin\n * characters and should either be removed or adapted for use\n * with languages with non-latin characters.\n *\n * @static\n * @implements {lunr.PipelineFunction}\n * @param {lunr.Token} token The token to pass through the filter\n * @returns {lunr.Token}\n * @see lunr.Pipeline\n */\nlunr.trimmer = function (token) {\n return token.update(function (s) {\n return s.replace(/^\\W+/, '').replace(/\\W+$/, '')\n })\n}\n\nlunr.Pipeline.registerFunction(lunr.trimmer, 'trimmer')\n/*!\n * lunr.TokenSet\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * A token set is used to store the unique list of all tokens\n * within an index. Token sets are also used to represent an\n * incoming query to the index, this query token set and index\n * token set are then intersected to find which tokens to look\n * up in the inverted index.\n *\n * A token set can hold multiple tokens, as in the case of the\n * index token set, or it can hold a single token as in the\n * case of a simple query token set.\n *\n * Additionally token sets are used to perform wildcard matching.\n * Leading, contained and trailing wildcards are supported, and\n * from this edit distance matching can also be provided.\n *\n * Token sets are implemented as a minimal finite state automata,\n * where both common prefixes and suffixes are shared between tokens.\n * This helps to reduce the space used for storing the token set.\n *\n * @constructor\n */\nlunr.TokenSet = function () {\n this.final = false\n this.edges = {}\n this.id = lunr.TokenSet._nextId\n lunr.TokenSet._nextId += 1\n}\n\n/**\n * Keeps track of the next, auto increment, identifier to assign\n * to a new tokenSet.\n *\n * TokenSets require a unique identifier to be correctly minimised.\n *\n * @private\n */\nlunr.TokenSet._nextId = 1\n\n/**\n * Creates a TokenSet instance from the given sorted array of words.\n *\n * @param {String[]} arr - A sorted array of strings to create the set from.\n * @returns {lunr.TokenSet}\n * @throws Will throw an error if the input array is not sorted.\n */\nlunr.TokenSet.fromArray = function (arr) {\n var builder = new lunr.TokenSet.Builder\n\n for (var i = 0, len = arr.length; i < len; i++) {\n builder.insert(arr[i])\n }\n\n builder.finish()\n return builder.root\n}\n\n/**\n * Creates a token set from a query clause.\n *\n * @private\n * @param {Object} clause - A single clause from lunr.Query.\n * @param {string} clause.term - The query clause term.\n * @param {number} [clause.editDistance] - The optional edit distance for the term.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.fromClause = function (clause) {\n if ('editDistance' in clause) {\n return lunr.TokenSet.fromFuzzyString(clause.term, clause.editDistance)\n } else {\n return lunr.TokenSet.fromString(clause.term)\n }\n}\n\n/**\n * Creates a token set representing a single string with a specified\n * edit distance.\n *\n * Insertions, deletions, substitutions and transpositions are each\n * treated as an edit distance of 1.\n *\n * Increasing the allowed edit distance will have a dramatic impact\n * on the performance of both creating and intersecting these TokenSets.\n * It is advised to keep the edit distance less than 3.\n *\n * @param {string} str - The string to create the token set from.\n * @param {number} editDistance - The allowed edit distance to match.\n * @returns {lunr.Vector}\n */\nlunr.TokenSet.fromFuzzyString = function (str, editDistance) {\n var root = new lunr.TokenSet\n\n var stack = [{\n node: root,\n editsRemaining: editDistance,\n str: str\n }]\n\n while (stack.length) {\n var frame = stack.pop()\n\n // no edit\n if (frame.str.length > 0) {\n var char = frame.str.charAt(0),\n noEditNode\n\n if (char in frame.node.edges) {\n noEditNode = frame.node.edges[char]\n } else {\n noEditNode = new lunr.TokenSet\n frame.node.edges[char] = noEditNode\n }\n\n if (frame.str.length == 1) {\n noEditNode.final = true\n }\n\n stack.push({\n node: noEditNode,\n editsRemaining: frame.editsRemaining,\n str: frame.str.slice(1)\n })\n }\n\n if (frame.editsRemaining == 0) {\n continue\n }\n\n // insertion\n if (\"*\" in frame.node.edges) {\n var insertionNode = frame.node.edges[\"*\"]\n } else {\n var insertionNode = new lunr.TokenSet\n frame.node.edges[\"*\"] = insertionNode\n }\n\n if (frame.str.length == 0) {\n insertionNode.final = true\n }\n\n stack.push({\n node: insertionNode,\n editsRemaining: frame.editsRemaining - 1,\n str: frame.str\n })\n\n // deletion\n // can only do a deletion if we have enough edits remaining\n // and if there are characters left to delete in the string\n if (frame.str.length > 1) {\n stack.push({\n node: frame.node,\n editsRemaining: frame.editsRemaining - 1,\n str: frame.str.slice(1)\n })\n }\n\n // deletion\n // just removing the last character from the str\n if (frame.str.length == 1) {\n frame.node.final = true\n }\n\n // substitution\n // can only do a substitution if we have enough edits remaining\n // and if there are characters left to substitute\n if (frame.str.length >= 1) {\n if (\"*\" in frame.node.edges) {\n var substitutionNode = frame.node.edges[\"*\"]\n } else {\n var substitutionNode = new lunr.TokenSet\n frame.node.edges[\"*\"] = substitutionNode\n }\n\n if (frame.str.length == 1) {\n substitutionNode.final = true\n }\n\n stack.push({\n node: substitutionNode,\n editsRemaining: frame.editsRemaining - 1,\n str: frame.str.slice(1)\n })\n }\n\n // transposition\n // can only do a transposition if there are edits remaining\n // and there are enough characters to transpose\n if (frame.str.length > 1) {\n var charA = frame.str.charAt(0),\n charB = frame.str.charAt(1),\n transposeNode\n\n if (charB in frame.node.edges) {\n transposeNode = frame.node.edges[charB]\n } else {\n transposeNode = new lunr.TokenSet\n frame.node.edges[charB] = transposeNode\n }\n\n if (frame.str.length == 1) {\n transposeNode.final = true\n }\n\n stack.push({\n node: transposeNode,\n editsRemaining: frame.editsRemaining - 1,\n str: charA + frame.str.slice(2)\n })\n }\n }\n\n return root\n}\n\n/**\n * Creates a TokenSet from a string.\n *\n * The string may contain one or more wildcard characters (*)\n * that will allow wildcard matching when intersecting with\n * another TokenSet.\n *\n * @param {string} str - The string to create a TokenSet from.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.fromString = function (str) {\n var node = new lunr.TokenSet,\n root = node\n\n /*\n * Iterates through all characters within the passed string\n * appending a node for each character.\n *\n * When a wildcard character is found then a self\n * referencing edge is introduced to continually match\n * any number of any characters.\n */\n for (var i = 0, len = str.length; i < len; i++) {\n var char = str[i],\n final = (i == len - 1)\n\n if (char == \"*\") {\n node.edges[char] = node\n node.final = final\n\n } else {\n var next = new lunr.TokenSet\n next.final = final\n\n node.edges[char] = next\n node = next\n }\n }\n\n return root\n}\n\n/**\n * Converts this TokenSet into an array of strings\n * contained within the TokenSet.\n *\n * This is not intended to be used on a TokenSet that\n * contains wildcards, in these cases the results are\n * undefined and are likely to cause an infinite loop.\n *\n * @returns {string[]}\n */\nlunr.TokenSet.prototype.toArray = function () {\n var words = []\n\n var stack = [{\n prefix: \"\",\n node: this\n }]\n\n while (stack.length) {\n var frame = stack.pop(),\n edges = Object.keys(frame.node.edges),\n len = edges.length\n\n if (frame.node.final) {\n /* In Safari, at this point the prefix is sometimes corrupted, see:\n * https://github.com/olivernn/lunr.js/issues/279 Calling any\n * String.prototype method forces Safari to \"cast\" this string to what\n * it's supposed to be, fixing the bug. */\n frame.prefix.charAt(0)\n words.push(frame.prefix)\n }\n\n for (var i = 0; i < len; i++) {\n var edge = edges[i]\n\n stack.push({\n prefix: frame.prefix.concat(edge),\n node: frame.node.edges[edge]\n })\n }\n }\n\n return words\n}\n\n/**\n * Generates a string representation of a TokenSet.\n *\n * This is intended to allow TokenSets to be used as keys\n * in objects, largely to aid the construction and minimisation\n * of a TokenSet. As such it is not designed to be a human\n * friendly representation of the TokenSet.\n *\n * @returns {string}\n */\nlunr.TokenSet.prototype.toString = function () {\n // NOTE: Using Object.keys here as this.edges is very likely\n // to enter 'hash-mode' with many keys being added\n //\n // avoiding a for-in loop here as it leads to the function\n // being de-optimised (at least in V8). From some simple\n // benchmarks the performance is comparable, but allowing\n // V8 to optimize may mean easy performance wins in the future.\n\n if (this._str) {\n return this._str\n }\n\n var str = this.final ? '1' : '0',\n labels = Object.keys(this.edges).sort(),\n len = labels.length\n\n for (var i = 0; i < len; i++) {\n var label = labels[i],\n node = this.edges[label]\n\n str = str + label + node.id\n }\n\n return str\n}\n\n/**\n * Returns a new TokenSet that is the intersection of\n * this TokenSet and the passed TokenSet.\n *\n * This intersection will take into account any wildcards\n * contained within the TokenSet.\n *\n * @param {lunr.TokenSet} b - An other TokenSet to intersect with.\n * @returns {lunr.TokenSet}\n */\nlunr.TokenSet.prototype.intersect = function (b) {\n var output = new lunr.TokenSet,\n frame = undefined\n\n var stack = [{\n qNode: b,\n output: output,\n node: this\n }]\n\n while (stack.length) {\n frame = stack.pop()\n\n // NOTE: As with the #toString method, we are using\n // Object.keys and a for loop instead of a for-in loop\n // as both of these objects enter 'hash' mode, causing\n // the function to be de-optimised in V8\n var qEdges = Object.keys(frame.qNode.edges),\n qLen = qEdges.length,\n nEdges = Object.keys(frame.node.edges),\n nLen = nEdges.length\n\n for (var q = 0; q < qLen; q++) {\n var qEdge = qEdges[q]\n\n for (var n = 0; n < nLen; n++) {\n var nEdge = nEdges[n]\n\n if (nEdge == qEdge || qEdge == '*') {\n var node = frame.node.edges[nEdge],\n qNode = frame.qNode.edges[qEdge],\n final = node.final && qNode.final,\n next = undefined\n\n if (nEdge in frame.output.edges) {\n // an edge already exists for this character\n // no need to create a new node, just set the finality\n // bit unless this node is already final\n next = frame.output.edges[nEdge]\n next.final = next.final || final\n\n } else {\n // no edge exists yet, must create one\n // set the finality bit and insert it\n // into the output\n next = new lunr.TokenSet\n next.final = final\n frame.output.edges[nEdge] = next\n }\n\n stack.push({\n qNode: qNode,\n output: next,\n node: node\n })\n }\n }\n }\n }\n\n return output\n}\nlunr.TokenSet.Builder = function () {\n this.previousWord = \"\"\n this.root = new lunr.TokenSet\n this.uncheckedNodes = []\n this.minimizedNodes = {}\n}\n\nlunr.TokenSet.Builder.prototype.insert = function (word) {\n var node,\n commonPrefix = 0\n\n if (word < this.previousWord) {\n throw new Error (\"Out of order word insertion\")\n }\n\n for (var i = 0; i < word.length && i < this.previousWord.length; i++) {\n if (word[i] != this.previousWord[i]) break\n commonPrefix++\n }\n\n this.minimize(commonPrefix)\n\n if (this.uncheckedNodes.length == 0) {\n node = this.root\n } else {\n node = this.uncheckedNodes[this.uncheckedNodes.length - 1].child\n }\n\n for (var i = commonPrefix; i < word.length; i++) {\n var nextNode = new lunr.TokenSet,\n char = word[i]\n\n node.edges[char] = nextNode\n\n this.uncheckedNodes.push({\n parent: node,\n char: char,\n child: nextNode\n })\n\n node = nextNode\n }\n\n node.final = true\n this.previousWord = word\n}\n\nlunr.TokenSet.Builder.prototype.finish = function () {\n this.minimize(0)\n}\n\nlunr.TokenSet.Builder.prototype.minimize = function (downTo) {\n for (var i = this.uncheckedNodes.length - 1; i >= downTo; i--) {\n var node = this.uncheckedNodes[i],\n childKey = node.child.toString()\n\n if (childKey in this.minimizedNodes) {\n node.parent.edges[node.char] = this.minimizedNodes[childKey]\n } else {\n // Cache the key for this node since\n // we know it can't change anymore\n node.child._str = childKey\n\n this.minimizedNodes[childKey] = node.child\n }\n\n this.uncheckedNodes.pop()\n }\n}\n/*!\n * lunr.Index\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * An index contains the built index of all documents and provides a query interface\n * to the index.\n *\n * Usually instances of lunr.Index will not be created using this constructor, instead\n * lunr.Builder should be used to construct new indexes, or lunr.Index.load should be\n * used to load previously built and serialized indexes.\n *\n * @constructor\n * @param {Object} attrs - The attributes of the built search index.\n * @param {Object} attrs.invertedIndex - An index of term/field to document reference.\n * @param {Object} attrs.fieldVectors - Field vectors\n * @param {lunr.TokenSet} attrs.tokenSet - An set of all corpus tokens.\n * @param {string[]} attrs.fields - The names of indexed document fields.\n * @param {lunr.Pipeline} attrs.pipeline - The pipeline to use for search terms.\n */\nlunr.Index = function (attrs) {\n this.invertedIndex = attrs.invertedIndex\n this.fieldVectors = attrs.fieldVectors\n this.tokenSet = attrs.tokenSet\n this.fields = attrs.fields\n this.pipeline = attrs.pipeline\n}\n\n/**\n * A result contains details of a document matching a search query.\n * @typedef {Object} lunr.Index~Result\n * @property {string} ref - The reference of the document this result represents.\n * @property {number} score - A number between 0 and 1 representing how similar this document is to the query.\n * @property {lunr.MatchData} matchData - Contains metadata about this match including which term(s) caused the match.\n */\n\n/**\n * Although lunr provides the ability to create queries using lunr.Query, it also provides a simple\n * query language which itself is parsed into an instance of lunr.Query.\n *\n * For programmatically building queries it is advised to directly use lunr.Query, the query language\n * is best used for human entered text rather than program generated text.\n *\n * At its simplest queries can just be a single term, e.g. `hello`, multiple terms are also supported\n * and will be combined with OR, e.g `hello world` will match documents that contain either 'hello'\n * or 'world', though those that contain both will rank higher in the results.\n *\n * Wildcards can be included in terms to match one or more unspecified characters, these wildcards can\n * be inserted anywhere within the term, and more than one wildcard can exist in a single term. Adding\n * wildcards will increase the number of documents that will be found but can also have a negative\n * impact on query performance, especially with wildcards at the beginning of a term.\n *\n * Terms can be restricted to specific fields, e.g. `title:hello`, only documents with the term\n * hello in the title field will match this query. Using a field not present in the index will lead\n * to an error being thrown.\n *\n * Modifiers can also be added to terms, lunr supports edit distance and boost modifiers on terms. A term\n * boost will make documents matching that term score higher, e.g. `foo^5`. Edit distance is also supported\n * to provide fuzzy matching, e.g. 'hello~2' will match documents with hello with an edit distance of 2.\n * Avoid large values for edit distance to improve query performance.\n *\n * Each term also supports a presence modifier. By default a term's presence in document is optional, however\n * this can be changed to either required or prohibited. For a term's presence to be required in a document the\n * term should be prefixed with a '+', e.g. `+foo bar` is a search for documents that must contain 'foo' and\n * optionally contain 'bar'. Conversely a leading '-' sets the terms presence to prohibited, i.e. it must not\n * appear in a document, e.g. `-foo bar` is a search for documents that do not contain 'foo' but may contain 'bar'.\n *\n * To escape special characters the backslash character '\\' can be used, this allows searches to include\n * characters that would normally be considered modifiers, e.g. `foo\\~2` will search for a term \"foo~2\" instead\n * of attempting to apply a boost of 2 to the search term \"foo\".\n *\n * @typedef {string} lunr.Index~QueryString\n * @example Simple single term query\n * hello\n * @example Multiple term query\n * hello world\n * @example term scoped to a field\n * title:hello\n * @example term with a boost of 10\n * hello^10\n * @example term with an edit distance of 2\n * hello~2\n * @example terms with presence modifiers\n * -foo +bar baz\n */\n\n/**\n * Performs a search against the index using lunr query syntax.\n *\n * Results will be returned sorted by their score, the most relevant results\n * will be returned first. For details on how the score is calculated, please see\n * the {@link https://lunrjs.com/guides/searching.html#scoring|guide}.\n *\n * For more programmatic querying use lunr.Index#query.\n *\n * @param {lunr.Index~QueryString} queryString - A string containing a lunr query.\n * @throws {lunr.QueryParseError} If the passed query string cannot be parsed.\n * @returns {lunr.Index~Result[]}\n */\nlunr.Index.prototype.search = function (queryString) {\n return this.query(function (query) {\n var parser = new lunr.QueryParser(queryString, query)\n parser.parse()\n })\n}\n\n/**\n * A query builder callback provides a query object to be used to express\n * the query to perform on the index.\n *\n * @callback lunr.Index~queryBuilder\n * @param {lunr.Query} query - The query object to build up.\n * @this lunr.Query\n */\n\n/**\n * Performs a query against the index using the yielded lunr.Query object.\n *\n * If performing programmatic queries against the index, this method is preferred\n * over lunr.Index#search so as to avoid the additional query parsing overhead.\n *\n * A query object is yielded to the supplied function which should be used to\n * express the query to be run against the index.\n *\n * Note that although this function takes a callback parameter it is _not_ an\n * asynchronous operation, the callback is just yielded a query object to be\n * customized.\n *\n * @param {lunr.Index~queryBuilder} fn - A function that is used to build the query.\n * @returns {lunr.Index~Result[]}\n */\nlunr.Index.prototype.query = function (fn) {\n // for each query clause\n // * process terms\n // * expand terms from token set\n // * find matching documents and metadata\n // * get document vectors\n // * score documents\n\n var query = new lunr.Query(this.fields),\n matchingFields = Object.create(null),\n queryVectors = Object.create(null),\n termFieldCache = Object.create(null),\n requiredMatches = Object.create(null),\n prohibitedMatches = Object.create(null)\n\n /*\n * To support field level boosts a query vector is created per\n * field. An empty vector is eagerly created to support negated\n * queries.\n */\n for (var i = 0; i < this.fields.length; i++) {\n queryVectors[this.fields[i]] = new lunr.Vector\n }\n\n fn.call(query, query)\n\n for (var i = 0; i < query.clauses.length; i++) {\n /*\n * Unless the pipeline has been disabled for this term, which is\n * the case for terms with wildcards, we need to pass the clause\n * term through the search pipeline. A pipeline returns an array\n * of processed terms. Pipeline functions may expand the passed\n * term, which means we may end up performing multiple index lookups\n * for a single query term.\n */\n var clause = query.clauses[i],\n terms = null,\n clauseMatches = lunr.Set.empty\n\n if (clause.usePipeline) {\n terms = this.pipeline.runString(clause.term, {\n fields: clause.fields\n })\n } else {\n terms = [clause.term]\n }\n\n for (var m = 0; m < terms.length; m++) {\n var term = terms[m]\n\n /*\n * Each term returned from the pipeline needs to use the same query\n * clause object, e.g. the same boost and or edit distance. The\n * simplest way to do this is to re-use the clause object but mutate\n * its term property.\n */\n clause.term = term\n\n /*\n * From the term in the clause we create a token set which will then\n * be used to intersect the indexes token set to get a list of terms\n * to lookup in the inverted index\n */\n var termTokenSet = lunr.TokenSet.fromClause(clause),\n expandedTerms = this.tokenSet.intersect(termTokenSet).toArray()\n\n /*\n * If a term marked as required does not exist in the tokenSet it is\n * impossible for the search to return any matches. We set all the field\n * scoped required matches set to empty and stop examining any further\n * clauses.\n */\n if (expandedTerms.length === 0 && clause.presence === lunr.Query.presence.REQUIRED) {\n for (var k = 0; k < clause.fields.length; k++) {\n var field = clause.fields[k]\n requiredMatches[field] = lunr.Set.empty\n }\n\n break\n }\n\n for (var j = 0; j < expandedTerms.length; j++) {\n /*\n * For each term get the posting and termIndex, this is required for\n * building the query vector.\n */\n var expandedTerm = expandedTerms[j],\n posting = this.invertedIndex[expandedTerm],\n termIndex = posting._index\n\n for (var k = 0; k < clause.fields.length; k++) {\n /*\n * For each field that this query term is scoped by (by default\n * all fields are in scope) we need to get all the document refs\n * that have this term in that field.\n *\n * The posting is the entry in the invertedIndex for the matching\n * term from above.\n */\n var field = clause.fields[k],\n fieldPosting = posting[field],\n matchingDocumentRefs = Object.keys(fieldPosting),\n termField = expandedTerm + \"/\" + field,\n matchingDocumentsSet = new lunr.Set(matchingDocumentRefs)\n\n /*\n * if the presence of this term is required ensure that the matching\n * documents are added to the set of required matches for this clause.\n *\n */\n if (clause.presence == lunr.Query.presence.REQUIRED) {\n clauseMatches = clauseMatches.union(matchingDocumentsSet)\n\n if (requiredMatches[field] === undefined) {\n requiredMatches[field] = lunr.Set.complete\n }\n }\n\n /*\n * if the presence of this term is prohibited ensure that the matching\n * documents are added to the set of prohibited matches for this field,\n * creating that set if it does not yet exist.\n */\n if (clause.presence == lunr.Query.presence.PROHIBITED) {\n if (prohibitedMatches[field] === undefined) {\n prohibitedMatches[field] = lunr.Set.empty\n }\n\n prohibitedMatches[field] = prohibitedMatches[field].union(matchingDocumentsSet)\n\n /*\n * Prohibited matches should not be part of the query vector used for\n * similarity scoring and no metadata should be extracted so we continue\n * to the next field\n */\n continue\n }\n\n /*\n * The query field vector is populated using the termIndex found for\n * the term and a unit value with the appropriate boost applied.\n * Using upsert because there could already be an entry in the vector\n * for the term we are working with. In that case we just add the scores\n * together.\n */\n queryVectors[field].upsert(termIndex, clause.boost, function (a, b) { return a + b })\n\n /**\n * If we've already seen this term, field combo then we've already collected\n * the matching documents and metadata, no need to go through all that again\n */\n if (termFieldCache[termField]) {\n continue\n }\n\n for (var l = 0; l < matchingDocumentRefs.length; l++) {\n /*\n * All metadata for this term/field/document triple\n * are then extracted and collected into an instance\n * of lunr.MatchData ready to be returned in the query\n * results\n */\n var matchingDocumentRef = matchingDocumentRefs[l],\n matchingFieldRef = new lunr.FieldRef (matchingDocumentRef, field),\n metadata = fieldPosting[matchingDocumentRef],\n fieldMatch\n\n if ((fieldMatch = matchingFields[matchingFieldRef]) === undefined) {\n matchingFields[matchingFieldRef] = new lunr.MatchData (expandedTerm, field, metadata)\n } else {\n fieldMatch.add(expandedTerm, field, metadata)\n }\n\n }\n\n termFieldCache[termField] = true\n }\n }\n }\n\n /**\n * If the presence was required we need to update the requiredMatches field sets.\n * We do this after all fields for the term have collected their matches because\n * the clause terms presence is required in _any_ of the fields not _all_ of the\n * fields.\n */\n if (clause.presence === lunr.Query.presence.REQUIRED) {\n for (var k = 0; k < clause.fields.length; k++) {\n var field = clause.fields[k]\n requiredMatches[field] = requiredMatches[field].intersect(clauseMatches)\n }\n }\n }\n\n /**\n * Need to combine the field scoped required and prohibited\n * matching documents into a global set of required and prohibited\n * matches\n */\n var allRequiredMatches = lunr.Set.complete,\n allProhibitedMatches = lunr.Set.empty\n\n for (var i = 0; i < this.fields.length; i++) {\n var field = this.fields[i]\n\n if (requiredMatches[field]) {\n allRequiredMatches = allRequiredMatches.intersect(requiredMatches[field])\n }\n\n if (prohibitedMatches[field]) {\n allProhibitedMatches = allProhibitedMatches.union(prohibitedMatches[field])\n }\n }\n\n var matchingFieldRefs = Object.keys(matchingFields),\n results = [],\n matches = Object.create(null)\n\n /*\n * If the query is negated (contains only prohibited terms)\n * we need to get _all_ fieldRefs currently existing in the\n * index. This is only done when we know that the query is\n * entirely prohibited terms to avoid any cost of getting all\n * fieldRefs unnecessarily.\n *\n * Additionally, blank MatchData must be created to correctly\n * populate the results.\n */\n if (query.isNegated()) {\n matchingFieldRefs = Object.keys(this.fieldVectors)\n\n for (var i = 0; i < matchingFieldRefs.length; i++) {\n var matchingFieldRef = matchingFieldRefs[i]\n var fieldRef = lunr.FieldRef.fromString(matchingFieldRef)\n matchingFields[matchingFieldRef] = new lunr.MatchData\n }\n }\n\n for (var i = 0; i < matchingFieldRefs.length; i++) {\n /*\n * Currently we have document fields that match the query, but we\n * need to return documents. The matchData and scores are combined\n * from multiple fields belonging to the same document.\n *\n * Scores are calculated by field, using the query vectors created\n * above, and combined into a final document score using addition.\n */\n var fieldRef = lunr.FieldRef.fromString(matchingFieldRefs[i]),\n docRef = fieldRef.docRef\n\n if (!allRequiredMatches.contains(docRef)) {\n continue\n }\n\n if (allProhibitedMatches.contains(docRef)) {\n continue\n }\n\n var fieldVector = this.fieldVectors[fieldRef],\n score = queryVectors[fieldRef.fieldName].similarity(fieldVector),\n docMatch\n\n if ((docMatch = matches[docRef]) !== undefined) {\n docMatch.score += score\n docMatch.matchData.combine(matchingFields[fieldRef])\n } else {\n var match = {\n ref: docRef,\n score: score,\n matchData: matchingFields[fieldRef]\n }\n matches[docRef] = match\n results.push(match)\n }\n }\n\n /*\n * Sort the results objects by score, highest first.\n */\n return results.sort(function (a, b) {\n return b.score - a.score\n })\n}\n\n/**\n * Prepares the index for JSON serialization.\n *\n * The schema for this JSON blob will be described in a\n * separate JSON schema file.\n *\n * @returns {Object}\n */\nlunr.Index.prototype.toJSON = function () {\n var invertedIndex = Object.keys(this.invertedIndex)\n .sort()\n .map(function (term) {\n return [term, this.invertedIndex[term]]\n }, this)\n\n var fieldVectors = Object.keys(this.fieldVectors)\n .map(function (ref) {\n return [ref, this.fieldVectors[ref].toJSON()]\n }, this)\n\n return {\n version: lunr.version,\n fields: this.fields,\n fieldVectors: fieldVectors,\n invertedIndex: invertedIndex,\n pipeline: this.pipeline.toJSON()\n }\n}\n\n/**\n * Loads a previously serialized lunr.Index\n *\n * @param {Object} serializedIndex - A previously serialized lunr.Index\n * @returns {lunr.Index}\n */\nlunr.Index.load = function (serializedIndex) {\n var attrs = {},\n fieldVectors = {},\n serializedVectors = serializedIndex.fieldVectors,\n invertedIndex = Object.create(null),\n serializedInvertedIndex = serializedIndex.invertedIndex,\n tokenSetBuilder = new lunr.TokenSet.Builder,\n pipeline = lunr.Pipeline.load(serializedIndex.pipeline)\n\n if (serializedIndex.version != lunr.version) {\n lunr.utils.warn(\"Version mismatch when loading serialised index. Current version of lunr '\" + lunr.version + \"' does not match serialized index '\" + serializedIndex.version + \"'\")\n }\n\n for (var i = 0; i < serializedVectors.length; i++) {\n var tuple = serializedVectors[i],\n ref = tuple[0],\n elements = tuple[1]\n\n fieldVectors[ref] = new lunr.Vector(elements)\n }\n\n for (var i = 0; i < serializedInvertedIndex.length; i++) {\n var tuple = serializedInvertedIndex[i],\n term = tuple[0],\n posting = tuple[1]\n\n tokenSetBuilder.insert(term)\n invertedIndex[term] = posting\n }\n\n tokenSetBuilder.finish()\n\n attrs.fields = serializedIndex.fields\n\n attrs.fieldVectors = fieldVectors\n attrs.invertedIndex = invertedIndex\n attrs.tokenSet = tokenSetBuilder.root\n attrs.pipeline = pipeline\n\n return new lunr.Index(attrs)\n}\n/*!\n * lunr.Builder\n * Copyright (C) 2020 Oliver Nightingale\n */\n\n/**\n * lunr.Builder performs indexing on a set of documents and\n * returns instances of lunr.Index ready for querying.\n *\n * All configuration of the index is done via the builder, the\n * fields to index, the document reference, the text processing\n * pipeline and document scoring parameters are all set on the\n * builder before indexing.\n *\n * @constructor\n * @property {string} _ref - Internal reference to the document reference field.\n * @property {string[]} _fields - Internal reference to the document fields to index.\n * @property {object} invertedIndex - The inverted index maps terms to document fields.\n * @property {object} documentTermFrequencies - Keeps track of document term frequencies.\n * @property {object} documentLengths - Keeps track of the length of documents added to the index.\n * @property {lunr.tokenizer} tokenizer - Function for splitting strings into tokens for indexing.\n * @property {lunr.Pipeline} pipeline - The pipeline performs text processing on tokens before indexing.\n * @property {lunr.Pipeline} searchPipeline - A pipeline for processing search terms before querying the index.\n * @property {number} documentCount - Keeps track of the total number of documents indexed.\n * @property {number} _b - A parameter to control field length normalization, setting this to 0 disabled normalization, 1 fully normalizes field lengths, the default value is 0.75.\n * @property {number} _k1 - A parameter to control how quickly an increase in term frequency results in term frequency saturation, the default value is 1.2.\n * @property {number} termIndex - A counter incremented for each unique term, used to identify a terms position in the vector space.\n * @property {array} metadataWhitelist - A list of metadata keys that have been whitelisted for entry in the index.\n */\nlunr.Builder = function () {\n this._ref = \"id\"\n this._fields = Object.create(null)\n this._documents = Object.create(null)\n this.invertedIndex = Object.create(null)\n this.fieldTermFrequencies = {}\n this.fieldLengths = {}\n this.tokenizer = lunr.tokenizer\n this.pipeline = new lunr.Pipeline\n this.searchPipeline = new lunr.Pipeline\n this.documentCount = 0\n this._b = 0.75\n this._k1 = 1.2\n this.termIndex = 0\n this.metadataWhitelist = []\n}\n\n/**\n * Sets the document field used as the document reference. Every document must have this field.\n * The type of this field in the document should be a string, if it is not a string it will be\n * coerced into a string by calling toString.\n *\n * The default ref is 'id'.\n *\n * The ref should _not_ be changed during indexing, it should be set before any documents are\n * added to the index. Changing it during indexing can lead to inconsistent results.\n *\n * @param {string} ref - The name of the reference field in the document.\n */\nlunr.Builder.prototype.ref = function (ref) {\n this._ref = ref\n}\n\n/**\n * A function that is used to extract a field from a document.\n *\n * Lunr expects a field to be at the top level of a document, if however the field\n * is deeply nested within a document an extractor function can be used to extract\n * the right field for indexing.\n *\n * @callback fieldExtractor\n * @param {object} doc - The document being added to the index.\n * @returns {?(string|object|object[])} obj - The object that will be indexed for this field.\n * @example Extracting a nested field\n * function (doc) { return doc.nested.field }\n */\n\n/**\n * Adds a field to the list of document fields that will be indexed. Every document being\n * indexed should have this field. Null values for this field in indexed documents will\n * not cause errors but will limit the chance of that document being retrieved by searches.\n *\n * All fields should be added before adding documents to the index. Adding fields after\n * a document has been indexed will have no effect on already indexed documents.\n *\n * Fields can be boosted at build time. This allows terms within that field to have more\n * importance when ranking search results. Use a field boost to specify that matches within\n * one field are more important than other fields.\n *\n * @param {string} fieldName - The name of a field to index in all documents.\n * @param {object} attributes - Optional attributes associated with this field.\n * @param {number} [attributes.boost=1] - Boost applied to all terms within this field.\n * @param {fieldExtractor} [attributes.extractor] - Function to extract a field from a document.\n * @throws {RangeError} fieldName cannot contain unsupported characters '/'\n */\nlunr.Builder.prototype.field = function (fieldName, attributes) {\n if (/\\//.test(fieldName)) {\n throw new RangeError (\"Field '\" + fieldName + \"' contains illegal character '/'\")\n }\n\n this._fields[fieldName] = attributes || {}\n}\n\n/**\n * A parameter to tune the amount of field length normalisation that is applied when\n * calculating relevance scores. A value of 0 will completely disable any normalisation\n * and a value of 1 will fully normalise field lengths. The default is 0.75. Values of b\n * will be clamped to the range 0 - 1.\n *\n * @param {number} number - The value to set for this tuning parameter.\n */\nlunr.Builder.prototype.b = function (number) {\n if (number < 0) {\n this._b = 0\n } else if (number > 1) {\n this._b = 1\n } else {\n this._b = number\n }\n}\n\n/**\n * A parameter that controls the speed at which a rise in term frequency results in term\n * frequency saturation. The default value is 1.2. Setting this to a higher value will give\n * slower saturation levels, a lower value will result in quicker saturation.\n *\n * @param {number} number - The value to set for this tuning parameter.\n */\nlunr.Builder.prototype.k1 = function (number) {\n this._k1 = number\n}\n\n/**\n * Adds a document to the index.\n *\n * Before adding fields to the index the index should have been fully setup, with the document\n * ref and all fields to index already having been specified.\n *\n * The document must have a field name as specified by the ref (by default this is 'id') and\n * it should have all fields defined for indexing, though null or undefined values will not\n * cause errors.\n *\n * Entire documents can be boosted at build time. Applying a boost to a document indicates that\n * this document should rank higher in search results than other documents.\n *\n * @param {object} doc - The document to add to the index.\n * @param {object} attributes - Optional attributes associated with this document.\n * @param {number} [attributes.boost=1] - Boost applied to all terms within this document.\n */\nlunr.Builder.prototype.add = function (doc, attributes) {\n var docRef = doc[this._ref],\n fields = Object.keys(this._fields)\n\n this._documents[docRef] = attributes || {}\n this.documentCount += 1\n\n for (var i = 0; i < fields.length; i++) {\n var fieldName = fields[i],\n extractor = this._fields[fieldName].extractor,\n field = extractor ? extractor(doc) : doc[fieldName],\n tokens = this.tokenizer(field, {\n fields: [fieldName]\n }),\n terms = this.pipeline.run(tokens),\n fieldRef = new lunr.FieldRef (docRef, fieldName),\n fieldTerms = Object.create(null)\n\n this.fieldTermFrequencies[fieldRef] = fieldTerms\n this.fieldLengths[fieldRef] = 0\n\n // store the length of this field for this document\n this.fieldLengths[fieldRef] += terms.length\n\n // calculate term frequencies for this field\n for (var j = 0; j < terms.length; j++) {\n var term = terms[j]\n\n if (fieldTerms[term] == undefined) {\n fieldTerms[term] = 0\n }\n\n fieldTerms[term] += 1\n\n // add to inverted index\n // create an initial posting if one doesn't exist\n if (this.invertedIndex[term] == undefined) {\n var posting = Object.create(null)\n posting[\"_index\"] = this.termIndex\n this.termIndex += 1\n\n for (var k = 0; k < fields.length; k++) {\n posting[fields[k]] = Object.create(null)\n }\n\n this.invertedIndex[term] = posting\n }\n\n // add an entry for this term/fieldName/docRef to the invertedIndex\n if (this.invertedIndex[term][fieldName][docRef] == undefined) {\n this.invertedIndex[term][fieldName][docRef] = Object.create(null)\n }\n\n // store all whitelisted metadata about this token in the\n // inverted index\n for (var l = 0; l < this.metadataWhitelist.length; l++) {\n var metadataKey = this.metadataWhitelist[l],\n metadata = term.metadata[metadataKey]\n\n if (this.invertedIndex[term][fieldName][docRef][metadataKey] == undefined) {\n this.invertedIndex[term][fieldName][docRef][metadataKey] = []\n }\n\n this.invertedIndex[term][fieldName][docRef][metadataKey].push(metadata)\n }\n }\n\n }\n}\n\n/**\n * Calculates the average document length for this index\n *\n * @private\n */\nlunr.Builder.prototype.calculateAverageFieldLengths = function () {\n\n var fieldRefs = Object.keys(this.fieldLengths),\n numberOfFields = fieldRefs.length,\n accumulator = {},\n documentsWithField = {}\n\n for (var i = 0; i < numberOfFields; i++) {\n var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),\n field = fieldRef.fieldName\n\n documentsWithField[field] || (documentsWithField[field] = 0)\n documentsWithField[field] += 1\n\n accumulator[field] || (accumulator[field] = 0)\n accumulator[field] += this.fieldLengths[fieldRef]\n }\n\n var fields = Object.keys(this._fields)\n\n for (var i = 0; i < fields.length; i++) {\n var fieldName = fields[i]\n accumulator[fieldName] = accumulator[fieldName] / documentsWithField[fieldName]\n }\n\n this.averageFieldLength = accumulator\n}\n\n/**\n * Builds a vector space model of every document using lunr.Vector\n *\n * @private\n */\nlunr.Builder.prototype.createFieldVectors = function () {\n var fieldVectors = {},\n fieldRefs = Object.keys(this.fieldTermFrequencies),\n fieldRefsLength = fieldRefs.length,\n termIdfCache = Object.create(null)\n\n for (var i = 0; i < fieldRefsLength; i++) {\n var fieldRef = lunr.FieldRef.fromString(fieldRefs[i]),\n fieldName = fieldRef.fieldName,\n fieldLength = this.fieldLengths[fieldRef],\n fieldVector = new lunr.Vector,\n termFrequencies = this.fieldTermFrequencies[fieldRef],\n terms = Object.keys(termFrequencies),\n termsLength = terms.length\n\n\n var fieldBoost = this._fields[fieldName].boost || 1,\n docBoost = this._documents[fieldRef.docRef].boost || 1\n\n for (var j = 0; j < termsLength; j++) {\n var term = terms[j],\n tf = termFrequencies[term],\n termIndex = this.invertedIndex[term]._index,\n idf, score, scoreWithPrecision\n\n if (termIdfCache[term] === undefined) {\n idf = lunr.idf(this.invertedIndex[term], this.documentCount)\n termIdfCache[term] = idf\n } else {\n idf = termIdfCache[term]\n }\n\n score = idf * ((this._k1 + 1) * tf) / (this._k1 * (1 - this._b + this._b * (fieldLength / this.averageFieldLength[fieldName])) + tf)\n score *= fieldBoost\n score *= docBoost\n scoreWithPrecision = Math.round(score * 1000) / 1000\n // Converts 1.23456789 to 1.234.\n // Reducing the precision so that the vectors take up less\n // space when serialised. Doing it now so that they behave\n // the same before and after serialisation. Also, this is\n // the fastest approach to reducing a number's precision in\n // JavaScript.\n\n fieldVector.insert(termIndex, scoreWithPrecision)\n }\n\n fieldVectors[fieldRef] = fieldVector\n }\n\n this.fieldVectors = fieldVectors\n}\n\n/**\n * Creates a token set of all tokens in the index using lunr.TokenSet\n *\n * @private\n */\nlunr.Builder.prototype.createTokenSet = function () {\n this.tokenSet = lunr.TokenSet.fromArray(\n Object.keys(this.invertedIndex).sort()\n )\n}\n\n/**\n * Builds the index, creating an instance of lunr.Index.\n *\n * This completes the indexing process and should only be called\n * once all documents have been added to the index.\n *\n * @returns {lunr.Index}\n */\nlunr.Builder.prototype.build = function () {\n this.calculateAverageFieldLengths()\n this.createFieldVectors()\n this.createTokenSet()\n\n return new lunr.Index({\n invertedIndex: this.invertedIndex,\n fieldVectors: this.fieldVectors,\n tokenSet: this.tokenSet,\n fields: Object.keys(this._fields),\n pipeline: this.searchPipeline\n })\n}\n\n/**\n * Applies a plugin to the index builder.\n *\n * A plugin is a function that is called with the index builder as its context.\n * Plugins can be used to customise or extend the behaviour of the index\n * in some way. A plugin is just a function, that encapsulated the custom\n * behaviour that should be applied when building the index.\n *\n * The plugin function will be called with the index builder as its argument, additional\n * arguments can also be passed when calling use. The function will be called\n * with the index builder as its context.\n *\n * @param {Function} plugin The plugin to apply.\n */\nlunr.Builder.prototype.use = function (fn) {\n var args = Array.prototype.slice.call(arguments, 1)\n args.unshift(this)\n fn.apply(this, args)\n}\n/**\n * Contains and collects metadata about a matching document.\n * A single instance of lunr.MatchData is returned as part of every\n * lunr.Index~Result.\n *\n * @constructor\n * @param {string} term - The term this match data is associated with\n * @param {string} field - The field in which the term was found\n * @param {object} metadata - The metadata recorded about this term in this field\n * @property {object} metadata - A cloned collection of metadata associated with this document.\n * @see {@link lunr.Index~Result}\n */\nlunr.MatchData = function (term, field, metadata) {\n var clonedMetadata = Object.create(null),\n metadataKeys = Object.keys(metadata || {})\n\n // Cloning the metadata to prevent the original\n // being mutated during match data combination.\n // Metadata is kept in an array within the inverted\n // index so cloning the data can be done with\n // Array#slice\n for (var i = 0; i < metadataKeys.length; i++) {\n var key = metadataKeys[i]\n clonedMetadata[key] = metadata[key].slice()\n }\n\n this.metadata = Object.create(null)\n\n if (term !== undefined) {\n this.metadata[term] = Object.create(null)\n this.metadata[term][field] = clonedMetadata\n }\n}\n\n/**\n * An instance of lunr.MatchData will be created for every term that matches a\n * document. However only one instance is required in a lunr.Index~Result. This\n * method combines metadata from another instance of lunr.MatchData with this\n * objects metadata.\n *\n * @param {lunr.MatchData} otherMatchData - Another instance of match data to merge with this one.\n * @see {@link lunr.Index~Result}\n */\nlunr.MatchData.prototype.combine = function (otherMatchData) {\n var terms = Object.keys(otherMatchData.metadata)\n\n for (var i = 0; i < terms.length; i++) {\n var term = terms[i],\n fields = Object.keys(otherMatchData.metadata[term])\n\n if (this.metadata[term] == undefined) {\n this.metadata[term] = Object.create(null)\n }\n\n for (var j = 0; j < fields.length; j++) {\n var field = fields[j],\n keys = Object.keys(otherMatchData.metadata[term][field])\n\n if (this.metadata[term][field] == undefined) {\n this.metadata[term][field] = Object.create(null)\n }\n\n for (var k = 0; k < keys.length; k++) {\n var key = keys[k]\n\n if (this.metadata[term][field][key] == undefined) {\n this.metadata[term][field][key] = otherMatchData.metadata[term][field][key]\n } else {\n this.metadata[term][field][key] = this.metadata[term][field][key].concat(otherMatchData.metadata[term][field][key])\n }\n\n }\n }\n }\n}\n\n/**\n * Add metadata for a term/field pair to this instance of match data.\n *\n * @param {string} term - The term this match data is associated with\n * @param {string} field - The field in which the term was found\n * @param {object} metadata - The metadata recorded about this term in this field\n */\nlunr.MatchData.prototype.add = function (term, field, metadata) {\n if (!(term in this.metadata)) {\n this.metadata[term] = Object.create(null)\n this.metadata[term][field] = metadata\n return\n }\n\n if (!(field in this.metadata[term])) {\n this.metadata[term][field] = metadata\n return\n }\n\n var metadataKeys = Object.keys(metadata)\n\n for (var i = 0; i < metadataKeys.length; i++) {\n var key = metadataKeys[i]\n\n if (key in this.metadata[term][field]) {\n this.metadata[term][field][key] = this.metadata[term][field][key].concat(metadata[key])\n } else {\n this.metadata[term][field][key] = metadata[key]\n }\n }\n}\n/**\n * A lunr.Query provides a programmatic way of defining queries to be performed\n * against a {@link lunr.Index}.\n *\n * Prefer constructing a lunr.Query using the {@link lunr.Index#query} method\n * so the query object is pre-initialized with the right index fields.\n *\n * @constructor\n * @property {lunr.Query~Clause[]} clauses - An array of query clauses.\n * @property {string[]} allFields - An array of all available fields in a lunr.Index.\n */\nlunr.Query = function (allFields) {\n this.clauses = []\n this.allFields = allFields\n}\n\n/**\n * Constants for indicating what kind of automatic wildcard insertion will be used when constructing a query clause.\n *\n * This allows wildcards to be added to the beginning and end of a term without having to manually do any string\n * concatenation.\n *\n * The wildcard constants can be bitwise combined to select both leading and trailing wildcards.\n *\n * @constant\n * @default\n * @property {number} wildcard.NONE - The term will have no wildcards inserted, this is the default behaviour\n * @property {number} wildcard.LEADING - Prepend the term with a wildcard, unless a leading wildcard already exists\n * @property {number} wildcard.TRAILING - Append a wildcard to the term, unless a trailing wildcard already exists\n * @see lunr.Query~Clause\n * @see lunr.Query#clause\n * @see lunr.Query#term\n * @example query term with trailing wildcard\n * query.term('foo', { wildcard: lunr.Query.wildcard.TRAILING })\n * @example query term with leading and trailing wildcard\n * query.term('foo', {\n * wildcard: lunr.Query.wildcard.LEADING | lunr.Query.wildcard.TRAILING\n * })\n */\n\nlunr.Query.wildcard = new String (\"*\")\nlunr.Query.wildcard.NONE = 0\nlunr.Query.wildcard.LEADING = 1\nlunr.Query.wildcard.TRAILING = 2\n\n/**\n * Constants for indicating what kind of presence a term must have in matching documents.\n *\n * @constant\n * @enum {number}\n * @see lunr.Query~Clause\n * @see lunr.Query#clause\n * @see lunr.Query#term\n * @example query term with required presence\n * query.term('foo', { presence: lunr.Query.presence.REQUIRED })\n */\nlunr.Query.presence = {\n /**\n * Term's presence in a document is optional, this is the default value.\n */\n OPTIONAL: 1,\n\n /**\n * Term's presence in a document is required, documents that do not contain\n * this term will not be returned.\n */\n REQUIRED: 2,\n\n /**\n * Term's presence in a document is prohibited, documents that do contain\n * this term will not be returned.\n */\n PROHIBITED: 3\n}\n\n/**\n * A single clause in a {@link lunr.Query} contains a term and details on how to\n * match that term against a {@link lunr.Index}.\n *\n * @typedef {Object} lunr.Query~Clause\n * @property {string[]} fields - The fields in an index this clause should be matched against.\n * @property {number} [boost=1] - Any boost that should be applied when matching this clause.\n * @property {number} [editDistance] - Whether the term should have fuzzy matching applied, and how fuzzy the match should be.\n * @property {boolean} [usePipeline] - Whether the term should be passed through the search pipeline.\n * @property {number} [wildcard=lunr.Query.wildcard.NONE] - Whether the term should have wildcards appended or prepended.\n * @property {number} [presence=lunr.Query.presence.OPTIONAL] - The terms presence in any matching documents.\n */\n\n/**\n * Adds a {@link lunr.Query~Clause} to this query.\n *\n * Unless the clause contains the fields to be matched all fields will be matched. In addition\n * a default boost of 1 is applied to the clause.\n *\n * @param {lunr.Query~Clause} clause - The clause to add to this query.\n * @see lunr.Query~Clause\n * @returns {lunr.Query}\n */\nlunr.Query.prototype.clause = function (clause) {\n if (!('fields' in clause)) {\n clause.fields = this.allFields\n }\n\n if (!('boost' in clause)) {\n clause.boost = 1\n }\n\n if (!('usePipeline' in clause)) {\n clause.usePipeline = true\n }\n\n if (!('wildcard' in clause)) {\n clause.wildcard = lunr.Query.wildcard.NONE\n }\n\n if ((clause.wildcard & lunr.Query.wildcard.LEADING) && (clause.term.charAt(0) != lunr.Query.wildcard)) {\n clause.term = \"*\" + clause.term\n }\n\n if ((clause.wildcard & lunr.Query.wildcard.TRAILING) && (clause.term.slice(-1) != lunr.Query.wildcard)) {\n clause.term = \"\" + clause.term + \"*\"\n }\n\n if (!('presence' in clause)) {\n clause.presence = lunr.Query.presence.OPTIONAL\n }\n\n this.clauses.push(clause)\n\n return this\n}\n\n/**\n * A negated query is one in which every clause has a presence of\n * prohibited. These queries require some special processing to return\n * the expected results.\n *\n * @returns boolean\n */\nlunr.Query.prototype.isNegated = function () {\n for (var i = 0; i < this.clauses.length; i++) {\n if (this.clauses[i].presence != lunr.Query.presence.PROHIBITED) {\n return false\n }\n }\n\n return true\n}\n\n/**\n * Adds a term to the current query, under the covers this will create a {@link lunr.Query~Clause}\n * to the list of clauses that make up this query.\n *\n * The term is used as is, i.e. no tokenization will be performed by this method. Instead conversion\n * to a token or token-like string should be done before calling this method.\n *\n * The term will be converted to a string by calling `toString`. Multiple terms can be passed as an\n * array, each term in the array will share the same options.\n *\n * @param {object|object[]} term - The term(s) to add to the query.\n * @param {object} [options] - Any additional properties to add to the query clause.\n * @returns {lunr.Query}\n * @see lunr.Query#clause\n * @see lunr.Query~Clause\n * @example adding a single term to a query\n * query.term(\"foo\")\n * @example adding a single term to a query and specifying search fields, term boost and automatic trailing wildcard\n * query.term(\"foo\", {\n * fields: [\"title\"],\n * boost: 10,\n * wildcard: lunr.Query.wildcard.TRAILING\n * })\n * @example using lunr.tokenizer to convert a string to tokens before using them as terms\n * query.term(lunr.tokenizer(\"foo bar\"))\n */\nlunr.Query.prototype.term = function (term, options) {\n if (Array.isArray(term)) {\n term.forEach(function (t) { this.term(t, lunr.utils.clone(options)) }, this)\n return this\n }\n\n var clause = options || {}\n clause.term = term.toString()\n\n this.clause(clause)\n\n return this\n}\nlunr.QueryParseError = function (message, start, end) {\n this.name = \"QueryParseError\"\n this.message = message\n this.start = start\n this.end = end\n}\n\nlunr.QueryParseError.prototype = new Error\nlunr.QueryLexer = function (str) {\n this.lexemes = []\n this.str = str\n this.length = str.length\n this.pos = 0\n this.start = 0\n this.escapeCharPositions = []\n}\n\nlunr.QueryLexer.prototype.run = function () {\n var state = lunr.QueryLexer.lexText\n\n while (state) {\n state = state(this)\n }\n}\n\nlunr.QueryLexer.prototype.sliceString = function () {\n var subSlices = [],\n sliceStart = this.start,\n sliceEnd = this.pos\n\n for (var i = 0; i < this.escapeCharPositions.length; i++) {\n sliceEnd = this.escapeCharPositions[i]\n subSlices.push(this.str.slice(sliceStart, sliceEnd))\n sliceStart = sliceEnd + 1\n }\n\n subSlices.push(this.str.slice(sliceStart, this.pos))\n this.escapeCharPositions.length = 0\n\n return subSlices.join('')\n}\n\nlunr.QueryLexer.prototype.emit = function (type) {\n this.lexemes.push({\n type: type,\n str: this.sliceString(),\n start: this.start,\n end: this.pos\n })\n\n this.start = this.pos\n}\n\nlunr.QueryLexer.prototype.escapeCharacter = function () {\n this.escapeCharPositions.push(this.pos - 1)\n this.pos += 1\n}\n\nlunr.QueryLexer.prototype.next = function () {\n if (this.pos >= this.length) {\n return lunr.QueryLexer.EOS\n }\n\n var char = this.str.charAt(this.pos)\n this.pos += 1\n return char\n}\n\nlunr.QueryLexer.prototype.width = function () {\n return this.pos - this.start\n}\n\nlunr.QueryLexer.prototype.ignore = function () {\n if (this.start == this.pos) {\n this.pos += 1\n }\n\n this.start = this.pos\n}\n\nlunr.QueryLexer.prototype.backup = function () {\n this.pos -= 1\n}\n\nlunr.QueryLexer.prototype.acceptDigitRun = function () {\n var char, charCode\n\n do {\n char = this.next()\n charCode = char.charCodeAt(0)\n } while (charCode > 47 && charCode < 58)\n\n if (char != lunr.QueryLexer.EOS) {\n this.backup()\n }\n}\n\nlunr.QueryLexer.prototype.more = function () {\n return this.pos < this.length\n}\n\nlunr.QueryLexer.EOS = 'EOS'\nlunr.QueryLexer.FIELD = 'FIELD'\nlunr.QueryLexer.TERM = 'TERM'\nlunr.QueryLexer.EDIT_DISTANCE = 'EDIT_DISTANCE'\nlunr.QueryLexer.BOOST = 'BOOST'\nlunr.QueryLexer.PRESENCE = 'PRESENCE'\n\nlunr.QueryLexer.lexField = function (lexer) {\n lexer.backup()\n lexer.emit(lunr.QueryLexer.FIELD)\n lexer.ignore()\n return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexTerm = function (lexer) {\n if (lexer.width() > 1) {\n lexer.backup()\n lexer.emit(lunr.QueryLexer.TERM)\n }\n\n lexer.ignore()\n\n if (lexer.more()) {\n return lunr.QueryLexer.lexText\n }\n}\n\nlunr.QueryLexer.lexEditDistance = function (lexer) {\n lexer.ignore()\n lexer.acceptDigitRun()\n lexer.emit(lunr.QueryLexer.EDIT_DISTANCE)\n return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexBoost = function (lexer) {\n lexer.ignore()\n lexer.acceptDigitRun()\n lexer.emit(lunr.QueryLexer.BOOST)\n return lunr.QueryLexer.lexText\n}\n\nlunr.QueryLexer.lexEOS = function (lexer) {\n if (lexer.width() > 0) {\n lexer.emit(lunr.QueryLexer.TERM)\n }\n}\n\n// This matches the separator used when tokenising fields\n// within a document. These should match otherwise it is\n// not possible to search for some tokens within a document.\n//\n// It is possible for the user to change the separator on the\n// tokenizer so it _might_ clash with any other of the special\n// characters already used within the search string, e.g. :.\n//\n// This means that it is possible to change the separator in\n// such a way that makes some words unsearchable using a search\n// string.\nlunr.QueryLexer.termSeparator = lunr.tokenizer.separator\n\nlunr.QueryLexer.lexText = function (lexer) {\n while (true) {\n var char = lexer.next()\n\n if (char == lunr.QueryLexer.EOS) {\n return lunr.QueryLexer.lexEOS\n }\n\n // Escape character is '\\'\n if (char.charCodeAt(0) == 92) {\n lexer.escapeCharacter()\n continue\n }\n\n if (char == \":\") {\n return lunr.QueryLexer.lexField\n }\n\n if (char == \"~\") {\n lexer.backup()\n if (lexer.width() > 0) {\n lexer.emit(lunr.QueryLexer.TERM)\n }\n return lunr.QueryLexer.lexEditDistance\n }\n\n if (char == \"^\") {\n lexer.backup()\n if (lexer.width() > 0) {\n lexer.emit(lunr.QueryLexer.TERM)\n }\n return lunr.QueryLexer.lexBoost\n }\n\n // \"+\" indicates term presence is required\n // checking for length to ensure that only\n // leading \"+\" are considered\n if (char == \"+\" && lexer.width() === 1) {\n lexer.emit(lunr.QueryLexer.PRESENCE)\n return lunr.QueryLexer.lexText\n }\n\n // \"-\" indicates term presence is prohibited\n // checking for length to ensure that only\n // leading \"-\" are considered\n if (char == \"-\" && lexer.width() === 1) {\n lexer.emit(lunr.QueryLexer.PRESENCE)\n return lunr.QueryLexer.lexText\n }\n\n if (char.match(lunr.QueryLexer.termSeparator)) {\n return lunr.QueryLexer.lexTerm\n }\n }\n}\n\nlunr.QueryParser = function (str, query) {\n this.lexer = new lunr.QueryLexer (str)\n this.query = query\n this.currentClause = {}\n this.lexemeIdx = 0\n}\n\nlunr.QueryParser.prototype.parse = function () {\n this.lexer.run()\n this.lexemes = this.lexer.lexemes\n\n var state = lunr.QueryParser.parseClause\n\n while (state) {\n state = state(this)\n }\n\n return this.query\n}\n\nlunr.QueryParser.prototype.peekLexeme = function () {\n return this.lexemes[this.lexemeIdx]\n}\n\nlunr.QueryParser.prototype.consumeLexeme = function () {\n var lexeme = this.peekLexeme()\n this.lexemeIdx += 1\n return lexeme\n}\n\nlunr.QueryParser.prototype.nextClause = function () {\n var completedClause = this.currentClause\n this.query.clause(completedClause)\n this.currentClause = {}\n}\n\nlunr.QueryParser.parseClause = function (parser) {\n var lexeme = parser.peekLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n switch (lexeme.type) {\n case lunr.QueryLexer.PRESENCE:\n return lunr.QueryParser.parsePresence\n case lunr.QueryLexer.FIELD:\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.TERM:\n return lunr.QueryParser.parseTerm\n default:\n var errorMessage = \"expected either a field or a term, found \" + lexeme.type\n\n if (lexeme.str.length >= 1) {\n errorMessage += \" with value '\" + lexeme.str + \"'\"\n }\n\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n}\n\nlunr.QueryParser.parsePresence = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n switch (lexeme.str) {\n case \"-\":\n parser.currentClause.presence = lunr.Query.presence.PROHIBITED\n break\n case \"+\":\n parser.currentClause.presence = lunr.Query.presence.REQUIRED\n break\n default:\n var errorMessage = \"unrecognised presence operator'\" + lexeme.str + \"'\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n var errorMessage = \"expecting term or field, found nothing\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.FIELD:\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.TERM:\n return lunr.QueryParser.parseTerm\n default:\n var errorMessage = \"expecting term or field, found '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseField = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n if (parser.query.allFields.indexOf(lexeme.str) == -1) {\n var possibleFields = parser.query.allFields.map(function (f) { return \"'\" + f + \"'\" }).join(', '),\n errorMessage = \"unrecognised field '\" + lexeme.str + \"', possible fields: \" + possibleFields\n\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n parser.currentClause.fields = [lexeme.str]\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n var errorMessage = \"expecting term, found nothing\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n return lunr.QueryParser.parseTerm\n default:\n var errorMessage = \"expecting term, found '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseTerm = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n parser.currentClause.term = lexeme.str.toLowerCase()\n\n if (lexeme.str.indexOf(\"*\") != -1) {\n parser.currentClause.usePipeline = false\n }\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n parser.nextClause()\n return\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n parser.nextClause()\n return lunr.QueryParser.parseTerm\n case lunr.QueryLexer.FIELD:\n parser.nextClause()\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.EDIT_DISTANCE:\n return lunr.QueryParser.parseEditDistance\n case lunr.QueryLexer.BOOST:\n return lunr.QueryParser.parseBoost\n case lunr.QueryLexer.PRESENCE:\n parser.nextClause()\n return lunr.QueryParser.parsePresence\n default:\n var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseEditDistance = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n var editDistance = parseInt(lexeme.str, 10)\n\n if (isNaN(editDistance)) {\n var errorMessage = \"edit distance must be numeric\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n parser.currentClause.editDistance = editDistance\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n parser.nextClause()\n return\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n parser.nextClause()\n return lunr.QueryParser.parseTerm\n case lunr.QueryLexer.FIELD:\n parser.nextClause()\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.EDIT_DISTANCE:\n return lunr.QueryParser.parseEditDistance\n case lunr.QueryLexer.BOOST:\n return lunr.QueryParser.parseBoost\n case lunr.QueryLexer.PRESENCE:\n parser.nextClause()\n return lunr.QueryParser.parsePresence\n default:\n var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\nlunr.QueryParser.parseBoost = function (parser) {\n var lexeme = parser.consumeLexeme()\n\n if (lexeme == undefined) {\n return\n }\n\n var boost = parseInt(lexeme.str, 10)\n\n if (isNaN(boost)) {\n var errorMessage = \"boost must be numeric\"\n throw new lunr.QueryParseError (errorMessage, lexeme.start, lexeme.end)\n }\n\n parser.currentClause.boost = boost\n\n var nextLexeme = parser.peekLexeme()\n\n if (nextLexeme == undefined) {\n parser.nextClause()\n return\n }\n\n switch (nextLexeme.type) {\n case lunr.QueryLexer.TERM:\n parser.nextClause()\n return lunr.QueryParser.parseTerm\n case lunr.QueryLexer.FIELD:\n parser.nextClause()\n return lunr.QueryParser.parseField\n case lunr.QueryLexer.EDIT_DISTANCE:\n return lunr.QueryParser.parseEditDistance\n case lunr.QueryLexer.BOOST:\n return lunr.QueryParser.parseBoost\n case lunr.QueryLexer.PRESENCE:\n parser.nextClause()\n return lunr.QueryParser.parsePresence\n default:\n var errorMessage = \"Unexpected lexeme type '\" + nextLexeme.type + \"'\"\n throw new lunr.QueryParseError (errorMessage, nextLexeme.start, nextLexeme.end)\n }\n}\n\n /**\n * export the module via AMD, CommonJS or as a browser global\n * Export code from https://github.com/umdjs/umd/blob/master/returnExports.js\n */\n ;(function (root, factory) {\n if (typeof define === 'function' && define.amd) {\n // AMD. Register as an anonymous module.\n define(factory)\n } else if (typeof exports === 'object') {\n /**\n * Node. Does not work with strict CommonJS, but\n * only CommonJS-like enviroments that support module.exports,\n * like Node.\n */\n module.exports = factory()\n } else {\n // Browser globals (root is window)\n root.lunr = factory()\n }\n }(this, function () {\n /**\n * Just return a value to define the module export.\n * This example returns an object, but the module\n * can return a function as the exported value.\n */\n return lunr\n }))\n})();\n", "/*!\n * escape-html\n * Copyright(c) 2012-2013 TJ Holowaychuk\n * Copyright(c) 2015 Andreas Lubbe\n * Copyright(c) 2015 Tiancheng \"Timothy\" Gu\n * MIT Licensed\n */\n\n'use strict';\n\n/**\n * Module variables.\n * @private\n */\n\nvar matchHtmlRegExp = /[\"'&<>]/;\n\n/**\n * Module exports.\n * @public\n */\n\nmodule.exports = escapeHtml;\n\n/**\n * Escape special characters in the given string of html.\n *\n * @param {string} string The string to escape for inserting into HTML\n * @return {string}\n * @public\n */\n\nfunction escapeHtml(string) {\n var str = '' + string;\n var match = matchHtmlRegExp.exec(str);\n\n if (!match) {\n return str;\n }\n\n var escape;\n var html = '';\n var index = 0;\n var lastIndex = 0;\n\n for (index = match.index; index < str.length; index++) {\n switch (str.charCodeAt(index)) {\n case 34: // \"\n escape = '"';\n break;\n case 38: // &\n escape = '&';\n break;\n case 39: // '\n escape = ''';\n break;\n case 60: // <\n escape = '<';\n break;\n case 62: // >\n escape = '>';\n break;\n default:\n continue;\n }\n\n if (lastIndex !== index) {\n html += str.substring(lastIndex, index);\n }\n\n lastIndex = index + 1;\n html += escape;\n }\n\n return lastIndex !== index\n ? html + str.substring(lastIndex, index)\n : html;\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A RTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport lunr from \"lunr\"\n\nimport \"~/polyfills\"\n\nimport { Search, SearchIndexConfig } from \"../../_\"\nimport {\n SearchMessage,\n SearchMessageType\n} from \"../message\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Add support for usage with `iframe-worker` polyfill\n *\n * While `importScripts` is synchronous when executed inside of a web worker,\n * it's not possible to provide a synchronous polyfilled implementation. The\n * cool thing is that awaiting a non-Promise is a noop, so extending the type\n * definition to return a `Promise` shouldn't break anything.\n *\n * @see https://bit.ly/2PjDnXi - GitHub comment\n */\ndeclare global {\n function importScripts(...urls: string[]): Promise | void\n}\n\n/* ----------------------------------------------------------------------------\n * Data\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nlet index: Search\n\n/* ----------------------------------------------------------------------------\n * Helper functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Fetch (= import) multi-language support through `lunr-languages`\n *\n * This function automatically imports the stemmers necessary to process the\n * languages, which are defined through the search index configuration.\n *\n * If the worker runs inside of an `iframe` (when using `iframe-worker` as\n * a shim), the base URL for the stemmers to be loaded must be determined by\n * searching for the first `script` element with a `src` attribute, which will\n * contain the contents of this script.\n *\n * @param config - Search index configuration\n *\n * @returns Promise resolving with no result\n */\nasync function setupSearchLanguages(\n config: SearchIndexConfig\n): Promise {\n let base = \"../lunr\"\n\n /* Detect `iframe-worker` and fix base URL */\n if (typeof parent !== \"undefined\" && \"IFrameWorker\" in parent) {\n const worker = document.querySelector(\"script[src]\")!\n const [path] = worker.src.split(\"/worker\")\n\n /* Prefix base with path */\n base = base.replace(\"..\", path)\n }\n\n /* Add scripts for languages */\n const scripts = []\n for (const lang of config.lang) {\n switch (lang) {\n\n /* Add segmenter for Japanese */\n case \"ja\":\n scripts.push(`${base}/tinyseg.js`)\n break\n\n /* Add segmenter for Hindi and Thai */\n case \"hi\":\n case \"th\":\n scripts.push(`${base}/wordcut.js`)\n break\n }\n\n /* Add language support */\n if (lang !== \"en\")\n scripts.push(`${base}/min/lunr.${lang}.min.js`)\n }\n\n /* Add multi-language support */\n if (config.lang.length > 1)\n scripts.push(`${base}/min/lunr.multi.min.js`)\n\n /* Load scripts synchronously */\n if (scripts.length)\n await importScripts(\n `${base}/min/lunr.stemmer.support.min.js`,\n ...scripts\n )\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Message handler\n *\n * @param message - Source message\n *\n * @returns Target message\n */\nexport async function handler(\n message: SearchMessage\n): Promise {\n switch (message.type) {\n\n /* Search setup message */\n case SearchMessageType.SETUP:\n await setupSearchLanguages(message.data.config)\n index = new Search(message.data)\n return {\n type: SearchMessageType.READY\n }\n\n /* Search query message */\n case SearchMessageType.QUERY:\n return {\n type: SearchMessageType.RESULT,\n data: index ? index.search(message.data) : { items: [] }\n }\n\n /* All other messages */\n default:\n throw new TypeError(\"Invalid message type\")\n }\n}\n\n/* ----------------------------------------------------------------------------\n * Worker\n * ------------------------------------------------------------------------- */\n\n/* @ts-expect-error - expose Lunr.js in global scope, or stemmers won't work */\nself.lunr = lunr\n\n/* Handle messages */\naddEventListener(\"message\", async ev => {\n postMessage(await handler(ev.data))\n})\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Polyfills\n * ------------------------------------------------------------------------- */\n\n/* Polyfill `Object.entries` */\nif (!Object.entries)\n Object.entries = function (obj: object) {\n const data: [string, string][] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n data.push([key, obj[key]])\n\n /* Return entries */\n return data\n }\n\n/* Polyfill `Object.values` */\nif (!Object.values)\n Object.values = function (obj: object) {\n const data: string[] = []\n for (const key of Object.keys(obj))\n // @ts-expect-error - ignore property access warning\n data.push(obj[key])\n\n /* Return values */\n return data\n }\n\n/* ------------------------------------------------------------------------- */\n\n/* Polyfills for `Element` */\nif (typeof Element !== \"undefined\") {\n\n /* Polyfill `Element.scrollTo` */\n if (!Element.prototype.scrollTo)\n Element.prototype.scrollTo = function (\n x?: ScrollToOptions | number, y?: number\n ): void {\n if (typeof x === \"object\") {\n this.scrollLeft = x.left!\n this.scrollTop = x.top!\n } else {\n this.scrollLeft = x!\n this.scrollTop = y!\n }\n }\n\n /* Polyfill `Element.replaceWith` */\n if (!Element.prototype.replaceWith)\n Element.prototype.replaceWith = function (\n ...nodes: Array\n ): void {\n const parent = this.parentNode\n if (parent) {\n if (nodes.length === 0)\n parent.removeChild(this)\n\n /* Replace children and create text nodes */\n for (let i = nodes.length - 1; i >= 0; i--) {\n let node = nodes[i]\n if (typeof node !== \"object\")\n node = document.createTextNode(node)\n else if (node.parentNode)\n node.parentNode.removeChild(node)\n\n /* Replace child or insert before previous sibling */\n if (!i)\n parent.replaceChild(node, this)\n else\n parent.insertBefore(this.previousSibling!, node)\n }\n }\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexDocument } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search document\n */\nexport interface SearchDocument extends SearchIndexDocument {\n parent?: SearchIndexDocument /* Parent article */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search document mapping\n */\nexport type SearchDocumentMap = Map\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search document mapping\n *\n * @param docs - Search index documents\n *\n * @returns Search document map\n */\nexport function setupSearchDocumentMap(\n docs: SearchIndexDocument[]\n): SearchDocumentMap {\n const documents = new Map()\n const parents = new Set()\n for (const doc of docs) {\n const [path, hash] = doc.location.split(\"#\")\n\n /* Extract location, title and tags */\n const location = doc.location\n const title = doc.title\n const tags = doc.tags\n\n /* Escape and cleanup text */\n const text = escapeHTML(doc.text)\n .replace(/\\s+(?=[,.:;!?])/g, \"\")\n .replace(/\\s+/g, \" \")\n\n /* Handle section */\n if (hash) {\n const parent = documents.get(path)!\n\n /* Ignore first section, override article */\n if (!parents.has(parent)) {\n parent.title = doc.title\n parent.text = text\n\n /* Remember that we processed the article */\n parents.add(parent)\n\n /* Add subsequent section */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n parent\n })\n }\n\n /* Add article */\n } else {\n documents.set(location, {\n location,\n title,\n text,\n ...tags && { tags }\n })\n }\n }\n return documents\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport escapeHTML from \"escape-html\"\n\nimport { SearchIndexConfig } from \"../_\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search highlight function\n *\n * @param value - Value\n *\n * @returns Highlighted value\n */\nexport type SearchHighlightFn = (value: string) => string\n\n/**\n * Search highlight factory function\n *\n * @param query - Query value\n *\n * @returns Search highlight function\n */\nexport type SearchHighlightFactoryFn = (query: string) => SearchHighlightFn\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Create a search highlighter\n *\n * @param config - Search index configuration\n * @param escape - Whether to escape HTML\n *\n * @returns Search highlight factory function\n */\nexport function setupSearchHighlighter(\n config: SearchIndexConfig, escape: boolean\n): SearchHighlightFactoryFn {\n const separator = new RegExp(config.separator, \"img\")\n const highlight = (_: unknown, data: string, term: string) => {\n return `${data}${term}`\n }\n\n /* Return factory function */\n return (query: string) => {\n query = query\n .replace(/[\\s*+\\-:~^]+/g, \" \")\n .trim()\n\n /* Create search term match expression */\n const match = new RegExp(`(^|${config.separator})(${\n query\n .replace(/[|\\\\{}()[\\]^$+*?.-]/g, \"\\\\$&\")\n .replace(separator, \"|\")\n })`, \"img\")\n\n /* Highlight string value */\n return value => (\n escape\n ? escapeHTML(value)\n : value\n )\n .replace(match, highlight)\n .replace(/<\\/mark>(\\s+)]*>/img, \"$1\")\n }\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search query clause\n */\nexport interface SearchQueryClause {\n presence: lunr.Query.presence /* Clause presence */\n term: string /* Clause term */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search query terms\n */\nexport type SearchQueryTerms = Record\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Parse a search query for analysis\n *\n * @param value - Query value\n *\n * @returns Search query clauses\n */\nexport function parseSearchQuery(\n value: string\n): SearchQueryClause[] {\n const query = new (lunr as any).Query([\"title\", \"text\"])\n const parser = new (lunr as any).QueryParser(value, query)\n\n /* Parse and return query clauses */\n parser.parse()\n return query.clauses\n}\n\n/**\n * Analyze the search query clauses in regard to the search terms found\n *\n * @param query - Search query clauses\n * @param terms - Search terms\n *\n * @returns Search query terms\n */\nexport function getSearchQueryTerms(\n query: SearchQueryClause[], terms: string[]\n): SearchQueryTerms {\n const clauses = new Set(query)\n\n /* Match query clauses against terms */\n const result: SearchQueryTerms = {}\n for (let t = 0; t < terms.length; t++)\n for (const clause of clauses)\n if (terms[t].startsWith(clause.term)) {\n result[clause.term] = true\n clauses.delete(clause)\n }\n\n /* Annotate unmatched non-stopword query clauses */\n for (const clause of clauses)\n if (lunr.stopWordFilter?.(clause.term as any))\n result[clause.term] = false\n\n /* Return query terms */\n return result\n}\n", "/*\n * Copyright (c) 2016-2022 Martin Donath \n *\n * Permission is hereby granted, free of charge, to any person obtaining a copy\n * of this software and associated documentation files (the \"Software\"), to\n * deal in the Software without restriction, including without limitation the\n * rights to use, copy, modify, merge, publish, distribute, sublicense, and/or\n * sell copies of the Software, and to permit persons to whom the Software is\n * furnished to do so, subject to the following conditions:\n *\n * The above copyright notice and this permission notice shall be included in\n * all copies or substantial portions of the Software.\n *\n * THE SOFTWARE IS PROVIDED \"AS IS\", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR\n * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,\n * FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE\n * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER\n * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING\n * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS\n * IN THE SOFTWARE.\n */\n\nimport {\n SearchDocument,\n SearchDocumentMap,\n setupSearchDocumentMap\n} from \"../document\"\nimport {\n SearchHighlightFactoryFn,\n setupSearchHighlighter\n} from \"../highlighter\"\nimport { SearchOptions } from \"../options\"\nimport {\n SearchQueryTerms,\n getSearchQueryTerms,\n parseSearchQuery\n} from \"../query\"\n\n/* ----------------------------------------------------------------------------\n * Types\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index configuration\n */\nexport interface SearchIndexConfig {\n lang: string[] /* Search languages */\n separator: string /* Search separator */\n}\n\n/**\n * Search index document\n */\nexport interface SearchIndexDocument {\n location: string /* Document location */\n title: string /* Document title */\n text: string /* Document text */\n tags?: string[] /* Document tags */\n boost?: number /* Document boost */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search index\n *\n * This interfaces describes the format of the `search_index.json` file which\n * is automatically built by the MkDocs search plugin.\n */\nexport interface SearchIndex {\n config: SearchIndexConfig /* Search index configuration */\n docs: SearchIndexDocument[] /* Search index documents */\n options: SearchOptions /* Search options */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search metadata\n */\nexport interface SearchMetadata {\n score: number /* Score (relevance) */\n terms: SearchQueryTerms /* Search query terms */\n}\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search result document\n */\nexport type SearchResultDocument = SearchDocument & SearchMetadata\n\n/**\n * Search result item\n */\nexport type SearchResultItem = SearchResultDocument[]\n\n/* ------------------------------------------------------------------------- */\n\n/**\n * Search result\n */\nexport interface SearchResult {\n items: SearchResultItem[] /* Search result items */\n suggestions?: string[] /* Search suggestions */\n}\n\n/* ----------------------------------------------------------------------------\n * Functions\n * ------------------------------------------------------------------------- */\n\n/**\n * Compute the difference of two lists of strings\n *\n * @param a - 1st list of strings\n * @param b - 2nd list of strings\n *\n * @returns Difference\n */\nfunction difference(a: string[], b: string[]): string[] {\n const [x, y] = [new Set(a), new Set(b)]\n return [\n ...new Set([...x].filter(value => !y.has(value)))\n ]\n}\n\n/* ----------------------------------------------------------------------------\n * Class\n * ------------------------------------------------------------------------- */\n\n/**\n * Search index\n */\nexport class Search {\n\n /**\n * Search document mapping\n *\n * A mapping of URLs (including hash fragments) to the actual articles and\n * sections of the documentation. The search document mapping must be created\n * regardless of whether the index was prebuilt or not, as Lunr.js itself\n * only stores the actual index.\n */\n protected documents: SearchDocumentMap\n\n /**\n * Search highlight factory function\n */\n protected highlight: SearchHighlightFactoryFn\n\n /**\n * The underlying Lunr.js search index\n */\n protected index: lunr.Index\n\n /**\n * Search options\n */\n protected options: SearchOptions\n\n /**\n * Create the search integration\n *\n * @param data - Search index\n */\n public constructor({ config, docs, options }: SearchIndex) {\n this.options = options\n\n /* Set up document map and highlighter factory */\n this.documents = setupSearchDocumentMap(docs)\n this.highlight = setupSearchHighlighter(config, false)\n\n /* Set separator for tokenizer */\n lunr.tokenizer.separator = new RegExp(config.separator)\n\n /* Create search index */\n this.index = lunr(function () {\n\n /* Set up multi-language support */\n if (config.lang.length === 1 && config.lang[0] !== \"en\") {\n this.use((lunr as any)[config.lang[0]])\n } else if (config.lang.length > 1) {\n this.use((lunr as any).multiLanguage(...config.lang))\n }\n\n /* Compute functions to be removed from the pipeline */\n const fns = difference([\n \"trimmer\", \"stopWordFilter\", \"stemmer\"\n ], options.pipeline)\n\n /* Remove functions from the pipeline for registered languages */\n for (const lang of config.lang.map(language => (\n language === \"en\" ? lunr : (lunr as any)[language]\n ))) {\n for (const fn of fns) {\n this.pipeline.remove(lang[fn])\n this.searchPipeline.remove(lang[fn])\n }\n }\n\n /* Set up reference */\n this.ref(\"location\")\n\n /* Set up fields */\n this.field(\"title\", { boost: 1e3 })\n this.field(\"text\")\n this.field(\"tags\", { boost: 1e6, extractor: doc => {\n const { tags = [] } = doc as SearchDocument\n return tags.reduce((list, tag) => [\n ...list,\n ...lunr.tokenizer(tag)\n ], [] as lunr.Token[])\n } })\n\n /* Index documents */\n for (const doc of docs)\n this.add(doc, { boost: doc.boost })\n })\n }\n\n /**\n * Search for matching documents\n *\n * The search index which MkDocs provides is divided up into articles, which\n * contain the whole content of the individual pages, and sections, which only\n * contain the contents of the subsections obtained by breaking the individual\n * pages up at `h1` ... `h6`. As there may be many sections on different pages\n * with identical titles (for example within this very project, e.g. \"Usage\"\n * or \"Installation\"), they need to be put into the context of the containing\n * page. For this reason, section results are grouped within their respective\n * articles which are the top-level results that are returned.\n *\n * @param query - Query value\n *\n * @returns Search results\n */\n public search(query: string): SearchResult {\n if (query) {\n try {\n const highlight = this.highlight(query)\n\n /* Parse query to extract clauses for analysis */\n const clauses = parseSearchQuery(query)\n .filter(clause => (\n clause.presence !== lunr.Query.presence.PROHIBITED\n ))\n\n /* Perform search and post-process results */\n const groups = this.index.search(`${query}*`)\n\n /* Apply post-query boosts based on title and search query terms */\n .reduce((item, { ref, score, matchData }) => {\n const document = this.documents.get(ref)\n if (typeof document !== \"undefined\") {\n const { location, title, text, tags, parent } = document\n\n /* Compute and analyze search query terms */\n const terms = getSearchQueryTerms(\n clauses,\n Object.keys(matchData.metadata)\n )\n\n /* Highlight title and text and apply post-query boosts */\n const boost = +!parent + +Object.values(terms).every(t => t)\n item.push({\n location,\n title: highlight(title),\n text: highlight(text),\n ...tags && { tags: tags.map(highlight) },\n score: score * (1 + boost),\n terms\n })\n }\n return item\n }, [])\n\n /* Sort search results again after applying boosts */\n .sort((a, b) => b.score - a.score)\n\n /* Group search results by page */\n .reduce((items, result) => {\n const document = this.documents.get(result.location)\n if (typeof document !== \"undefined\") {\n const ref = \"parent\" in document\n ? document.parent!.location\n : document.location\n items.set(ref, [...items.get(ref) || [], result])\n }\n return items\n }, new Map())\n\n /* Generate search suggestions, if desired */\n let suggestions: string[] | undefined\n if (this.options.suggestions) {\n const titles = this.index.query(builder => {\n for (const clause of clauses)\n builder.term(clause.term, {\n fields: [\"title\"],\n presence: lunr.Query.presence.REQUIRED,\n wildcard: lunr.Query.wildcard.TRAILING\n })\n })\n\n /* Retrieve suggestions for best match */\n suggestions = titles.length\n ? Object.keys(titles[0].matchData.metadata)\n : []\n }\n\n /* Return items and suggestions */\n return {\n items: [...groups.values()],\n ...typeof suggestions !== \"undefined\" && { suggestions }\n }\n\n /* Log errors to console (for now) */\n } catch {\n console.warn(`Invalid query: ${query} \u2013 see https://bit.ly/2s3ChXG`)\n }\n }\n\n /* Return nothing in case of error or empty query */\n return { items: [] }\n }\n}\n"], - "mappings": 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\ No newline at end of file diff --git a/contributors.html b/contributors.html new file mode 100644 index 0000000..a1d2444 --- /dev/null +++ b/contributors.html @@ -0,0 +1,775 @@ + + + + + + + + + +Introduction to NGS data analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Jose Alejandro Romero Herrera :custom-orcid: :simple-github:

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    CRediT table

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    CRediT roleInitials
    Conceptualization
    Data curation
    Formal Analysis
    Funding acquisition
    Investigation
    Methodology
    Project administration
    Resources
    Software
    Supervision
    Validation
    Visualization
    Writing - original draft
    Writing - review & editing
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    + + + + + \ No newline at end of file diff --git a/datasets/datapolicy.html b/datasets/datapolicy.html new file mode 100644 index 0000000..19f37bf --- /dev/null +++ b/datasets/datapolicy.html @@ -0,0 +1,762 @@ + + + + + + + + + + +Introduction to NGS data analysis - Data policy + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Data policy

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    Published
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    January 1, 2024

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    With respect to person-specific datasets

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    A priority of the Sandbox is to guide health data science learning using real-world-similar datasets. A major component is addressing how to analyze and leverage person-specific data, such as electronic health records, without invading personal privacy or straying from GDPR guidelines on sensitive data use. We are therefore focused on using either publicly accessible datasets (that are generally well anonymized to enable such release) or we are using/creating synthetic datasets that mimic real-world datasets without replicating real people’s data such that they can be identified. In either case, it is essential for Sandbox users to treat person-specific data respectfully and be aware of the additional responsibility and limitations of working with this type of data as part of their career in health data science.

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    We recommend that users interested in this type of data complete an ethics course on research using health datasets before digging into any analysis. A well regarded course that is also often required for using public databases that contain person-specific data is the Human Subject and Data Research Ethics course designed by the Massachusetts Institute of Technology. The course is hosted at CITI, the Collaborative Institutional Training Initiative. Completing the course is free of charge and provides you with a certificate which you may need to upload to certain databases to gain access. Set up an account at CITI, add an Institutional affiliation with ‘Massachusetts Institute of Technology Affiliates’, and then find and complete the course titled ‘Data or Specimens Only Research’ to obtain a certificate (in pdf form).

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    Public domain data

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    The intended scope of the Sandbox is broad, and we will be pulling from many different public access databases (especially for training modules on omics analysis). Databases can be topically broad, giant repositories or field-specific, and each may have its own usage rules. We plan to provide our own copies of publically available datasets where allowed to ensure compatibility with the linked module is preserved, but some datasets may need to be downloaded by users themselves under specific access / distribution restrictions. Many omics datasets do not present significant data sensitivity concerns in comparison to real-world data such as electronic health records (EHRs) and clinical trial datasets.

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    There are large public de-identified EHR datasets that serve as benchmark resources for teaching and comparing new methods with old, but these are not numerous and often have restricted usage and sharing terms in addition to being quite dated. Historical approaches to dataset anonymization and de-identification have been substantially challenged in the age of digitalized healthcare and increasing data integration, which means meaningfully large ‘anonymized’ datasets are now rarely released.

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    Synthetic data

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    Via our collaborators and broader network, the Sandbox has the opportunity to simulate/synthesize data resembling different databases and registries from the Danish health sector. We are exploring methods of creating useful synthetic datasets with national and EU-level data access policies and GDPR restrictions in mind, while developing initial datasets using publicly available data from Danish research studies and other resources.

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    Ultimately, a new era of synthetic data is rapidly developing. The funded Sandbox proposal focused on generating synthetic data using mechanistic models, agent-based models, or draws from multivariate distributions (such as copulas), which are methods that do not present any significant GDPR-related concerns with sharing the produced datasets as they are derived from population-level characteristics and prior knowledge. However, new deep learning-based methods of data synthesis can theoretically learn complex, nonlinear patterns within a sensitive dataset and generate a synthetic dataset that replicates these patterns. This is a really promising approach for sharing high utility synthetic datasets, but it also elevates risk of accidentally sharing too much about the real dataset and skirting the boundaries of GDPR and ethical data handling. There is an inherent trade-off between privacy preservation and similarity of the synthetic dataset to the original dataset, with method development focused on moving closer to the ideal zone of high privacy AND high similarity. The figure at right is a rough approximation of this relationship versus current families of synthesis methods.

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    Please see Synthetic Data for more information about our approach to this technology.

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    + + + + + \ No newline at end of file diff --git a/datasets/datasets.html b/datasets/datasets.html new file mode 100644 index 0000000..9d824bf --- /dev/null +++ b/datasets/datasets.html @@ -0,0 +1,725 @@ + + + + + + + + + +Introduction to NGS data analysis - Datasets + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Datasets

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    Datasets

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    Here we provide details of datasets used in our various modules as well as a specific guide on using electronic health record datasets.

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    Datasets

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    Data policy with respect to person-specific datasets

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    A priority of the Sandbox is to guide health data science learning using real-world-similar datasets. A major component is addressing how to analyze and leverage person-specific data, such as electronic health records, without invading personal privacy or straying from GDPR guidelines on sensitive data use. We are therefore focused on using either publicly accessible datasets (that are generally well anonymized to enable such release) or we are using/creating synthetic datasets that mimic real-world datasets without replicating real people’s data such that they can be identified. In either case, it is essential for Sandbox users to treat person-specific data respectfully and be aware of the additional responsibility and limitations of working with this type of data as part of their career in health data science.

    +

    We recommend that users interested in this type of data complete an ethics course on research using health datasets before digging into any analysis. A well regarded course that is also often required for using public databases that contain person-specific data is the Human Subject and Data Research Ethics course designed by the Massachusetts Institute of Technology. The course is hosted at CITI, the Collaborative Institutional Training Initiative. Completing the course is free of charge and provides you with a certificate which you may need to upload to certain databases to gain access. Set up an account at CITI, add an Institutional affiliation with ‘Massachusetts Institute of Technology Affiliates’, and then find and complete the course titled ‘Data or Specimens Only Research’ to obtain a certificate (in pdf form).

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    Public domain data

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    The intended scope of the Sandbox is broad, and we will be pulling from many different public access databases in our development of teaching modules. There are classical datasets that serve as benchmark resources for teaching and comparing new methods with old, and also brand new datasets that will support modules on emerging technologies (such as spatial single cell RNA-seq analysis). Databases can be topically broad giant repositories or field-specific, and each may have its own usage rules. We plan to provide our own copies of publically available datasets where allowed to ensure compatibility with the linked module is preserved, but some datasets may need to be downloaded by users themselves under specific access / distribution restrictions.

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    Synthetic/Simulated data

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    The Sandbox is focused on supporting Danish health data science education and research. Via our collaborators and broader network, we have the opportunity to simulate/synthesize data resembling different databases and registries from the Danish health sector in addition to using traditional data simulation techniques to replicate general datasets. We are exploring methods of creating useful synthetic datasets with local access guidelines/GDPR restrictions in mind, while developing initial datasets using published data from Danish studies and publically available resources.

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    + + + + + \ No newline at end of file diff --git a/datasets/synthdata.html b/datasets/synthdata.html new file mode 100644 index 0000000..e4dba48 --- /dev/null +++ b/datasets/synthdata.html @@ -0,0 +1,796 @@ + + + + + + + + + + +Introduction to NGS data analysis - Synthetic data + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Synthetic data

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    Published
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    January 1, 2024

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    progress and challenges

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    Defining synthetic data

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    It is necessary to clarify what we mean when we refer to synthetic data within the Sandbox project. While the term has been used for decades to describe all kinds of ‘non-real’ data including those derived from models and simulations, developments in deep generative modeling have dramatically expanded our understanding of what synthetic data can be. In the age of deepfakes and news articles written entirely by ChatGPT, synthetic data derived from deep learning is in a wholly different class from data simulated with a mechanistic or agent-based model.

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    The Sandbox is actually interested in any form of synthetic data - our highest priority is providing safe-to-use data to trainees and researchers that does not raise any concerns about sensitive data with respect to the EU’s General Data Protection Regulation (GDPR) and local Danish data regulations. So, we are using both old school and new school forms of data synthesis. However, the discussion on this page is heavily weighted towards our interest in new school synthesis - with our connections to generative modeling researchers and high quality data, we are naturally interested in figuring out a safe way to deploy synthetic datasets derived from deep learning and other high similarity approaches.

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    +The TLDR for synthetic data in the Sandbox +
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    - The development of synthetic datasets should be viewed as a research project. The technology is generally untested with few examples of public roll-out, and its deployment should be future-proofed as much as possible against attacks and potential sensitive data disclosure.
+- Synthetic data generation and evaluation approaches should be tailored     to each dataset of interest. With current technology, it is unlikely that high quality, safe-to-share datasets will be produced at any kind of production scale without a massive effort devoted to pre-processing, data harmonization, and customized routines for different families of datasets.
+- The Sandbox is not openly sharing any synthetic datasets generated from person-specific sensitive data. We think these datasets will be useful to approved researchers that ideally gain access via an approved data portal with registration and data use agreements with relevant data authorities. We are not currently that portal.
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    Generating synthetic data

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    We have explored the performance of copulas, multiple imputation, sequential synthesis, and several generative adversarial network (GAN) approaches with a cancer dataset which we were developing for a course in the MS in Personal Medicine program at University of Copenhagen. We quickly discovered that factors such as missingness, collinearity, and the ratio of patients to features cause just as many problems for synthetic data generation as they do in predictive modeling. We are currently evaluating the above techniques as well as additional deep learning approaches such as variational autoencoders (VAEs) and Bayesian graphs against a collection of benchmark health datasets to better understand the positives and negatives of each technique when faced with common challenges in real world health data.

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    Recently, a few interesting libraries / pipelines have been released that enable testing of different synthetic data generation approaches alongside a range of evaluation metrics. We are actively exploring these tools as we test different generation approaches and examining their implementation of evaluation metrics. We plan to add additional components and features as we resolve challenges with different target datasets.

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    Evaluating synthetic data

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    There are 3 key principles to consider when judging the overall quality of a synthetic dataset: fidelity to the original dataset, risk to privacy, and prediction utility. Fidelity and utility are often grouped together as similarity to the original data which exists in a trade-off with privacy - the more similar your synthetic dataset to the original, the higher your risk to patient privacy. However, the distinction between them is important as they can be achieved independently of each other depending on the project frame. Fidelity refers to reproduction of the multivariate shape and structure of the original data (including complex nonlinear relationships) while utility refers to how well the synthetic dataset matches the predictive accuracy of the original dataset. Risk to privacy includes both risk of patient reidentification and risk of sensitive information disclosure about a patient. There are many proposed evaluation metrics for measuring different aspects of these three qualities. We are actively investigating the performance of these metrics against our different datasets.

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    We should point out that while using quantitative metrics to assess privacy preservation is a critical step in creating a synthetic dataset, positive results do not absolve us from any concerns regarding risk to privacy in the synthetic data. Regulatory guidelines regarding the safety of synthetic data and the ability to openly share it are extremely unclear. No authorities have specified quantitative cut-offs using these metrics that enable open release, for example. For this reason, we have developed our own internal guidelines for how to handle this aspect of the project, which are based on a comprehensive examination of relevant EU and Danish legislation (i.e. the GDPR, the Artificial Intelligence Act, the Danish Health Law, and the Danish Data Protection Act). We continue work on synthesis with hope that new legislation such as the development of the European Health Data Space will provide further guidance in the future.

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    Rules for synthetic data in the Sandbox

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    We are currently focused on exploring methods and metrics by developing reproducible, well documented examples and use cases of synthetic data in partnership with other researchers, legal advisors, and data authorities. We’re relying primarily on publicly available tabular health datasets in this exploration phase, but we will also work with sensitive data in the future. Our rules aim to preserve the trust of the public in how their health data is handled by data authorities and researchers.

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    +Sandbox Rules for Synthetic Data +
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    1. Creation of synthetic data involves processing sensitive data, and this requires obtaining project approvals from data authorities when performing this work on sensitive data. Any synthetic data work with restricted-access, sensitive data by the Sandbox will only be conducted with these approvals in place in the frame of a research project.
+2. Goals for each synthetic dataset project should be defined at project initiation: how will the synthetic dataset be used, who is the intended audience, and how might it be shared? This frame should govern every consequent decision for that dataset and be shared alongside the final dataset.
+3. Quantitative metrics for fidelity, utility, and privacy preservation should be implemented for each dataset and shared alongside the final dataset.
+4. A cost-benefit analysis should be performed after the project is completed - is any risk to privacy appropriately balanced by value of the dataset in achieving its stated aims and contributing to the public good?
+5. Data authorities with ethical and strategic stakes in who accesses the synthetic dataset should be included in decisions about how it is used and who is allowed to access it. 
+6. Synthetic datasets created from person-specific sensitive data rather than population characteristics can still pose privacy risks, and any users of the dataset should be approved and registered. The Sandbox will not release any such datasets publicly and will instead work with appropriate data authorities to decide how such datasets should be governed in a responsible way.
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    Data filtering

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    Each person works on its own personal folder, which contains a dataset. As a reminder, these are the personal folders

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    NameSample folder
    Andersen, Albert LundGifu_ctr_1
    Bagger, AndreasGifu_ctr_2
    Hansen, Mads WürglerGifu_ctr_ 3
    Milo, LasseGifu_ctr_4
    Reimick, Sebastian HaunstrupGifu_R7A_1
    Hemmingsen, Jonas KlejsGifu_R7A_2
    Skovmøller, Emma HvitfeldtGifu_R7A_3
    Sørensen, Emma FrasezGifu_R7A_4
    Agersnap, Simon NørregaardHAR1_ctr_1
    Schmidt, AlinaHAR1_ctr_2
    Henriksen, Frederik OskarHAR1_ctr_3
    Lundby, Josephine MarieHAR1_ctr_4
    Nørholm, AnneHAR1_R7A_1
    Odgaard, Louise NyrupHAR1_R7A_2
    Sørensen, Sara SejerHAR1_R7A_3
    Lønskov, JonasHAR1_R7A_4
    Niklassen, Jacob HansenGifu_ctr_1_bis
    Øllgaard, Ann Mai Brøndum HolmGifu_ctr_2_bis
    Overgaard, Morten ØgelundGifu_R7A_1_bis
    Sørensen, Elisabeth AstaGifu_R7A_2_bis
    Rey, IsabelHAR1_ctr_1_bis
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    Instructions

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      Open a new session of jupyterlab in the same way as in the tutorial session

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      Find your way to your personal folder, which is inside 426401/Students_analysis

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      Start filtering your data using the notebook filtering.ipynb. This is a copy of the first part of the tutorial, so be careful about small changes you have to made (e.g. condition name, thresholds). For the condition name created in the metadata at the beginning of the tutorial, here we use one of Gifu_Control, Gifu_Infected, HAR1_Control, HAR1_Infected (depending on the dataset you have assigned), so that it is easy to integrated all datasets at the end.

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    4. When you are done and you saved your data at the end (keep the filename filtered.h5Seurat), write when you are done at this google docs under the sheet Filtering, so we all know when we are ready to proceed to data integration.
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    Quality Control and Alignment of raw reads

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    This first exercise will be executed on Galaxy, an interactive platform to run bioinformatics workflows. We will replicate this lesson with computer code later in this course. Galaxy has the possibility of working with a free account.

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    Biological introduction

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    White clover (Trifolium repens) is an allotetraploid. This means that it contains genomes -originating from two different species within the same nucleus. Normally, white clover is an -outbreeding species, but a self-compatible line was used for sequencing the white clover -genome. This line is -designated S10 in your data, indicating that this is the 10th self-fertilized generation. In -addition, you have data from a wild clover accession (ecotype) called Tienshan (Ti), which is -collected from Chinese mountains and is adapted to alpine conditions.

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    -Figure: Characterisation of the white clover population. T.Repens is a hybrid of T.Occidentale and T.Pallescens

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    Exercise guide

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    Prepare the tools and data

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    1. Install IGV on your computer from here. This is a genome browser you will use to look at some files.
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    3. Find the course data by going to this web address and by clicking on Import this history (top left corner of the page).
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    Note: If usegalaxy.org has availability problems, you can use the other server https://usegalaxy.eu/ and get the data at this link. You might need to create an account there as well.

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    Data

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    You will be working with two types of sequencing data. -The first is PacBio Hifi reads, which are long and accurate. You can find them under -Hifi_reads_white_clover.fastq. -The second type is Illumina RNA-seq reads, which are short and accurate and should be aligned -using a spliced aligner, such as STAR.

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    There are 24 of these files, 12 for each of the two genotypes mentioned -before. The files are named [genotype]_[treatment]_[replicate].fastq. Treatment 1 is before and -treatment 2 is after exposure to frost, respectively.

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    In addition to the sequencing data, there are also three reference files: one for homologous contig 1 (referencing T. occidentale-derived subgenome), one for contig 2 (T. -pallescens-derived subgenome) and one for both Contigs 1 and 2. The reference files are in fasta format.

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    The file white_clover_genes.gtf contains the gene annotations for the two contigs.

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    Workflow illustration

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    Through Galaxy, we build a workflow applying tools to the data. We will look at the quality of the raw reads for both PacBio HiFi and Illumina RNA-seq reads. Afterwards, we align to references, using two different tools for the two types of data. Finally, we will look at the alignments on a genome browser. We will work then on a computing cluster through uCloud to analyze the aligned data in some of the upcoming lessons of the course.

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    Galaxy Workflow

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    When you import the files, what you actually import is a History - a sequence of files and softwares applied on the data. You can see the history on the right side of your usegalaxy.org webpage with green panels. Here, we only have the starting data, and you will build the rest of your history through various tools.

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    On the left side of the screen, you have a menu with various available tools organized by category. All those softwares are also available on a classical computing command line (we will try those as well).

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    Quality control

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    1 Run FastQC on the PacBio Hifi reads and on two of the Illumina RNA-seq libraries. FastQC does quality control of the raw sequence data, providing an overview of the data which can help identify if there are any problems that should be addressed before further analysis.

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    In the tool menu, click on FASTQ quality control --> FASTQC read quality reports. You will see a window with tool parameters: for the first option (raw read data from history), choose multiple files and select Hifi_reads_white_clover.fastq plus other fastq files you want to see the quality of (example in figure below). Then click on the button Run Tool. -

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    You will notice that some new elements are added to your history. Part of them are FastQC producing a text file, while others are FastQC producing a webpage report. The reports are ready when coloured in green: click on the eye symbol of a history item to read a report.

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    2 FastQC provides a report for each sample. To have a better comparison between -the Hifi and Illumina data, we would combine the three FastQC reports into one using MultiQC.

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    Choose the MultiQC tool from FASTQ quality control --> MultiQC aggregate results from .... In the options, select FastQC as the used tool for the logsselect FastQC as the tool used to generate the output, and then select the items of FastQC of your history producing RawData (Figure below). In this way, you build a pipeline from the previous reports to the new tool you are using. Now click on Run Tool.

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    The tool will be now running in your history. When it is done, click on the eye symbol to see the report.

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    select the three “RawData” outputs generated by FastQC. Visualize the Webpage generated by -MultiQC. -Hint: You can find a “Help” button that offers additional information about the plots for each panel.

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    -Focus on the following panels: “Per base sequence quality”, “Per sequence quality scores”…. (“Per base sequence content” always gives a FAIL for RNA-seq data). What do you notice with respect to the sequence quality scores? And are there any other quality issues worth noting? - -

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    Hifi Data Alignment

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    3 Map the PacBio Hifi reads (Hifi_reads_white_clover.fastq) to the white clover reference sequence (Contigs 1 and 2) using minimap2 (Map with minimap2). Find Genomics Analysis --> Mapping --> Map with minimap2. In the options, do not leave Use a built-in genome index, but select the option for having a genome from history. Choose then DNA_Contig1_2.fasta as the reference sequence.

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    Under the profile with preset options, choose PacBio/Oxford Nanopore read to reference mapping (map-pb). Then click on Run Tool.

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    4 Run the same alignment, but choose as preset options Long assembly to reference mapping. Divergence is far below 20% (asm20).

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    Rename then the two alignments using the edit function (pen symbol in the history). Use for example names Contig1_2_mappb and Contig1_2_asm20, to distinguish alignment options and reference genome.

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    5 The aligned genomes are not sorted by coordinates. Sort the alignments using Samtools sort (Find the tool under Genomic file manipulation --> SAM/BAM --> Samtools sort ...). In the options, choose the two aligned files with multiple selection. Then click on Run Tool.

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    6 Download the two alignments to your computer. To do so, click on the disk symbol of each file in your history, and for each download both the Dataset (alignments in bam format) and their index files (in bai format). Download as well the reference genome in fasta format (DNA_Contig1_2.fasta from the history).

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    7 Open IGV on your computer. Load the reference first: go on Genome --> Load genome from file and select the fasta file you downloaded. Then load the two alignments: go on File --> Load from file and select the bam and bai files you downloaded, together. You can now visualize the alignments.

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    - Look at the alignments in IGV. What do you notice about the alignments? What is the difference between the two alignments? Do you think one of them is better than the other? Choose on of the two alignments for the next steps. - -

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    8 Repeat the alignment with Minimap2 (using the chosen alignment option from the question above) and the sorting, but using the reference genomes for Contig 1 and for Contig 2 searaately. Note: you can run all at once by choosing multiple reference genomes in the options!

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    - Download the two references for Contig 1 and 2, and the two sorted alignments. Load the references from the menu `Genomes` in IGV, and then open the two alignments using the menu `File` in IGV. - -- Why do you see fluctuations in coverage and large regions without any apparent subgenome -SNPs? - -- What are the major differences between the stats for the reads mapped to Contigs1&2 -versus contig1 and contig2? What is your interpretation of the differences? - -

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    RNA Data Alignment

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    9 First, group the 24 RNA-seq libraries into two dataset lists, one list of pairs for S10 libraries and -another for Tienshan libraries. so we can work with multiple samples simultaneously. -You can do this by selecting the libraries for each genotype and choosing Build Lists of Dataset -Pairs.

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    The grouping suggested by Galaxy is wrong, because the paired reads are paired according to _1 and _2 in their names. Change those two with R1 and R2, click on Unpair all, and then click on the suggested corrected pairs with the buttons Pair these datasets.

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    Your sequences will be substituted by two elements in your history. Here we chose for example to name them S10 and TI.

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    10 Do alignment of the RNA-seq lists of raw files to the reference DNA_Contig1_2.fasta using STAR. Go to Genomics analysis --> RNA-seq --> RNA STAR Gapped-read mapper for RNA-seq data. In the options use:

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    11 Use MultiQC to see the quality of the output. The alignment of STAR produces log files which can be used for quality reports. Go on Genomic File Manipulation --> MultiQC. In the options select the tool STAR. Then Insert STAR output, as type of output the Log, and choose the two logs listing collections of STAR alignments. Then click on Run Tool.

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    View the report to see the alignment statistics.

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    Final note: `Galaxy can also be used to create an automatic workflow that will map the data. This workflow can be useful when running multiple samples. You can -generate a workflow from the analysis already completed in a history, by going to Settings → -Extract workflow. You can also create a workflow from scratch using the Workflow editor.

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    Introduction to Next Generation Sequencing data

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    Computing and didactical support from the Danish Health Data Science Sandbox

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    Course material

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    The material for this course is organized in four separated jupyter notebooks in both bash, python and R where you will benefit of an interactive coding setup on jupyterlab. Each lesson is in the menu above.

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    First exercise

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    The first exercise lesson is executed with the web interface usegalaxy.org. Click on 1.Galaxy Exercise in the menu for instructions)

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    Following exercises

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    The following exercise lessons will work on a computing environment with jupyterlab. Use 2.Instructions to find out how to run it, selecting the computing environment you need (danish clusters uCloud and GenomeDK, your PC, or another cluster).

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    Compiled exercises

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    if you need to have a look at the exercises as a reference, then the menu 3.Compiled exercises contains all the compiled exercises on jupyterlab in a document format, from which you can also copy-paste the code.

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    Course overview

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    After the course, you will have knowledge of bioinformatics methods for analyzing genomes using NGS data, including knowledge of the existing types of genome data, how the different types of data can be displayed and analyzed, the current methods for genome assembly and analysis, their accuracy and how they can be used. The course will enable you to devise and run a project that makes use of NGS data.

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    • Prerequisites: This is an introductory course that needs a basic understanding of the biology behind sequencing, and not necessarily programming experience (though this would help!).
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    -Syllabus: - Describe key challenges in the analysis of NGS data

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    - Explain the theoretical foundation for methods that use NGS for assembly and analysis of genomes
 
+- Discuss the bioinformatic methods for genome analysis and hypothesize what drives the outcome of the methods
 
+- Review original literature within the subjects and relate the discussed topics to analysis scenarios
 
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    Introduction to Next Generation Sequencing data
    
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    A course of the Summer School of Aarhus University
    
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    Computing and didactical support from the Danish Health Data Science Sandbox
    
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    The material for this course is organized in four separated jupyter notebooks in both bash, python and R where you will benefit of an interactive coding setup on jupyterlab. 
    
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    Overview
    
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    After the course, you will have knowledge of bioinformatics methods for analyzing genomes using NGS data, including knowledge of the existing types of genome data, how the different types of data can be displayed and analyzed, the current methods for genome assembly and analysis, their accuracy and how they can be used. The course will enable you to devise and run a project that makes use of NGS data.
    
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    📚 Prerequisites: This is an introductory course that needs a basic understanding of the biology behind sequencing, and not necessarily programming experience (though this would help!).
    
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    💬 Syllabus:   
    
-    1. Describe key challenges in the analysis of NGS data 
    
-    2. Explain the theoretical foundation for methods that use NGS for assembly and analysis of genomes
    
-    3. Discuss the bioinformatic methods for genome analysis and hypothesize what drives the outcome of the methods
    
-    4. Review original literature within the subjects and relate the discussed topics to analysis scenarios
    
-    5. Apply bioinformatics tools within the selected application areas and reflect on the results, formulating your own conclusion in the proposed tasks
    
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    🕰 Total Time Estimation: 20 hours  
    
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    📁 Supporting Materials:  
    
+- Apply bioinformatics tools within the selected application areas and reflect on the results, formulating your own conclusion in the proposed tasks
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    • Time: 20 hours (for reading through the code, executing it, answering questions). The material fits 4-5 days lessons.

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    • Supporting Materials:

      • jupyter notebooks for interactive coding
      • lecture slides from the instructor
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    You can find the links to the material in the table at the bottom of this page.

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    🖍 Course authors and instructors:

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    Mikkel H Schierup -Stig U Andersen

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    Samuele Soraggi -Peter S Porsborg -Adrián G Repollés

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    📋 License: Tutorial Content is licensed under Creative Commons Attribution 4.0 International License

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    📝 Citation: If you use any of this material for your research, please cite this course with the DOI below, and acknowledge the Health Data Science Sandbox project of the Novo Nordisk Foundation (grant number NNF20OC0063268). It is of great help to support the project. -DOI

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    📧 Contact: Samuele Soraggi (samuele at birc.au.dk).

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    Course structure and Instructions

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    The course exercises are organized in four exercise modules.

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    The first one is executed with the web interface usegalaxy.org. Click on 1.Galaxy Exercise in the menu for instructions)

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    Afterwards, we will work on a computing environment to use jupyterlab. Use 2.Instructions for instructions.

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    The menu 3.Course exercises contains all the compiled exercises as a reference.

    -

    Course material 2022

    -

    Here you find a table with the instructor's slides from 2022.

    - +
    +

    Course material 2022

    +

    Here you find a table with the instructor’s slides from 2022.

    +
    - + - + - + - + - + - + - + - + - + - + - + - + - +
    Topic Slide Notebook
    Sequencing technologies link--–
    Mapping to reference link Notebook
    Data visualization link--–
    SNPs and structural variants link Notebook
    RNA sequencing link Notebook
    De-novo assembly link--–
    Microbiomes and metagenomics link--–
    Single cell RNA sequencing link Notebook
    -

    Course material 2023 (on its way after the course's end)

    -

    Here you find a table with the instructor's slides and a link to the compiled notebooks, that you can also run on your own following the instructions in this webpage. Data alignment can also be performed on the Galaxy interactive webpage (see the galaxy exercise in this webpage).

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    - - - - - - - - - - - - - - \ No newline at end of file + +
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    Course material 2024

    +

    Here you find a table with the instructor’s slides and a link to the compiled notebooks, that you can also run on your own following the instructions in this webpage. Data alignment can also be performed on the Galaxy interactive webpage (see the galaxy exercise in this webpage).

    + + +
    + + +
    + + + + + + + \ No newline at end of file diff --git a/instructions.html b/instructions.html deleted file mode 100644 index 4a9c137..0000000 --- a/instructions.html +++ /dev/null @@ -1,649 +0,0 @@ - - - - - - - - - - - - - - - - - - - - Instructions - Introduction to NGS data analysis - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
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    Instructions

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    You have various options to run the course material. You can execute it on a supercomputing system or on your own computer.

    -

    Access the material on uCloud

    -

    Ucloud is an interactive online platform from the University of Southern Danmark eScience center that allows users to execute softwares and computer code directly from their browser. If you are enrolled in a danish university or hospital, you can access the platform for free and try the course.

    -

    Please follow these instructions to access uCloud and get access to the course:

    -
      -
    • -

      To access uCloud for the first time, go to the ucloud webpage and log in by pressing on the green button, choosing your institution, and writing your institutional credentials. If you have a mail address from a danish institution or university, you should be able to login with your institutional credentials.

      -
      • -
    • -

      If you are participating in the NGS Summer Course 2023 in Aarhus, click AFTER logging in on this link. This will add you to a project on uCloud, where we have data and extra computing credit for the course. You should see a message on your browser where you have to accept the invitation to the project.

      -
      • -
    • -

      Click on the uCloud symbol on the top-left corner of the uCloud webpage. You should see a dashboard window similar to the one below. The dashboard is a home page you will always see when opening uCloud. You can use the menu on the left to navigate to different sections of uCloud (File explorer, applications, etc.) -

      -
      • -
    • -

      On top of the uCloud interface you have My Workspace. That is your private space where you have some free hundreds of CPU hours and GBs of memory to run different applications (that you can see by using the menu Apps on the left).

      -
      • -
    • -

      Click on Apps and find the application called Genomics Courses. Here choose the course Intro to NGS data, and use the other options to choose, for example, how many resources you want to use (we suggest at least 8 vCPUs)

      -
      • -
    -

    Run the docker container

    -

    With Docker, you can create containers that will work in the same way on all the machines. The results of the course are exactly reproducible if you use such a Docker container. We created a container for the course that already contains packages and course material installed. You need to download Docker Desktop at this link. We suggest you have at least 8GB of RAM and 20GB of hard disk space.

    -
      -
    • -

      When Docker Desktop is installed, you can use the command line to retrieve the container from the web: -docker pull samuelesoraggi/ngs-summer-aarhus:2022.08.01

      -
      • -
    • -

      You can now execute the container. You will see a web address in the output of the command line: you need to copy that into your web browser to see jupyterlab.

      -
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    docker run --rm -it -p 8888:8888 samuelesoraggi/ngs-summer-aarhus:2022.08.01

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    AlphaFold

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    + + + +
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    + + + +
    + + +
    +

    AlphaFold

    +

    :fontawesome-brands-github: GitHub Repository

    +

    Updated: January 2022
    +Status: Under expansion

    +

    This module will contain a basic standalone tutorial on how to run the newly implemented AlphaFold app in the Sandbox (UCloud version).

    +

    Intended use: The aim of this repository is to on-board users for AlphaFold on Computerome/UCloud.

    +

    !!! abstract “Syllabus” 1. Introduction to protein structural analysis 2. Evaluating predicted structures (AlphaFold DB) 3. Using the AlphaFold app to predict new structures (AlphaFold) 4. Replicating an AlphaFold study 5. Future developments possible with AlphaFold

    +

    !!! info “Workshop requirements” Knowledge of Python and Jupyter notebooks

    +
    +

    Acknowledgements

    + + + +
    +
    + +
    + +
    + + + + + \ No newline at end of file diff --git a/modules/EHRs.html b/modules/EHRs.html new file mode 100644 index 0000000..47f693b --- /dev/null +++ b/modules/EHRs.html @@ -0,0 +1,726 @@ + + + + + + + + + +Introduction to NGS data analysis - EHRs + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
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    + +
    +
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    EHRs

    +
    + + + +
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    + + + +
    + + +
    +

    Electronic Health Records

    +

    Electronic health records (EHRs) are digital records kept in the public health sector that record the medical histories of individuals, and access is normally highly restricted to preserve patient privacy. This data is sometimes also shared (partly or in full) in secondary patient registries that support research of a specific disease or condition (such as cystic fibrosis). These datasets are extraordinarily valuable in the development of predictive models used in precision medicine.

    +

    Modules linked to EHR analysis are currently under development.

    + + +
    + +
    + +
    + + + + + \ No newline at end of file diff --git a/modules/bulk_rnaseq.html b/modules/bulk_rnaseq.html new file mode 100644 index 0000000..e9bca6d --- /dev/null +++ b/modules/bulk_rnaseq.html @@ -0,0 +1,756 @@ + + + + + + + + + +Introduction to NGS data analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Bulk RNAseq

    +
    + + + +
    + + + + +
    + + + +
    + + +
    +

    Introduction to bulk RNAseq analysis workshop

    +
    +:material-web-plus: Course Page +
    +

    This workshop material includes a tutorial on how to approach RNAseq data, starting from your count matrix. Thus, the workshop only briefly touches upon laboratory protocols, library preparation, and experimental design of RNA sequencing experiments, mainly for the purpose of outlining considerations in the downstream bioinformatic analysis. This workshop is based on the materials developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC), a collection of modified tutorials from the DESeq2 and R language vignettes.

    +

    Intended use: The aim of this repository is to run a comprehensive but introductory workshop on bulk-RNAseq bioinformatic analyses. Each of the modules of this workshop is accompanied by a powerpoint slideshow explaining the steps and the theory behind a typical bioinformatics analysis (ideally with a teacher). Many of the slides are annotated with extra information and/or point to original sources for extra reading material.

    +
    +

    Goals

    +

    By the end of this workshop, you should be able to analyse your own bulk RNAseq count matrix:

    +
      +
    • Normalize your data.
      • +
    • Explore your samples with PCAs and heatmaps.
      • +
    • Perform Differential Expression Analysis.
      • +
    • Annotate your results.
      • +
    +

    !!! agenda “Syllabus” 1. Course Introduction 2. Setup 3. Experimental planning 4. Data Explanation 5. Preprocessing 6. RNAseq counts 7. Exploratory analysis 8. Differential Expression Analysis 9. Functional Analysis 10. Summarized workflow

    +

    !!! info “Workshop prerequisites” - Knowledge of R, Rstudio and Rmarkdown. It is recommended that you have at least followed our workshop R basics - Basic knowledge of RNAseq technology - Basic knowledge of data science and statistics such as PCA, clustering and statistical testing

    +
    +

    Acknowledgements

    + + + +
    +
    +
    + +
    + +
    + + + + + \ No newline at end of file diff --git a/modules/clinProteomics_0122.html b/modules/clinProteomics_0122.html new file mode 100644 index 0000000..b710b8a --- /dev/null +++ b/modules/clinProteomics_0122.html @@ -0,0 +1,772 @@ + + + + + + + + + +Introduction to NGS data analysis - Clinical Proteomics + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
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    Clinical Proteomics

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    + + +
    +

    Clinical Proteomics

    +

    :fontawesome-brands-github: GitHub Repository

    +

    Updated: January 2021
    +Status: Under expansion

    +

    The general strategy for the clinical proteomics module is to provide software, computing resources, datsets and storage using UCloud. Written material (instructions etc.), example notebooks and other auxiliary files will be provided in a Github repository.

    +
      +
    • Proteomics Sandbox app will be used for GUI programs +
        +
      • Primarily for identification / quantification
        • +
      • FragPipe / MSFragger for database search (and perhaps open search)
        • +
      • PDV for visualizing spectral matches
        • +
      • SearchGUI and PeptideShaker also available
        • +
      • +
    • JupyterLab app for data analysis after quantification +
        +
      • Init script to activate conda environment and install custom kernel
        • +
      • Notebooks provided through Github (https://github.com/hds-sandbox/proteomics-course)
        • +
      • +
    • Datasets, (installed) software and JSON config files stored in UCloud project folders +
        +
      • Students currently need to be project members
        • +
      • +
    +

    Intended use: Self-guided introduction to basic proteomics

    +

    !!! abstract “Syllabus” 1. Identify and quantify peptides/proteins * “Database search” using MSFragger/FragPipe or MaxQuant * Visualize peptide spectrum matches using e.g. PDV, IDPicker, IPSA, … 2. Quality control analysis 3. Bioinformatics * Reintegrate clinical metadata * JupyterLab / RStudio + e.g. PolySTest / VSClust / … 4. PhosphoProteomics

    +

    !!! info “Workshop requirements” Knowledge of Python and Jupyter Notebooks

    +
    +

    Other learning resources

    + +
    +

    Acknowledgements

    + + + +
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    + +
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    + + + + + \ No newline at end of file diff --git a/modules/course_template.html b/modules/course_template.html new file mode 100644 index 0000000..0f2fc06 --- /dev/null +++ b/modules/course_template.html @@ -0,0 +1,766 @@ + + + + + + + + + +Introduction to NGS data analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
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    + + + + +

    +Course Template +

    +

    Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nulla et euismod nulla. Curabitur feugiat, tortor non consequat finibus, justo purus auctor massa, nec semper lorem quam in massa.

    +

    +Authors +

    +

    Jennifer Bartell Jose Alejandro Romero Herrera Samuele Soraggi

    +
    +

    !!! abstract “Overview” 💬 Questions:
    +- Why are we doing this?
    +- What is the meaning of life?

    +
    &#128477; **Objectives:**  
+- Be the best person you can be  
+- Know your enemy  
+
+&#128368; **Time Estimation:** X hours  
+
+&#128193; **Supporting Materials:**  
+
+&#128203; **License:** [Tutorial Content is licensed under Creative Commons Attribution 4.0 International License](https://creativecommons.org/licenses/by/4.0/)
    +
    +

    Introduction

    +
    +

    Look at this!

    +
    +

    Lorem markdownum voluntas et praeteritae aliquando Cauno thyrso inevitabile est, interdum fingit educat, aliquo ungues solito sermo. Miscent pulveris me fletus moenia sed simul aequoris removit, te incursu.

    +
      +
    • Incursurus liquidis Troiae
      • +
    • En ad staminaque ullam
      • +
    • Pellis erat collo Hectoreis cadavera quia draconem
      • +
    +
    +
    +

    Agenda

    +

    !!! note “In this tutorial, we will cover:” * First item * Second item

    +
    +
    +

    Section 1

    +

    Lorem markdownum voluntas et praeteritae aliquando Cauno thyrso inevitabile est, interdum fingit educat, aliquo ungues solito sermo. Miscent pulveris me fletus moenia sed simul aequoris removit, te incursu.

    +

    ??? question “How does this thing work?”

    +
    By looking at it long enough!
    +
    +
    +

    Section 2

    +

    Lorem markdownum voluntas et praeteritae aliquando Cauno thyrso inevitabile est, interdum fingit educat, aliquo ungues solito sermo. Miscent pulveris me fletus moenia sed simul aequoris removit, te incursu.

    +

    ??? note

    +
    Lorem ipsum dolor sit amet, consectetur adipiscing elit. Nulla et euismod
+nulla. Curabitur feugiat, tortor non consequat finibus, justo purus auctor
+massa, nec semper lorem quam in massa.
    +
    +
    +

    Section 3

    +

    Lorem markdownum voluntas et praeteritae aliquando Cauno thyrso inevitabile est, interdum fingit educat, aliquo ungues solito sermo. Miscent pulveris me fletus moenia sed simul aequoris removit, te incursu.

    +

    !!! info “Are you using an Apple chip?”

    +
    Continue to do so.
    + + +
    + +
    + +
    + + + + + \ No newline at end of file diff --git a/modules/genomics.html b/modules/genomics.html new file mode 100644 index 0000000..cbc64d4 --- /dev/null +++ b/modules/genomics.html @@ -0,0 +1,726 @@ + + + + + + + + + +Introduction to NGS data analysis - Genomics + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Genomics

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    +

    Genomics

    +

    Genomics is the study of genomes, the complete set of an organism’s DNA. Genomics research now encompasses functional and structural studies, epigenomics, and metagenomics, and genomic medicine is under active implementation and extension in the health sector.

    +

    Modules linked to genomics topics are currently under construction.

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    + +
    + + + + + \ No newline at end of file diff --git a/modules/index.html b/modules/index.html new file mode 100644 index 0000000..c118301 --- /dev/null +++ b/modules/index.html @@ -0,0 +1,833 @@ + + + + + + + + + +Introduction to NGS data analysis - Training modules + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Training modules

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    Modified
    +
    +

    May 15, 2024

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    + +
    + + + +
    + + +

    Sandbox resources have been organized as training modules focused on key topics in health data science. We are constantly adding additional resources and have plans to create additional modules on medical imaging and wearable device data. Feel free to adapt these resources for your own purposes (with credit to the National Health Data Science Sandbox project and other projects they acknowledge in the specific materials).

    +

    You can access our training modules through:

    +
      +
    • In-person workshops and courses at host universities (check News for announcements)
      • +
    • Course/workshop repositories on our GitHub page - some tool assembly may be required!
      • +
    • Independently accessible Sandbox apps on UCloud, the academic (interactive) HPC at University of Southern Denmark
      • +
    • Independently accessible Sandbox apps on GenomeDK, the bioinformatics high-throughput HPC at University of Aarhus
      • +
    • Virtual machines deployed on the Course Platform at Computerome, the academic HPC at the Technical University of Denmark (Sandbox rollout still under development!) tutorials and guides and popular tools for analysis and visualization. Email us with any questions, comments or suggestions for new workshops!
      • +
    +

     

    +
    +

    Data Carpentry and management

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    +
    +

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    +
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    +

    Computing skills are an important foundation for health data science (and using the above training modules), but formal training is often lacking as biomedical researchers navigate increasingly difficult computational tasks in their projects. These skills range from programming to the use of high-performance computers (HPC) to proper research data management.

    + +

     

    +
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    Genomics

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    +
    +

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    +
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    +

    Genomics is the study of genomes, the complete set of an organism’s DNA. Genomics research now encompasses functional and structural studies, epigenomics, and metagenomics, and genomic medicine is under active implementation and extension in the health sector.

    +

    Use the Genomics Sandbox App on UCloud to explore the resources below:

    + +

     

    +
    +
    +

    Transcriptomics

    +
    +
    +
    +

    +
    +
    +
    +

    Transcriptomics is the study of transcriptomes, which investigates RNA transcripts within a cell or tissue to determine what genes are being expressed and in what proportion. These RNA transcripts include mRNAs, tRNA, rRNA, and other non-coding RNA present in a cell.

    +

    Use the Transcriptomics Sandbox App on UCloud to explore these resources:

    +
      +
    • Bulk RNAseq (last update: June 2023)
      • +
    • Single-Cell RNAseq (last update: May 2023)
      • +
    • Cirrocumulus (a popular tool for visualizing different types of RNA-seq data and downstream analysis)
      • +
    • RNAseq in RStudio (RStudio session with pre-installed RNAseq analysis packages for exploring with your own uploaded data)
      • +
    +

     

    +
    +
    +

    Proteomics

    +
    +
    +
    +

    +
    +
    +
    +

    Proteomics is the study of proteins that are produced by an organism. Proteomics allows us to analyze protein composition and structure, which have great importance in determining their function.

    +

    Use the Proteomics Sandbox App on UCloud to explore pre-installed tools for proteomics analysis and other resources:

    + +

    We also offer a tutorial on UCloud’s ColabFold app, a tool that allows predictions with AlphaFold2 or RoseTTAFold.

    + +

     

    +
    +
    +

    Electronic Health Records

    +
    +
    +
    +

    +
    +
    +
    +

    Electronic health records (EHRs) are digital records kept in the public health sector that record the medical histories of individuals, and access is normally highly restricted to preserve patient privacy. This data is sometimes also shared (partly or in full) in secondary patient registries that support research on a specific disease or condition (such as breast cancer or cystic fibrosis). These datasets are extraordinarily valuable in the development of predictive models used in precision medicine.

    +

    The chronic lymphocytic leukemia synthetic dataset listed below is generated solely from public data. It is of low utility, so we don’t recommend its use beyond the course it was designed for (with much explanation for the students on its construction and caveats). Please see Synthetic Data for more information.

    +
      +
    • Chronic Lymphocytic Leukemia synthetic dataset created for use in “Fra realworld data til personlig medicin”, a course from the University of Copenhagen’s MS in Personlig Medicin (last update: January 2023)
      • +
    • Intro to EHR analysis (workshop under development)
      • +
    + + +
    + +
    + +
    + + + + + \ No newline at end of file diff --git a/modules/proteomics.html b/modules/proteomics.html new file mode 100644 index 0000000..00c216a --- /dev/null +++ b/modules/proteomics.html @@ -0,0 +1,725 @@ + + + + + + + + + +Introduction to NGS data analysis - Proteomics + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Proteomics

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    +

    Proteomics

    +

    Proteomics is the study of proteins summed across a complete sample (ranging from a single cell to a whole organism). High-throughput measurement is conducted using mass spectrometry techniques and protein arrays, and provides insight into protein expression profiles and interactions.

    + + +
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    + + + + + \ No newline at end of file diff --git a/modules/transcriptomics.html b/modules/transcriptomics.html new file mode 100644 index 0000000..11c5d71 --- /dev/null +++ b/modules/transcriptomics.html @@ -0,0 +1,725 @@ + + + + + + + + + +Introduction to NGS data analysis - Transcriptomics + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Transcriptomics

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    + + +
    +

    Transcriptomics

    +

    Transcriptomics is the study of RNA transcripts and provides insight into gene expression patterns. State-of-the-art approaches rely on high-throughput sequencing of transcripts sampled by various methods.

    + + +
    + +
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    News

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    Sandbox data scientists routinely lead or contribute to courses and workshops at host universities in Denmark. Check out upcoming events here! All our past events are listed in the table below.

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    +Workshop: Digging into the Health Data Science Sandbox + +18-19 April 2024 + +KU + +Jennifer Bartell +
    +Course support at SDU + +9 February 2024 + +SDU + +Jacob Fredegaard Hansen +
    +DDSA PhD meetup and D3A conference + +1 February 2024 + +DDSA + +Jennifer Bartell +
    +A primer for Synthetic health data + +31 January 2024 + +  + +Jennifer Bartell +
    +NNF Collaborative Data Science award news: the SE3D project! + +12 December 2023 + +KU + +Jennifer Bartell +
    +Updates from SDU + +9 November 2023 + +SDU + +Jacob Fredegaard Hansen +
    +A course on RDS for NGS data + +7 November 2023 + +DTU + +Jose AR Herrera +
    +From Data Chaos to Data Harmony + +7 November 2023 + +DeiC conference + +Jennifer Bartell +
    +‘Digging into the Health Data Science Sandbox’ workshop + +7 September 2023 + +AU + +Jennifer Bartell +
    +Sandbox workshop in Aarhus + +29 August 2023 + +AU + +Samuele Soraggi +
    +Workshop on bulkRNA-seq data + +19 June 2023 + +KU + +Jennifer Bartell +
    +Sandbox App updates on UCloud rolled out + +31 May 2023 + +KU + +Jennifer Bartell +
    +Second bulk RNA-seq course at the University of Copenhagen + +18 January 2023 + +KU + +Jennifer Bartell +
    +Sandbox support for Spring 2023 courses + +10 January 2023 + +KU + +Jennifer Bartell +
    +Soft launch of the new Course Platform at Computerome + +8 January 2023 + +KU + +Jesper R Christiansen +
    +Sandbox support for ‘Advanced Statistical Learning’ + +30 November 2022 + +AU + +Samuele Soraggi +
    +Sandbox support within ‘Workshops in Applied Bioinformatics’ at SDU + +15 November 2022 + +SDU + +Jacob Fredegaard Hansen +
    +Transcriptomics Sandbox app launched on UCloud! + +15 November 2022 + +KU + +Jose AR Herrera +
    +Genomics Sandbox app launched on UCloud! + +6 September 2022 + +AU + +Samuele Soraggi +
    +Bulk RNA-seq course at University of Copenhagen + +18 August 2022 + +KU + +Jennifer Bartell +
    +Genomics course at Aarhus University + +1 June 2022 + +AU + +Samuele Soraggi +
    +Basics of Personalized Medicine - final wrap-up + +22 April 2022 + +AAU + +Jennifer Bartell +
    +Basics of Personalized Medicine - MSc course + +1 April 2022 + +AAU + +Jennifer Bartell +
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    Basics of Personalized Medicine - MSc course

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    personalized-medicine
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    AAU
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    + Basics of Personalized Medicine - MS in Personal Medicine program +
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    Published
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    April 1, 2022

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    The first course supported by the Sandbox is launching this month - ‘Basics of Personalized Medicine’ - where students in the new Master in Personal Medicine program at University of Copenhagen are introduced to predictive modeling using electronic health records.

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    Basics of Personalized Medicine - final wrap-up

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    personalized-medicine
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    AAU
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    + Basics of Personalized Medicine - final wrap-up +
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    Published
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    April 22, 2022

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    Our first course, Basics of Personalized Medicine, wrapped up this month with student project presentations which described their approaches to analysis of the synthetic Chronic Lymphocytic Leukemia dataset created for the course. Course reviews highlighted the helpfulness of Sandbox staff in troubleshooting R problems and the tremendous amount that students learned about predictive modeling.

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    + + + + + \ No newline at end of file diff --git a/news/past/2022-06-01-genomics-au.html b/news/past/2022-06-01-genomics-au.html new file mode 100644 index 0000000..5287d3c --- /dev/null +++ b/news/past/2022-06-01-genomics-au.html @@ -0,0 +1,733 @@ + + + + + + + + + + + +Introduction to NGS data analysis - Genomics course at Aarhus University + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Genomics course at Aarhus University

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    genomics
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    AU
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    + Genomics course at Aarhus University +
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    Published
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    June 1, 2022

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    A month-long course in Genomics taught by Professors Mikkel Schierup and Stig Andersen has started with lead supercomputing support on UCloud by Sandbox data scientist and course instructor Samuele Soraggi. Computational exercises in NGS analysis were deployed in a UCloud project for use by 47 graduate students with primarily molecular biology and clinical backgrounds and no prior supercomputing experience! Post-course update: We received many positive reviews on use of the Genomics Sandbox training materials on UCloud!

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    Bulk RNA-seq course at University of Copenhagen

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    transcriptomics
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    course
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    KU
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    HeaDS
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    reNEW
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    + Bulk RNA-seq course at University of Copenhagen +
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    Published
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    August 18, 2022

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    Today we began teaching our brand new bulk RNA-seq course to researchers (from PhD students to professors) at SUND at the University of Copenhagen. We had 32 workshop participants join us for two days of lectures and exercises on UCloud. We’d like to extend our thanks to our workshop collaborators, data scientists from the SUND DataLab at KU’s Center for Health Data Science as well as the genomics platform at the NNF Center for Stem Cell Medicine (reNEW).

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    For those that could not enroll for this session, you can find the relevant material here.

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    Genomics Sandbox app launched on UCloud!

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    genomics
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    + Genomics Sandbox app launched on UCloud! +
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    September 6, 2022

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    We have deployed our first standalone Sandbox app on UCloud! Please see the Access page for instructions on how to find our Sandbox apps on UCloud - this first one is titled ‘Genomics Sandbox’ and module documentation is linked from the UCloud app page as well as here in Modules.

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    Sandbox support within ‘Workshops in Applied Bioinformatics’ at SDU

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    + Sandbox support for a workshop in the series ‘Workshops in Applied Bioinformatics’ at SDU +
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    November 15, 2022

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    Sandbox data scientist Jacob Fredegaard Hansen created a tutorial on how to use ColabFold for a one day workshop as part of the ‘Workshops in Applied Bioinformatics’ series taught by Sandbox collaborator Veit Schwammle. The material is accessible on the Sandbox website (see Modules, Proteomics) for any UCloud user alongside the UCloud ColabFold App.

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    Sandbox support for ‘Advanced Statistical Learning’

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    + Sandbox support for ‘Advanced Statistical Learning’ +
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    November 30, 2022

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    Sandbox data scientist Samuele Soraggi spent two weeks teaching for the Fall 2023 course ‘Advanced Statistical Learning’ taught by Prof. Asger Hobolth at Aarhus University.

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    Transcriptomics Sandbox app launched on UCloud!

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    November 15, 2022

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    We have deployed our second standalone Sandbox app on UCloud! Please see the Access page for instructions on how to find our Sandbox apps on UCloud - This one is titled ‘Transcriptomics Sandbox’ and module documentation is linked from the UCloud app page as well as here in Modules.

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    Soft launch of the new Course Platform at Computerome

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    January 8, 2023

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    Sandbox data scientist Jesper Roy Christiansen has been integral to the development of a new ‘Course Platform’ at Computerome, the HPC platform at the Technical University of Denmark. Built as a collaboration between the Sandbox and Computerome, the Course Platform will host its first users, students in ‘Fra real-world data til personlig medicin’, a course of KU’s MS in Personlig Medicin. Sandbox coordinator Jennifer Bartell and Sandbox PI Martin Boegsted have also been involved in testing this new system during course setup. See the above link as well as HPC Access for more details on this platform and how you can also use this new platform to host courses (with or without Sandbox involvement!).

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    Sandbox support for Spring 2023 courses

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    personalized-medicine
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    single-cell
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    HeaDS
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    January 10, 2023

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    The Health Data Science sandbox is working with the following courses during spring 2023:

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    • Sandbox support for Population Genomics
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    Exercises for an MS course on Population Genomics taught by Prof. Kasper Munch at Aarhus University are being implemented on UCloud by Sandbox data scientist Samuele Soraggi. Students will explore the training materials on UCloud during the Spring 2023 semester, after which the materials will be accessible to any UCloud user via the Genomics Sandbox App.

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    • Fra real-world data til personlig medicin with Course Platform & Sandbox support The second round of the course ‘Fra real-world data til personlig medicin’ in KU’s MS in Personlig Medicin begins in January with an introduction to CLL-TIM, a predictive model for chronic lymphocytic leukemia deployed by Prof. Carsten Niemann, an introduction by Sandbox coordinator Jennifer Bartell to the new Course Platform at Computerome built with Sandbox help for hosting courses with HPC resources, and an introduction to building predictive models using TidyModels in R by Prof. Rasmus Broendum. The course will run through April with 10 continuing education students building their own predictive models using a new and improved synthetic CLL dataset developed by Sandbox data scientist Sander Boisen Valentin. Jennifer and Rasmus are also manning the Sandbox Slack workspace to field student questions about the dataset and their model building.

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    • Sandbox support for ‘Single-cell, Single-Molecule: The Next Level in Cell Biology’ An NNF-funded course, ‘Single-cell, Single-Molecule: The Next Level in Cell Biology’ combining experimental and computational approaches to RNA sequencing is starting at Aarhus University. In addition to course-responsible professor Stig Andersen and co-teachers Victoria Birkedal and Thomas Boesen, Sandbox PI Mikkel Schierup will be contributing along with Sandbox data scientist Samuele Soraggi. Samuele is adapting the Transcriptomics App material on UCloud to supply tutorials and exercises for this hefty course as well as serving as a teaching assistant. The course materials will be available to all users of the Transcriptomics Sandbox App on UCloud in the future.

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    Second bulk RNA-seq course at the University of Copenhagen

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    workshop
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    course
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    KU
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    nextflow
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    + Second bulk RNA-seq course at the University of Copenhagen +
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    Published
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    January 18, 2023

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    On 18th of January we taught the second iteration of our bulk RNA-seq course to researchers (from PhD students to professors) at SUND at the University of Copenhagen. We had ~50 workshop participants joining us for three days of lectures and exercises on UCloud. This time, we introduced preprocessing theory (read QC, alignment and quantification) and the use of automated workflows using the nf-core rnaseq pipeline.

    +

    For those that could not enroll for this session, you can find the updated material here. We have moved the datasets and slides to a zenodo repository

    +

    We’d like to extend our thanks to our workshop collaborators, data scientists from the SUND DataLab at KU’s Center for Health Data Science as well as the genomics platform at the NNF Center for Stem Cell Medicine (reNEW).

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    Sandbox App updates on UCloud rolled out

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    genomics
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    transcriptomics
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    proteomics
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    ucloud
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    KU
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    HeaDS
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    reNEW
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    transcriptomics
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    + Sandbox App updates on UCloud rolled out +
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    Published
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    May 31, 2023

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    New versions of the Genomics Sandbox App, the Transcriptomics Sandbox App, and the Proteomics Sandbox App have all been launched on UCloud this month! Check out the new components in the training modules such as a GWAS module in Genomics and new tools in Transcriptomics and Proteomics. Updates were also informed by the different courses supported during Spring 2023. With these courses wrapping up this month, the associated new training materials have also been included in the new versions of the apps.

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    Workshop on bulkRNA-seq data

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    workshop
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    KU
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    HeaDS
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    reNEW
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    transcriptomics
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    + 3 days of bulk RNA-seq at the University of Copenhagen +
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    Published
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    June 19, 2023

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    Our teaching team (from the Sandbox, the HeaDS DataLab, and reNEW’s genomics platform) hosted another 3 day workshop on bulk RNA-seq. The 34 participants used the updated version of the UCloud Transcriptomics App which provided the smoothest experience yet for both trainers and trainees. A new goal for the next course run is to add a student project to support independent implementation and exploration of the course content.

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    Sandbox workshop in Aarhus

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    workshop
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    AU
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    + 3 days of Sandbox demos at Aarhus University +
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    Published
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    August 29, 2023

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    Sandbox data scientist Samuele Soraggi hosted a three day speed run through Sandbox apps at the Bioinformatics Research Center. The 26 participants joined for genomics, transcriptomics, and/or proteomics app demos depending on their interests. This thorough omics demo had maxed out participant sign-ups and an enthusiastic crew enjoyed the sessions alongside a bit of networking across disciplines. We plan to host more of these type of workshops given the event’s success!

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    ‘Digging into the Health Data Science Sandbox’ workshop

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    conference
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    AU
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    + ‘Digging into the Health Data Science Sandbox’ at the Danish Bioinformatics Conference 2023 (Aarhus University) +
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    Published
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    September 7, 2023

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    The full team of Sandbox data scientists hosted a 4 hour workshop at the Danish Bioinformatics conference where they gave a taster session of each of our 3 omics apps. We learned that multi-omics analysis were a substantial draw for the crowd at the DBC and are making plans to address this interest in future events.

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    + + + + + \ No newline at end of file diff --git a/news/past/2023-10-25-RDM_NGS.html b/news/past/2023-10-25-RDM_NGS.html new file mode 100644 index 0000000..d0befdf --- /dev/null +++ b/news/past/2023-10-25-RDM_NGS.html @@ -0,0 +1,734 @@ + + + + + + + + + + + +Introduction to NGS data analysis - A course on RDS for NGS data + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    A course on RDS for NGS data

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    course
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    data-management
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    DTU
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    + +
    +
    + ‘Research Data Management for NGS Data’ with DeiC (Technical University of Denmark) +
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    Published
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    +

    November 7, 2023

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    Sandbox data scientist Jose Alejandro Romero Herrera ran the first instance of a new module on research data management practices he developed specifically for NGS data. Twelve participants were hosted in conjunction with DeiC at DTU, and were exposed to tools like bash, conda, git, and cookie cutter in their quest to organize their omics data.

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    From Data Chaos to Data Harmony

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    conference
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    data-management
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    talk
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    + From Data Chaos to Data Harmony: Managing NGS Data in a Wetlab - at the annual DeiC conference +
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    Published
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    +

    November 7, 2023

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    Sandbox data scientist Jose Alejandro Romero Herrera gave a talk in the Data Management speaker track at the annual Danish E-Infrastructure Consortium (DeiC) conference in Kolding, Denmark. The talk was well received at the biggest DeiC conference ever (250 participants).

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    + + + + + \ No newline at end of file diff --git a/news/past/2023-11-09-proteomics_biostat_SDU.html b/news/past/2023-11-09-proteomics_biostat_SDU.html new file mode 100644 index 0000000..f1121b3 --- /dev/null +++ b/news/past/2023-11-09-proteomics_biostat_SDU.html @@ -0,0 +1,734 @@ + + + + + + + + + + + +Introduction to NGS data analysis - Updates from SDU + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    +

    Updates from SDU

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    +
    proteomics
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    course
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    SDU
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    +
    + +
    +
    + Updated Proteomics Sandbox App supporting of a Biostatistics course at SDU +
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    Published
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    +

    November 9, 2023

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    The Proteomics Sandbox Application has recently undergone a significant update, enhancing its security features to ensure safer usage for its users. In this latest iteration, Sandbox data scientist Jacob Fredegaard Hansen has expanded the app’s software suite by introducing two new tools: DIA-NN and MZmine, catering to the metabolomics field. Furthermore, the pre-existing software within the application has been refreshed and updated to the latest versions, ensuring that the Proteomics Sandbox Application remains at the cutting-edge of the field. Excitingly, this application will be actively utilized in the course “BMB831: Biostatistics in R II” at the University of Southern Denmark throughout this autumn, showcasing its relevance and applicability in academic settings.

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    + + + + + \ No newline at end of file diff --git a/news/past/2023-12-12-SE3D.html b/news/past/2023-12-12-SE3D.html new file mode 100644 index 0000000..b42dbae --- /dev/null +++ b/news/past/2023-12-12-SE3D.html @@ -0,0 +1,729 @@ + + + + + + + + + + +Introduction to NGS data analysis - NNF Collaborative Data Science award news: the SE3D project! + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    NNF Collaborative Data Science award news: the SE3D project!

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    novo-nordisk-foundation
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    AAU
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    KU
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    Published
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    December 12, 2023

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    Today we got the news that we will be able to hire 5 new research staff focused on synthetic health data over the next 4 years. The SE3D project - Synthetic health data: ethical development and deployment via deep learning approaches - will be led by Sandbox PIs Martin Boegsted (AAU) and Anders Krogh (KU) alongside Sandbox project lead Jennifer Bartell (KU) and a new collaborator, Prof. Jan Trzaskowski from AAU Law. We’re really excited to set up this research arm that shares so many Sandbox interests and potential for interaction. The project starts from 1 May 2024, with much thanks to the NNF for their continued support of our ideas. Look out for job ads in the spring from KU and AAU!

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    A primer for Synthetic health data

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    manuscript
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    synthetic-data
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    KU
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    AAU
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    Published
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    +

    January 31, 2024

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    In collaboration with Prof. Henning Langberg at KU Public Health and funding from Erhvervsfyrtaarn Sund Vaegt, Jennifer Bartell has developed a manuscript that discusses technical, regulatory, and deployment solutions and challenges for synthetic health data from a broad perspective. This manuscript was developed in collaboration with Sandbox partners Sander Boisen Valentin and Martin Boegsted of AAU, and we plan to submit it to a journal soon. For now, check out our manuscript on arXiv!

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    DDSA PhD meetup and D3A conference

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    conference
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    DDSA
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    Published
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    February 1, 2024

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    Several Sandbox staff represented the project at both the DDSA PhD Meetup with a practical presentation on research data management and with posters at D3A, the national data science meeting. It was nice to meet up in person and also make new connections with the excellent cadre of conference attendees. Thanks to the DDSA secretariat for their invitation and organizational efforts.

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    Course support at SDU

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    proteomics
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    SDU
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    course
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    Published
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    February 9, 2024

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    During the Spring Semester 2024, Sandbox data scientist Jacob Fredegaard Hansen will be assisting with teaching and tools in the course BMB834: Protein Structure, Dynamics, and Modelling at the University of Southern Denmark. Here, Jacob will provide Sandbox support, and materials will be used for applying computational methods for protein structure retrieval and visualization, as well as for applying high-performance computing (HPC) methods for protein structure modeling.ß

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    Workshop: Digging into the Health Data Science Sandbox

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    KU
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    workshop
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    course
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    HPC
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    RDM
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    Published
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    April 18, 2024

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    This workshop offers an introduction to the training materials and tools of the Health Data Science Sandbox, a national infrastructure project. The Sandbox team is building training resources and guides for learning bioinformatics, predictive modeling in precision medicine, high performance computing and data carpentry that is accessible to all Danish university employees (PhD students and up) via academic supercomputing infrastructure.

    +

    You will be introduced to our current training set-up, meet our helpful data scientists, be guided through how to use our apps, and can make requests for the next topic we tackle!

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    Intro to NGS data analysis - Summer School

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    +
    Genomics
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    AU
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    course
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    + +
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    + Fully booked +
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    Author
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    Samuele Soraggi

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    Published
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    July 1, 2024

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    This workshop is a regularly hosted summer school to teach NGS data analysis, and is taught by Stig Andersen, Mikkel Schierup, and Samuele Soraggi (supporting via the HDS Sandbox). You can find additional information here.

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    HPC launch

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    HPC
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    RDM
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    KU
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    course
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    + Click to sign-up +
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    Author
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    JB

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    Published
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    October 30, 2024

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    Sign-up.

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    HPC Pipes

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    snakemake
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    conda
    +
    KU
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    course
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    +
    + +
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    + Click to sign-up +
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    Author
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    ARM and JB

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    +
    Published
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    +

    November 15, 2024

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    + + +

    Sign-up.

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    + +
    + + + + + \ No newline at end of file diff --git a/news/upcoming/ngs-july-24.png b/news/upcoming/ngs-july-24.png new file mode 100644 index 0000000..1f9bcce Binary files /dev/null and b/news/upcoming/ngs-july-24.png differ diff --git a/recommended/recommended.html b/recommended/recommended.html new file mode 100644 index 0000000..bd24732 --- /dev/null +++ b/recommended/recommended.html @@ -0,0 +1,726 @@ + + + + + + + + + +Introduction to NGS data analysis - Recommended + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Recommended

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    + + + + +
    + +
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"enum": [ - "Dosis" - ] - }, - { - "title": "Dr Sugiyama", - "markdownDescription": "https://fonts.google.com/specimen/Dr+Sugiyama", - "enum": [ - "Dr Sugiyama" - ] - }, - { - "title": "Duru Sans", - "markdownDescription": "https://fonts.google.com/specimen/Duru+Sans", - "enum": [ - "Duru Sans" - ] - }, - { - "title": "Dynalight", - "markdownDescription": "https://fonts.google.com/specimen/Dynalight", - "enum": [ - "Dynalight" - ] - }, - { - "title": "EB Garamond", - "markdownDescription": "https://fonts.google.com/specimen/EB+Garamond", - "enum": [ - "EB Garamond" - ] - }, - { - "title": "Eagle Lake", - "markdownDescription": "https://fonts.google.com/specimen/Eagle+Lake", - "enum": [ - "Eagle Lake" - ] - }, - { - "title": "East Sea Dokdo", - "markdownDescription": "https://fonts.google.com/specimen/East+Sea+Dokdo", - "enum": [ - "East Sea Dokdo" - ] - }, - { - "title": "Eater", - "markdownDescription": "https://fonts.google.com/specimen/Eater", - "enum": [ - "Eater" - ] - }, - { - "title": "Economica", - "markdownDescription": "https://fonts.google.com/specimen/Economica", - "enum": [ - "Economica" - ] - }, - { - "title": "Eczar", - "markdownDescription": "https://fonts.google.com/specimen/Eczar", - "enum": [ - "Eczar" - ] - }, - { - "title": "El Messiri", - "markdownDescription": "https://fonts.google.com/specimen/El+Messiri", - "enum": [ - "El Messiri" - ] - }, - { - "title": "Electrolize", - "markdownDescription": "https://fonts.google.com/specimen/Electrolize", - "enum": [ - "Electrolize" - ] - }, - { - "title": "Elsie", - "markdownDescription": "https://fonts.google.com/specimen/Elsie", - "enum": [ - "Elsie" - ] - }, - { - "title": "Elsie Swash Caps", - "markdownDescription": "https://fonts.google.com/specimen/Elsie+Swash+Caps", - "enum": [ - "Elsie Swash Caps" - ] - }, - { - "title": "Emblema One", - "markdownDescription": "https://fonts.google.com/specimen/Emblema+One", - "enum": [ - "Emblema One" - ] - }, - { - "title": "Emilys Candy", - "markdownDescription": "https://fonts.google.com/specimen/Emilys+Candy", - 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"enum": [ - "Exo" - ] - }, - { - "title": "Exo 2", - "markdownDescription": "https://fonts.google.com/specimen/Exo+2", - "enum": [ - "Exo 2" - ] - }, - { - "title": "Expletus Sans", - "markdownDescription": "https://fonts.google.com/specimen/Expletus+Sans", - "enum": [ - "Expletus Sans" - ] - }, - { - "title": "Fahkwang", - "markdownDescription": "https://fonts.google.com/specimen/Fahkwang", - "enum": [ - "Fahkwang" - ] - }, - { - "title": "Fanwood Text", - "markdownDescription": "https://fonts.google.com/specimen/Fanwood+Text", - "enum": [ - "Fanwood Text" - ] - }, - { - "title": "Farro", - "markdownDescription": "https://fonts.google.com/specimen/Farro", - "enum": [ - "Farro" - ] - }, - { - "title": "Farsan", - "markdownDescription": "https://fonts.google.com/specimen/Farsan", - "enum": [ - "Farsan" - ] - }, - { - "title": "Fascinate", - "markdownDescription": "https://fonts.google.com/specimen/Fascinate", - "enum": [ - "Fascinate" - ] - }, - { - "title": "Fascinate Inline", - "markdownDescription": "https://fonts.google.com/specimen/Fascinate+Inline", - 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"enum": [ - "Fenix" - ] - }, - { - "title": "Finger Paint", - "markdownDescription": "https://fonts.google.com/specimen/Finger+Paint", - "enum": [ - "Finger Paint" - ] - }, - { - "title": "Fira Code", - "markdownDescription": "https://fonts.google.com/specimen/Fira+Code", - "enum": [ - "Fira Code" - ] - }, - { - "title": "Fira Mono", - "markdownDescription": "https://fonts.google.com/specimen/Fira+Mono", - "enum": [ - "Fira Mono" - ] - }, - { - "title": "Fira Sans", - "markdownDescription": "https://fonts.google.com/specimen/Fira+Sans", - "enum": [ - "Fira Sans" - ] - }, - { - "title": "Fira Sans Condensed", - "markdownDescription": "https://fonts.google.com/specimen/Fira+Sans+Condensed", - "enum": [ - "Fira Sans Condensed" - ] - }, - { - "title": "Fira Sans Extra Condensed", - "markdownDescription": "https://fonts.google.com/specimen/Fira+Sans+Extra+Condensed", - "enum": [ - "Fira Sans Extra Condensed" - ] - }, - { - "title": "Fjalla One", - "markdownDescription": "https://fonts.google.com/specimen/Fjalla+One", - 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"markdownDescription": "https://fonts.google.com/specimen/Frank+Ruhl+Libre", - "enum": [ - "Frank Ruhl Libre" - ] - }, - { - "title": "Freckle Face", - "markdownDescription": "https://fonts.google.com/specimen/Freckle+Face", - "enum": [ - "Freckle Face" - ] - }, - { - "title": "Fredericka the Great", - "markdownDescription": "https://fonts.google.com/specimen/Fredericka+the+Great", - "enum": [ - "Fredericka the Great" - ] - }, - { - "title": "Fredoka One", - "markdownDescription": "https://fonts.google.com/specimen/Fredoka+One", - "enum": [ - "Fredoka One" - ] - }, - { - "title": "Freehand", - "markdownDescription": "https://fonts.google.com/specimen/Freehand", - "enum": [ - "Freehand" - ] - }, - { - "title": "Fresca", - "markdownDescription": "https://fonts.google.com/specimen/Fresca", - "enum": [ - "Fresca" - ] - }, - { - "title": "Frijole", - "markdownDescription": "https://fonts.google.com/specimen/Frijole", - "enum": [ - "Frijole" - ] - }, - { - "title": "Fruktur", - "markdownDescription": "https://fonts.google.com/specimen/Fruktur", - "enum": [ - "Fruktur" - ] - }, - { - "title": "Fugaz One", - "markdownDescription": "https://fonts.google.com/specimen/Fugaz+One", - "enum": [ - "Fugaz One" - ] - }, - { - "title": "GFS Didot", - "markdownDescription": "https://fonts.google.com/specimen/GFS+Didot", - "enum": [ - "GFS Didot" - ] - }, - { - "title": "GFS Neohellenic", - "markdownDescription": "https://fonts.google.com/specimen/GFS+Neohellenic", - "enum": [ - "GFS Neohellenic" - ] - }, - { - "title": "Gabriela", - "markdownDescription": "https://fonts.google.com/specimen/Gabriela", - "enum": [ - "Gabriela" - ] - }, - { - "title": "Gaegu", - "markdownDescription": "https://fonts.google.com/specimen/Gaegu", - "enum": [ - "Gaegu" - ] - }, - { - "title": "Gafata", - "markdownDescription": "https://fonts.google.com/specimen/Gafata", - "enum": [ - "Gafata" - ] - }, - { - "title": "Galada", - "markdownDescription": "https://fonts.google.com/specimen/Galada", - "enum": [ - "Galada" - ] - }, - { - "title": "Galdeano", - "markdownDescription": "https://fonts.google.com/specimen/Galdeano", - "enum": [ - "Galdeano" - ] - }, - { - "title": "Galindo", - "markdownDescription": "https://fonts.google.com/specimen/Galindo", - "enum": [ - "Galindo" - ] - }, - { - "title": "Gamja Flower", - "markdownDescription": "https://fonts.google.com/specimen/Gamja+Flower", - "enum": [ - "Gamja Flower" - ] - }, - { - "title": "Gayathri", - "markdownDescription": "https://fonts.google.com/specimen/Gayathri", - "enum": [ - "Gayathri" - ] - }, - { - "title": "Gelasio", - "markdownDescription": "https://fonts.google.com/specimen/Gelasio", - "enum": [ - "Gelasio" - ] - }, - { - "title": "Gentium Basic", - "markdownDescription": "https://fonts.google.com/specimen/Gentium+Basic", - "enum": [ - "Gentium Basic" - ] - }, - { - "title": "Gentium Book Basic", - "markdownDescription": "https://fonts.google.com/specimen/Gentium+Book+Basic", - "enum": [ - "Gentium Book Basic" - ] - }, - { - "title": "Geo", - "markdownDescription": "https://fonts.google.com/specimen/Geo", - "enum": [ - "Geo" - ] - }, - { - "title": "Geostar", - "markdownDescription": "https://fonts.google.com/specimen/Geostar", - "enum": [ - "Geostar" - ] - }, - { - "title": "Geostar Fill", - "markdownDescription": "https://fonts.google.com/specimen/Geostar+Fill", - "enum": [ - "Geostar Fill" - ] - }, - { - "title": "Germania One", - "markdownDescription": "https://fonts.google.com/specimen/Germania+One", - "enum": [ - "Germania One" - ] - }, - { - "title": "Gidugu", - "markdownDescription": "https://fonts.google.com/specimen/Gidugu", - "enum": [ - "Gidugu" - ] - }, - { - "title": "Gilda Display", - "markdownDescription": "https://fonts.google.com/specimen/Gilda+Display", - "enum": [ - "Gilda Display" - ] - }, - { - "title": "Girassol", - "markdownDescription": "https://fonts.google.com/specimen/Girassol", - "enum": [ - "Girassol" - ] - }, - { - "title": "Give You Glory", - "markdownDescription": "https://fonts.google.com/specimen/Give+You+Glory", - "enum": [ - "Give You Glory" - ] - }, - { - "title": "Glass Antiqua", - "markdownDescription": "https://fonts.google.com/specimen/Glass+Antiqua", - "enum": [ - "Glass Antiqua" - ] - }, - { - "title": "Glegoo", - "markdownDescription": "https://fonts.google.com/specimen/Glegoo", - "enum": [ - "Glegoo" - ] - }, - { - "title": "Gloria Hallelujah", - "markdownDescription": "https://fonts.google.com/specimen/Gloria+Hallelujah", - "enum": [ - "Gloria Hallelujah" - ] - }, - { - "title": "Goblin One", - "markdownDescription": "https://fonts.google.com/specimen/Goblin+One", - "enum": [ - "Goblin One" - ] - }, - { - "title": "Gochi Hand", - "markdownDescription": "https://fonts.google.com/specimen/Gochi+Hand", - "enum": [ - "Gochi Hand" - ] - }, - { - "title": "Gorditas", - "markdownDescription": "https://fonts.google.com/specimen/Gorditas", - "enum": [ - "Gorditas" - ] - }, - { - "title": "Gothic A1", - "markdownDescription": "https://fonts.google.com/specimen/Gothic+A1", - "enum": [ - "Gothic A1" - ] - }, - { - "title": "Gotu", - "markdownDescription": "https://fonts.google.com/specimen/Gotu", - "enum": [ - "Gotu" - ] - }, - { - "title": "Goudy Bookletter 1911", - "markdownDescription": "https://fonts.google.com/specimen/Goudy+Bookletter+1911", - "enum": [ - "Goudy Bookletter 1911" - ] - }, - { - "title": "Graduate", - "markdownDescription": "https://fonts.google.com/specimen/Graduate", - "enum": [ - "Graduate" - ] - }, - { - "title": "Grand Hotel", - "markdownDescription": "https://fonts.google.com/specimen/Grand+Hotel", - "enum": [ - "Grand Hotel" - ] - }, - { - "title": "Grandstander", - "markdownDescription": "https://fonts.google.com/specimen/Grandstander", - "enum": [ - "Grandstander" - ] - }, - { - "title": "Gravitas One", - "markdownDescription": "https://fonts.google.com/specimen/Gravitas+One", - "enum": [ - "Gravitas One" - ] - }, - { - "title": "Great Vibes", - "markdownDescription": "https://fonts.google.com/specimen/Great+Vibes", - "enum": [ - "Great Vibes" - ] - }, - { - "title": "Grenze", - "markdownDescription": "https://fonts.google.com/specimen/Grenze", - "enum": [ - "Grenze" - ] - }, - { - "title": "Grenze Gotisch", - "markdownDescription": "https://fonts.google.com/specimen/Grenze+Gotisch", - "enum": [ - "Grenze Gotisch" - ] - }, - { - "title": "Griffy", - "markdownDescription": "https://fonts.google.com/specimen/Griffy", - "enum": [ - "Griffy" - ] - }, - { - "title": "Gruppo", - "markdownDescription": "https://fonts.google.com/specimen/Gruppo", - "enum": [ - "Gruppo" - ] - }, - { - "title": "Gudea", - "markdownDescription": "https://fonts.google.com/specimen/Gudea", - "enum": [ - "Gudea" - ] - }, - { - "title": "Gugi", - "markdownDescription": "https://fonts.google.com/specimen/Gugi", - "enum": [ - "Gugi" - ] - }, - { - "title": "Gupter", - "markdownDescription": "https://fonts.google.com/specimen/Gupter", - "enum": [ - "Gupter" - ] - }, - { - "title": "Gurajada", - "markdownDescription": "https://fonts.google.com/specimen/Gurajada", - "enum": [ - "Gurajada" - ] - }, - { - "title": "Habibi", - "markdownDescription": "https://fonts.google.com/specimen/Habibi", - "enum": [ - "Habibi" - ] - }, - { - "title": "Halant", - "markdownDescription": "https://fonts.google.com/specimen/Halant", - "enum": [ - "Halant" - ] - }, - { - "title": "Hammersmith One", - "markdownDescription": "https://fonts.google.com/specimen/Hammersmith+One", - "enum": [ - "Hammersmith One" - ] - }, - { - "title": "Hanalei", - "markdownDescription": "https://fonts.google.com/specimen/Hanalei", - "enum": [ - "Hanalei" - ] - }, - { - "title": "Hanalei Fill", - "markdownDescription": "https://fonts.google.com/specimen/Hanalei+Fill", - "enum": [ - "Hanalei Fill" - ] - }, - { - "title": "Handlee", - "markdownDescription": "https://fonts.google.com/specimen/Handlee", - "enum": [ - "Handlee" - ] - }, - { - "title": "Hanuman", - "markdownDescription": "https://fonts.google.com/specimen/Hanuman", - "enum": [ - "Hanuman" - ] - }, - { - "title": "Happy Monkey", - "markdownDescription": "https://fonts.google.com/specimen/Happy+Monkey", - "enum": [ - "Happy Monkey" - ] - }, - { - "title": "Harmattan", - "markdownDescription": "https://fonts.google.com/specimen/Harmattan", - "enum": [ - "Harmattan" - ] - }, - { - "title": "Headland One", - 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"markdownDescription": "https://fonts.google.com/specimen/IM+Fell+Double+Pica+SC", - "enum": [ - "IM Fell Double Pica SC" - ] - }, - { - "title": "IM Fell English", - "markdownDescription": "https://fonts.google.com/specimen/IM+Fell+English", - "enum": [ - "IM Fell English" - ] - }, - { - "title": "IM Fell English SC", - "markdownDescription": "https://fonts.google.com/specimen/IM+Fell+English+SC", - "enum": [ - "IM Fell English SC" - ] - }, - { - "title": "IM Fell French Canon", - "markdownDescription": "https://fonts.google.com/specimen/IM+Fell+French+Canon", - "enum": [ - "IM Fell French Canon" - ] - }, - { - "title": "IM Fell French Canon SC", - "markdownDescription": "https://fonts.google.com/specimen/IM+Fell+French+Canon+SC", - "enum": [ - "IM Fell French Canon SC" - ] - }, - { - "title": "IM Fell Great Primer", - "markdownDescription": "https://fonts.google.com/specimen/IM+Fell+Great+Primer", - "enum": [ - "IM Fell Great Primer" - ] - }, - { - "title": "IM Fell Great Primer SC", - "markdownDescription": "https://fonts.google.com/specimen/IM+Fell+Great+Primer+SC", - "enum": [ - "IM Fell Great Primer SC" - ] - }, - { - "title": "Ibarra Real Nova", - "markdownDescription": "https://fonts.google.com/specimen/Ibarra+Real+Nova", - "enum": [ - "Ibarra Real Nova" - ] - }, - { - "title": "Iceberg", - "markdownDescription": "https://fonts.google.com/specimen/Iceberg", - "enum": [ - "Iceberg" - ] - }, - { - "title": "Iceland", - "markdownDescription": "https://fonts.google.com/specimen/Iceland", - "enum": [ - "Iceland" - ] - }, - { - "title": "Imprima", - "markdownDescription": "https://fonts.google.com/specimen/Imprima", - "enum": [ - "Imprima" - ] - }, - { - "title": "Inconsolata", - "markdownDescription": "https://fonts.google.com/specimen/Inconsolata", - "enum": [ - "Inconsolata" - ] - }, - { - "title": "Inder", - "markdownDescription": "https://fonts.google.com/specimen/Inder", - "enum": [ - "Inder" - ] - }, - { - "title": "Indie Flower", - "markdownDescription": "https://fonts.google.com/specimen/Indie+Flower", - "enum": [ - "Indie Flower" - ] - }, - { - "title": "Inika", - "markdownDescription": "https://fonts.google.com/specimen/Inika", - "enum": [ - "Inika" - ] - }, - { - "title": "Inknut Antiqua", - "markdownDescription": "https://fonts.google.com/specimen/Inknut+Antiqua", - "enum": [ - "Inknut Antiqua" - ] - }, - { - "title": "Inria Sans", - "markdownDescription": "https://fonts.google.com/specimen/Inria+Sans", - "enum": [ - "Inria Sans" - ] - }, - { - "title": "Inria Serif", - "markdownDescription": "https://fonts.google.com/specimen/Inria+Serif", - "enum": [ - "Inria Serif" - ] - }, - { - "title": "Inter", - "markdownDescription": "https://fonts.google.com/specimen/Inter", - "enum": [ - "Inter" - ] - }, - { - "title": "Irish Grover", - "markdownDescription": "https://fonts.google.com/specimen/Irish+Grover", - "enum": [ - "Irish Grover" - ] - }, - { - "title": "Istok Web", - "markdownDescription": "https://fonts.google.com/specimen/Istok+Web", - "enum": [ - "Istok Web" - ] - }, - { - "title": "Italiana", - "markdownDescription": "https://fonts.google.com/specimen/Italiana", - "enum": [ - "Italiana" - ] - }, - { - "title": "Italianno", - "markdownDescription": "https://fonts.google.com/specimen/Italianno", - "enum": [ - "Italianno" - ] - }, - { - "title": "Itim", - "markdownDescription": "https://fonts.google.com/specimen/Itim", - "enum": [ - "Itim" - ] - }, - { - "title": "Jacques Francois", - "markdownDescription": "https://fonts.google.com/specimen/Jacques+Francois", - "enum": [ - "Jacques Francois" - ] - }, - { - "title": "Jacques Francois Shadow", - "markdownDescription": "https://fonts.google.com/specimen/Jacques+Francois+Shadow", - "enum": [ - "Jacques Francois Shadow" - ] - }, - { - "title": "Jaldi", - "markdownDescription": "https://fonts.google.com/specimen/Jaldi", - "enum": [ - "Jaldi" - ] - }, - { - "title": "Jim Nightshade", - "markdownDescription": "https://fonts.google.com/specimen/Jim+Nightshade", - "enum": [ - "Jim Nightshade" - ] - }, - { - "title": "Jockey One", - "markdownDescription": "https://fonts.google.com/specimen/Jockey+One", - "enum": [ - "Jockey One" - ] - }, - { - "title": "Jolly Lodger", - "markdownDescription": "https://fonts.google.com/specimen/Jolly+Lodger", - "enum": [ - "Jolly Lodger" - ] - }, - { - "title": "Jomhuria", - "markdownDescription": "https://fonts.google.com/specimen/Jomhuria", - "enum": [ - "Jomhuria" - ] - }, - { - "title": "Jomolhari", - "markdownDescription": "https://fonts.google.com/specimen/Jomolhari", - "enum": [ - "Jomolhari" - ] - }, - { - "title": "Josefin Sans", - "markdownDescription": "https://fonts.google.com/specimen/Josefin+Sans", - "enum": [ - "Josefin Sans" - ] - }, - { - "title": "Josefin Slab", - "markdownDescription": "https://fonts.google.com/specimen/Josefin+Slab", - "enum": [ - "Josefin Slab" - ] - }, - { - "title": "Jost", - "markdownDescription": "https://fonts.google.com/specimen/Jost", - "enum": [ - "Jost" - ] - }, - { - "title": "Joti One", - "markdownDescription": "https://fonts.google.com/specimen/Joti+One", - "enum": [ - "Joti One" - ] - }, - { - "title": "Jua", - "markdownDescription": "https://fonts.google.com/specimen/Jua", - "enum": [ - "Jua" - ] - }, - { - "title": "Judson", - "markdownDescription": "https://fonts.google.com/specimen/Judson", - "enum": [ - "Judson" - ] - }, - { - "title": "Julee", - "markdownDescription": "https://fonts.google.com/specimen/Julee", - "enum": [ - "Julee" - ] - }, - { - "title": "Julius Sans One", - "markdownDescription": "https://fonts.google.com/specimen/Julius+Sans+One", - "enum": [ - "Julius Sans One" - ] - }, - { - "title": "Junge", - "markdownDescription": "https://fonts.google.com/specimen/Junge", - "enum": [ - "Junge" - ] - }, - { - "title": "Jura", - "markdownDescription": "https://fonts.google.com/specimen/Jura", - "enum": [ - "Jura" - ] - }, - { - "title": "Just Another Hand", - "markdownDescription": "https://fonts.google.com/specimen/Just+Another+Hand", - "enum": [ - "Just Another Hand" - ] - }, - { - "title": "Just Me Again Down Here", - "markdownDescription": "https://fonts.google.com/specimen/Just+Me+Again+Down+Here", - "enum": [ - "Just Me Again Down Here" - ] - }, - { - "title": "K2D", - "markdownDescription": "https://fonts.google.com/specimen/K2D", - "enum": [ - "K2D" - ] - }, - { - "title": "Kadwa", - "markdownDescription": "https://fonts.google.com/specimen/Kadwa", - "enum": [ - "Kadwa" - ] - }, - { - "title": "Kalam", - "markdownDescription": "https://fonts.google.com/specimen/Kalam", - "enum": [ - "Kalam" - ] - }, - { - "title": "Kameron", - "markdownDescription": "https://fonts.google.com/specimen/Kameron", - "enum": [ - "Kameron" - ] - }, - { - "title": "Kanit", - "markdownDescription": "https://fonts.google.com/specimen/Kanit", - "enum": [ - "Kanit" - ] - }, - { - "title": "Kantumruy", - "markdownDescription": "https://fonts.google.com/specimen/Kantumruy", - "enum": [ - "Kantumruy" - ] - }, - { - "title": "Karla", - "markdownDescription": "https://fonts.google.com/specimen/Karla", - "enum": [ - "Karla" - ] - }, - { - "title": "Karma", - "markdownDescription": "https://fonts.google.com/specimen/Karma", - "enum": [ - "Karma" - ] - }, - { - "title": "Katibeh", - "markdownDescription": "https://fonts.google.com/specimen/Katibeh", - "enum": [ - "Katibeh" - ] - }, - { - "title": "Kaushan Script", - "markdownDescription": "https://fonts.google.com/specimen/Kaushan+Script", - "enum": [ - "Kaushan Script" - ] - }, - { - "title": "Kavivanar", - "markdownDescription": "https://fonts.google.com/specimen/Kavivanar", - "enum": [ - "Kavivanar" - ] - }, - { - "title": "Kavoon", - "markdownDescription": "https://fonts.google.com/specimen/Kavoon", - "enum": [ - "Kavoon" - ] - }, - { - "title": "Kdam Thmor", - "markdownDescription": "https://fonts.google.com/specimen/Kdam+Thmor", - "enum": [ - "Kdam Thmor" - ] - }, - { - "title": "Keania One", - "markdownDescription": "https://fonts.google.com/specimen/Keania+One", - "enum": [ - "Keania One" - ] - }, - { - "title": "Kelly Slab", - "markdownDescription": "https://fonts.google.com/specimen/Kelly+Slab", - "enum": [ - "Kelly Slab" - ] - }, - { - "title": "Kenia", - "markdownDescription": "https://fonts.google.com/specimen/Kenia", - "enum": [ - "Kenia" - ] - }, - { - "title": "Khand", - "markdownDescription": "https://fonts.google.com/specimen/Khand", - "enum": [ - "Khand" - ] - }, - { - "title": "Khmer", - "markdownDescription": "https://fonts.google.com/specimen/Khmer", - "enum": [ - "Khmer" - ] - }, - { - "title": "Khula", - "markdownDescription": "https://fonts.google.com/specimen/Khula", - "enum": [ - "Khula" - ] - }, - { - "title": "Kirang Haerang", - "markdownDescription": "https://fonts.google.com/specimen/Kirang+Haerang", - "enum": [ - "Kirang Haerang" - ] - }, - { - "title": "Kite One", - "markdownDescription": "https://fonts.google.com/specimen/Kite+One", - "enum": [ - "Kite One" - ] - }, - { - "title": "Knewave", - "markdownDescription": "https://fonts.google.com/specimen/Knewave", - "enum": [ - "Knewave" - ] - }, - { - "title": "KoHo", - "markdownDescription": "https://fonts.google.com/specimen/KoHo", - "enum": [ - "KoHo" - ] - }, - { - "title": "Kodchasan", - "markdownDescription": "https://fonts.google.com/specimen/Kodchasan", - "enum": [ - "Kodchasan" - ] - }, - { - "title": "Kosugi", - "markdownDescription": "https://fonts.google.com/specimen/Kosugi", - "enum": [ - "Kosugi" - ] - }, - { - "title": "Kosugi Maru", - "markdownDescription": "https://fonts.google.com/specimen/Kosugi+Maru", - "enum": [ - "Kosugi Maru" - ] - }, - { - "title": "Kotta One", - "markdownDescription": "https://fonts.google.com/specimen/Kotta+One", - "enum": [ - "Kotta One" - ] - }, - { - "title": "Koulen", - "markdownDescription": "https://fonts.google.com/specimen/Koulen", - "enum": [ - "Koulen" - ] - }, - { - "title": "Kranky", - "markdownDescription": "https://fonts.google.com/specimen/Kranky", - "enum": [ - "Kranky" - ] - }, - { - "title": "Kreon", - "markdownDescription": "https://fonts.google.com/specimen/Kreon", - "enum": [ - "Kreon" - ] - }, - { - "title": "Kristi", - "markdownDescription": "https://fonts.google.com/specimen/Kristi", - "enum": [ - "Kristi" - ] - }, - { - "title": "Krona One", - "markdownDescription": "https://fonts.google.com/specimen/Krona+One", - "enum": [ - "Krona One" - ] - }, - { - "title": "Krub", - "markdownDescription": "https://fonts.google.com/specimen/Krub", - "enum": [ - "Krub" - ] - }, - { - "title": "Kufam", - "markdownDescription": "https://fonts.google.com/specimen/Kufam", - "enum": [ - "Kufam" - ] - }, - { - "title": "Kulim Park", - "markdownDescription": "https://fonts.google.com/specimen/Kulim+Park", - "enum": [ - "Kulim Park" - ] - }, - { - "title": "Kumar One", - "markdownDescription": "https://fonts.google.com/specimen/Kumar+One", - "enum": [ - "Kumar One" - ] - }, - { - "title": "Kumar One Outline", - "markdownDescription": "https://fonts.google.com/specimen/Kumar+One+Outline", - "enum": [ - "Kumar One Outline" - ] - }, - { - "title": "Kumbh Sans", - "markdownDescription": "https://fonts.google.com/specimen/Kumbh+Sans", - "enum": [ - "Kumbh Sans" - ] - }, - { - "title": "Kurale", - 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"enum": [ - "Lateef" - ] - }, - { - "title": "Lato", - "markdownDescription": "https://fonts.google.com/specimen/Lato", - "enum": [ - "Lato" - ] - }, - { - "title": "League Script", - "markdownDescription": "https://fonts.google.com/specimen/League+Script", - "enum": [ - "League Script" - ] - }, - { - "title": "Leckerli One", - "markdownDescription": "https://fonts.google.com/specimen/Leckerli+One", - "enum": [ - "Leckerli One" - ] - }, - { - "title": "Ledger", - "markdownDescription": "https://fonts.google.com/specimen/Ledger", - "enum": [ - "Ledger" - ] - }, - { - "title": "Lekton", - "markdownDescription": "https://fonts.google.com/specimen/Lekton", - "enum": [ - "Lekton" - ] - }, - { - "title": "Lemon", - "markdownDescription": "https://fonts.google.com/specimen/Lemon", - "enum": [ - "Lemon" - ] - }, - { - "title": "Lemonada", - "markdownDescription": "https://fonts.google.com/specimen/Lemonada", - "enum": [ - "Lemonada" - ] - }, - { - "title": "Lexend Deca", - "markdownDescription": "https://fonts.google.com/specimen/Lexend+Deca", - "enum": [ - "Lexend Deca" - ] - }, - { - "title": "Lexend Exa", - "markdownDescription": "https://fonts.google.com/specimen/Lexend+Exa", - "enum": [ - "Lexend Exa" - ] - }, - { - "title": "Lexend Giga", - "markdownDescription": "https://fonts.google.com/specimen/Lexend+Giga", - "enum": [ - "Lexend Giga" - ] - }, - { - "title": "Lexend Mega", - "markdownDescription": "https://fonts.google.com/specimen/Lexend+Mega", - "enum": [ - "Lexend Mega" - ] - }, - { - "title": "Lexend Peta", - "markdownDescription": "https://fonts.google.com/specimen/Lexend+Peta", - "enum": [ - "Lexend Peta" - ] - }, - { - "title": "Lexend Tera", - "markdownDescription": "https://fonts.google.com/specimen/Lexend+Tera", - "enum": [ - "Lexend Tera" - ] - }, - { - "title": "Lexend Zetta", - "markdownDescription": "https://fonts.google.com/specimen/Lexend+Zetta", - "enum": [ - "Lexend Zetta" - ] - }, - { - "title": "Libre Barcode 128", - "markdownDescription": "https://fonts.google.com/specimen/Libre+Barcode+128", - "enum": [ - 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"enum": [ - "Libre Baskerville" - ] - }, - { - "title": "Libre Caslon Display", - "markdownDescription": "https://fonts.google.com/specimen/Libre+Caslon+Display", - "enum": [ - "Libre Caslon Display" - ] - }, - { - "title": "Libre Caslon Text", - "markdownDescription": "https://fonts.google.com/specimen/Libre+Caslon+Text", - "enum": [ - "Libre Caslon Text" - ] - }, - { - "title": "Libre Franklin", - "markdownDescription": "https://fonts.google.com/specimen/Libre+Franklin", - "enum": [ - "Libre Franklin" - ] - }, - { - "title": "Life Savers", - "markdownDescription": "https://fonts.google.com/specimen/Life+Savers", - "enum": [ - "Life Savers" - ] - }, - { - "title": "Lilita One", - "markdownDescription": "https://fonts.google.com/specimen/Lilita+One", - "enum": [ - "Lilita One" - ] - }, - { - "title": "Lily Script One", - "markdownDescription": "https://fonts.google.com/specimen/Lily+Script+One", - "enum": [ - "Lily Script One" - ] - }, - { - "title": "Limelight", - "markdownDescription": "https://fonts.google.com/specimen/Limelight", - "enum": [ - "Limelight" - ] - }, - { - "title": "Linden Hill", - "markdownDescription": "https://fonts.google.com/specimen/Linden+Hill", - "enum": [ - "Linden Hill" - ] - }, - { - "title": "Literata", - "markdownDescription": "https://fonts.google.com/specimen/Literata", - "enum": [ - "Literata" - ] - }, - { - "title": "Liu Jian Mao Cao", - "markdownDescription": "https://fonts.google.com/specimen/Liu+Jian+Mao+Cao", - "enum": [ - "Liu Jian Mao Cao" - ] - }, - { - "title": "Livvic", - "markdownDescription": "https://fonts.google.com/specimen/Livvic", - "enum": [ - "Livvic" - ] - }, - { - "title": "Lobster", - "markdownDescription": "https://fonts.google.com/specimen/Lobster", - "enum": [ - "Lobster" - ] - }, - { - "title": "Lobster Two", - "markdownDescription": "https://fonts.google.com/specimen/Lobster+Two", - "enum": [ - "Lobster Two" - ] - }, - { - "title": "Londrina Outline", - "markdownDescription": "https://fonts.google.com/specimen/Londrina+Outline", - "enum": [ - "Londrina Outline" - ] - }, - { - "title": "Londrina Shadow", - "markdownDescription": "https://fonts.google.com/specimen/Londrina+Shadow", - "enum": [ - "Londrina Shadow" - ] - }, - { - "title": "Londrina Sketch", - "markdownDescription": "https://fonts.google.com/specimen/Londrina+Sketch", - "enum": [ - "Londrina Sketch" - ] - }, - { - "title": "Londrina Solid", - "markdownDescription": "https://fonts.google.com/specimen/Londrina+Solid", - "enum": [ - "Londrina Solid" - ] - }, - { - "title": "Long Cang", - "markdownDescription": "https://fonts.google.com/specimen/Long+Cang", - "enum": [ - "Long Cang" - ] - }, - { - "title": "Lora", - "markdownDescription": "https://fonts.google.com/specimen/Lora", - "enum": [ - "Lora" - ] - }, - { - "title": "Love Ya Like A Sister", - "markdownDescription": "https://fonts.google.com/specimen/Love+Ya+Like+A+Sister", - "enum": [ - "Love Ya Like A Sister" - ] - }, - { - "title": "Loved by the King", - "markdownDescription": "https://fonts.google.com/specimen/Loved+by+the+King", - 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"markdownDescription": "https://fonts.google.com/specimen/Martel", - "enum": [ - "Martel" - ] - }, - { - "title": "Martel Sans", - "markdownDescription": "https://fonts.google.com/specimen/Martel+Sans", - "enum": [ - "Martel Sans" - ] - }, - { - "title": "Marvel", - "markdownDescription": "https://fonts.google.com/specimen/Marvel", - "enum": [ - "Marvel" - ] - }, - { - "title": "Mate", - "markdownDescription": "https://fonts.google.com/specimen/Mate", - "enum": [ - "Mate" - ] - }, - { - "title": "Mate SC", - "markdownDescription": "https://fonts.google.com/specimen/Mate+SC", - "enum": [ - "Mate SC" - ] - }, - { - "title": "Material Icons", - "markdownDescription": "https://fonts.google.com/specimen/Material+Icons", - "enum": [ - "Material Icons" - ] - }, - { - "title": "Maven Pro", - "markdownDescription": "https://fonts.google.com/specimen/Maven+Pro", - "enum": [ - "Maven Pro" - ] - }, - { - "title": "McLaren", - "markdownDescription": "https://fonts.google.com/specimen/McLaren", - "enum": [ - "McLaren" - ] - }, - { - "title": "Meddon", - "markdownDescription": "https://fonts.google.com/specimen/Meddon", - "enum": [ - "Meddon" - ] - }, - { - "title": "MedievalSharp", - "markdownDescription": "https://fonts.google.com/specimen/MedievalSharp", - "enum": [ - "MedievalSharp" - ] - }, - { - "title": "Medula One", - "markdownDescription": "https://fonts.google.com/specimen/Medula+One", - "enum": [ - "Medula One" - ] - }, - { - "title": "Meera Inimai", - "markdownDescription": "https://fonts.google.com/specimen/Meera+Inimai", - "enum": [ - "Meera Inimai" - ] - }, - { - "title": "Megrim", - "markdownDescription": "https://fonts.google.com/specimen/Megrim", - "enum": [ - "Megrim" - ] - }, - { - "title": "Meie Script", - "markdownDescription": "https://fonts.google.com/specimen/Meie+Script", - "enum": [ - "Meie Script" - ] - }, - { - "title": "Merienda", - "markdownDescription": "https://fonts.google.com/specimen/Merienda", - "enum": [ - "Merienda" - ] - }, - { - "title": "Merienda One", - "markdownDescription": "https://fonts.google.com/specimen/Merienda+One", - "enum": [ - "Merienda One" - ] - }, - { - "title": "Merriweather", - "markdownDescription": "https://fonts.google.com/specimen/Merriweather", - "enum": [ - "Merriweather" - ] - }, - { - "title": "Merriweather Sans", - "markdownDescription": "https://fonts.google.com/specimen/Merriweather+Sans", - "enum": [ - "Merriweather Sans" - ] - }, - { - "title": "Metal", - "markdownDescription": "https://fonts.google.com/specimen/Metal", - "enum": [ - "Metal" - ] - }, - { - "title": "Metal Mania", - "markdownDescription": "https://fonts.google.com/specimen/Metal+Mania", - "enum": [ - "Metal Mania" - ] - }, - { - "title": "Metamorphous", - "markdownDescription": "https://fonts.google.com/specimen/Metamorphous", - "enum": [ - "Metamorphous" - ] - }, - { - "title": "Metrophobic", - "markdownDescription": "https://fonts.google.com/specimen/Metrophobic", - "enum": [ - "Metrophobic" - ] - }, - { - "title": "Michroma", - "markdownDescription": "https://fonts.google.com/specimen/Michroma", - "enum": [ - "Michroma" - ] - }, - { - "title": "Milonga", - "markdownDescription": "https://fonts.google.com/specimen/Milonga", - "enum": [ - "Milonga" - ] - }, - { - "title": "Miltonian", - "markdownDescription": "https://fonts.google.com/specimen/Miltonian", - "enum": [ - "Miltonian" - ] - }, - { - "title": "Miltonian Tattoo", - "markdownDescription": "https://fonts.google.com/specimen/Miltonian+Tattoo", - "enum": [ - "Miltonian Tattoo" - ] - }, - { - "title": "Mina", - "markdownDescription": "https://fonts.google.com/specimen/Mina", - "enum": [ - "Mina" - ] - }, - { - "title": "Miniver", - "markdownDescription": "https://fonts.google.com/specimen/Miniver", - "enum": [ - "Miniver" - ] - }, - { - "title": "Miriam Libre", - "markdownDescription": "https://fonts.google.com/specimen/Miriam+Libre", - "enum": [ - "Miriam Libre" - ] - }, - { - "title": "Mirza", - "markdownDescription": "https://fonts.google.com/specimen/Mirza", - "enum": [ - "Mirza" - ] - }, - { - "title": "Miss Fajardose", - "markdownDescription": "https://fonts.google.com/specimen/Miss+Fajardose", - "enum": [ - "Miss Fajardose" - ] - }, - { - "title": "Mitr", - "markdownDescription": "https://fonts.google.com/specimen/Mitr", - "enum": [ - "Mitr" - ] - }, - { - "title": "Modak", - "markdownDescription": "https://fonts.google.com/specimen/Modak", - "enum": [ - "Modak" - ] - }, - { - "title": "Modern Antiqua", - "markdownDescription": "https://fonts.google.com/specimen/Modern+Antiqua", - "enum": [ - "Modern Antiqua" - ] - }, - { - "title": "Mogra", - "markdownDescription": "https://fonts.google.com/specimen/Mogra", - "enum": [ - "Mogra" - ] - }, - { - "title": "Molengo", - "markdownDescription": "https://fonts.google.com/specimen/Molengo", - "enum": [ - "Molengo" - ] - }, - { - "title": "Molle", - "markdownDescription": "https://fonts.google.com/specimen/Molle", - "enum": [ - "Molle" - ] - }, - { - "title": "Monda", - "markdownDescription": "https://fonts.google.com/specimen/Monda", - "enum": [ - "Monda" - ] - }, - { - "title": "Monofett", - "markdownDescription": "https://fonts.google.com/specimen/Monofett", - "enum": [ - "Monofett" - ] - }, - { - "title": "Monoton", - "markdownDescription": "https://fonts.google.com/specimen/Monoton", - "enum": [ - "Monoton" - ] - }, - { - "title": "Monsieur La Doulaise", - "markdownDescription": "https://fonts.google.com/specimen/Monsieur+La+Doulaise", - "enum": [ - "Monsieur La Doulaise" - ] - }, - { - "title": "Montaga", - "markdownDescription": "https://fonts.google.com/specimen/Montaga", - "enum": [ - "Montaga" - ] - }, - { - "title": "Montez", - "markdownDescription": "https://fonts.google.com/specimen/Montez", - "enum": [ - "Montez" - ] - }, - { - "title": "Montserrat", - "markdownDescription": "https://fonts.google.com/specimen/Montserrat", - "enum": [ - "Montserrat" - ] - }, - { - "title": "Montserrat Alternates", - "markdownDescription": "https://fonts.google.com/specimen/Montserrat+Alternates", - "enum": [ - "Montserrat Alternates" - ] - }, - { - "title": "Montserrat Subrayada", - "markdownDescription": "https://fonts.google.com/specimen/Montserrat+Subrayada", - "enum": [ - "Montserrat Subrayada" - ] - }, - { - "title": "Moul", - "markdownDescription": "https://fonts.google.com/specimen/Moul", - "enum": [ - "Moul" - ] - }, - { - "title": "Moulpali", - "markdownDescription": "https://fonts.google.com/specimen/Moulpali", - "enum": [ - "Moulpali" - ] - }, - { - "title": "Mountains of Christmas", - "markdownDescription": "https://fonts.google.com/specimen/Mountains+of+Christmas", - "enum": [ - "Mountains of Christmas" - ] - }, - { - "title": "Mouse Memoirs", - "markdownDescription": "https://fonts.google.com/specimen/Mouse+Memoirs", - "enum": [ - "Mouse Memoirs" - ] - }, - { - "title": "Mr Bedfort", - "markdownDescription": "https://fonts.google.com/specimen/Mr+Bedfort", - "enum": [ - "Mr Bedfort" - ] - }, - { - "title": "Mr Dafoe", - "markdownDescription": "https://fonts.google.com/specimen/Mr+Dafoe", - "enum": [ - "Mr Dafoe" - ] - 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] - }, - { - "title": "Mulish", - "markdownDescription": "https://fonts.google.com/specimen/Mulish", - "enum": [ - "Mulish" - ] - }, - { - "title": "MuseoModerno", - "markdownDescription": "https://fonts.google.com/specimen/MuseoModerno", - "enum": [ - "MuseoModerno" - ] - }, - { - "title": "Mystery Quest", - "markdownDescription": "https://fonts.google.com/specimen/Mystery+Quest", - "enum": [ - "Mystery Quest" - ] - }, - { - "title": "NTR", - "markdownDescription": "https://fonts.google.com/specimen/NTR", - "enum": [ - "NTR" - ] - }, - { - "title": "Nanum Brush Script", - "markdownDescription": "https://fonts.google.com/specimen/Nanum+Brush+Script", - "enum": [ - "Nanum Brush Script" - ] - }, - { - "title": "Nanum Gothic", - "markdownDescription": "https://fonts.google.com/specimen/Nanum+Gothic", - "enum": [ - "Nanum Gothic" - ] - }, - { - "title": "Nanum Gothic Coding", - "markdownDescription": "https://fonts.google.com/specimen/Nanum+Gothic+Coding", - "enum": [ - "Nanum Gothic Coding" - ] - }, - { - "title": "Nanum Myeongjo", - "markdownDescription": "https://fonts.google.com/specimen/Nanum+Myeongjo", - "enum": [ - "Nanum Myeongjo" - ] - }, - { - "title": "Nanum Pen Script", - "markdownDescription": "https://fonts.google.com/specimen/Nanum+Pen+Script", - "enum": [ - "Nanum Pen Script" - ] - }, - { - "title": "Neucha", - "markdownDescription": "https://fonts.google.com/specimen/Neucha", - "enum": [ - "Neucha" - ] - }, - { - "title": "Neuton", - "markdownDescription": "https://fonts.google.com/specimen/Neuton", - "enum": [ - "Neuton" - ] - }, - { - "title": "New Rocker", - "markdownDescription": "https://fonts.google.com/specimen/New+Rocker", - "enum": [ - "New Rocker" - ] - }, - { - "title": "News Cycle", - "markdownDescription": "https://fonts.google.com/specimen/News+Cycle", - "enum": [ - "News Cycle" - ] - }, - { - "title": "Niconne", - "markdownDescription": "https://fonts.google.com/specimen/Niconne", - "enum": [ - "Niconne" - ] - }, - { - "title": "Niramit", - "markdownDescription": "https://fonts.google.com/specimen/Niramit", - "enum": [ - "Niramit" - ] - }, - { - "title": "Nixie One", - "markdownDescription": "https://fonts.google.com/specimen/Nixie+One", - "enum": [ - "Nixie One" - ] - }, - { - "title": "Nobile", - "markdownDescription": "https://fonts.google.com/specimen/Nobile", - "enum": [ - "Nobile" - ] - }, - { - "title": "Nokora", - "markdownDescription": "https://fonts.google.com/specimen/Nokora", - "enum": [ - "Nokora" - ] - }, - { - "title": "Norican", - "markdownDescription": "https://fonts.google.com/specimen/Norican", - "enum": [ - "Norican" - ] - }, - { - "title": "Nosifer", - "markdownDescription": "https://fonts.google.com/specimen/Nosifer", - "enum": [ - "Nosifer" - ] - }, - { - "title": "Notable", - "markdownDescription": "https://fonts.google.com/specimen/Notable", - "enum": [ - "Notable" - ] - }, - { - "title": "Nothing You Could Do", - "markdownDescription": "https://fonts.google.com/specimen/Nothing+You+Could+Do", - "enum": [ - "Nothing You Could Do" - ] - }, - { - "title": "Noticia Text", - "markdownDescription": "https://fonts.google.com/specimen/Noticia+Text", - "enum": [ - "Noticia Text" - ] - }, - { - "title": "Noto Sans", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Sans", - "enum": [ - "Noto Sans" - ] - }, - { - "title": "Noto Sans HK", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Sans+HK", - "enum": [ - "Noto Sans HK" - ] - }, - { - "title": "Noto Sans JP", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Sans+JP", - "enum": [ - "Noto Sans JP" - ] - }, - { - "title": "Noto Sans KR", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Sans+KR", - "enum": [ - "Noto Sans KR" - ] - }, - { - "title": "Noto Sans SC", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Sans+SC", - "enum": [ - "Noto Sans SC" - ] - }, - { - "title": "Noto Sans TC", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Sans+TC", - "enum": [ - "Noto Sans TC" - ] - }, - { - "title": "Noto Serif", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Serif", - "enum": [ - "Noto Serif" - ] - }, - { - "title": "Noto Serif JP", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Serif+JP", - "enum": [ - "Noto Serif JP" - ] - }, - { - "title": "Noto Serif KR", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Serif+KR", - "enum": [ - "Noto Serif KR" - ] - }, - { - "title": "Noto Serif SC", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Serif+SC", - "enum": [ - "Noto Serif SC" - ] - }, - { - "title": "Noto Serif TC", - "markdownDescription": "https://fonts.google.com/specimen/Noto+Serif+TC", - "enum": [ - "Noto Serif TC" - ] - }, - { - "title": "Nova Cut", - "markdownDescription": "https://fonts.google.com/specimen/Nova+Cut", - "enum": [ - "Nova Cut" - ] - }, - { - "title": "Nova Flat", - "markdownDescription": "https://fonts.google.com/specimen/Nova+Flat", - "enum": [ - "Nova Flat" - ] - }, - { - "title": "Nova Mono", - "markdownDescription": "https://fonts.google.com/specimen/Nova+Mono", - "enum": [ - 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"enum": [ - "Oleo Script Swash Caps" - ] - }, - { - "title": "Open Sans", - "markdownDescription": "https://fonts.google.com/specimen/Open+Sans", - "enum": [ - "Open Sans" - ] - }, - { - "title": "Open Sans Condensed", - "markdownDescription": "https://fonts.google.com/specimen/Open+Sans+Condensed", - "enum": [ - "Open Sans Condensed" - ] - }, - { - "title": "Oranienbaum", - "markdownDescription": "https://fonts.google.com/specimen/Oranienbaum", - "enum": [ - "Oranienbaum" - ] - }, - { - "title": "Orbitron", - "markdownDescription": "https://fonts.google.com/specimen/Orbitron", - "enum": [ - "Orbitron" - ] - }, - { - "title": "Oregano", - "markdownDescription": "https://fonts.google.com/specimen/Oregano", - "enum": [ - "Oregano" - ] - }, - { - "title": "Orienta", - "markdownDescription": "https://fonts.google.com/specimen/Orienta", - "enum": [ - "Orienta" - ] - }, - { - "title": "Original Surfer", - "markdownDescription": "https://fonts.google.com/specimen/Original+Surfer", - "enum": [ - 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"enum": [ - "Playball" - ] - }, - { - "title": "Playfair Display", - "markdownDescription": "https://fonts.google.com/specimen/Playfair+Display", - "enum": [ - "Playfair Display" - ] - }, - { - "title": "Playfair Display SC", - "markdownDescription": "https://fonts.google.com/specimen/Playfair+Display+SC", - "enum": [ - "Playfair Display SC" - ] - }, - { - "title": "Podkova", - "markdownDescription": "https://fonts.google.com/specimen/Podkova", - "enum": [ - "Podkova" - ] - }, - { - "title": "Poiret One", - "markdownDescription": "https://fonts.google.com/specimen/Poiret+One", - "enum": [ - "Poiret One" - ] - }, - { - "title": "Poller One", - "markdownDescription": "https://fonts.google.com/specimen/Poller+One", - "enum": [ - "Poller One" - ] - }, - { - "title": "Poly", - "markdownDescription": "https://fonts.google.com/specimen/Poly", - "enum": [ - "Poly" - ] - }, - { - "title": "Pompiere", - "markdownDescription": "https://fonts.google.com/specimen/Pompiere", - "enum": [ - "Pompiere" - 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"enum": [ - "Rakkas" - ] - }, - { - "title": "Raleway", - "markdownDescription": "https://fonts.google.com/specimen/Raleway", - "enum": [ - "Raleway" - ] - }, - { - "title": "Raleway Dots", - "markdownDescription": "https://fonts.google.com/specimen/Raleway+Dots", - "enum": [ - "Raleway Dots" - ] - }, - { - "title": "Ramabhadra", - "markdownDescription": "https://fonts.google.com/specimen/Ramabhadra", - "enum": [ - "Ramabhadra" - ] - }, - { - "title": "Ramaraja", - "markdownDescription": "https://fonts.google.com/specimen/Ramaraja", - "enum": [ - "Ramaraja" - ] - }, - { - "title": "Rambla", - "markdownDescription": "https://fonts.google.com/specimen/Rambla", - "enum": [ - "Rambla" - ] - }, - { - "title": "Rammetto One", - "markdownDescription": "https://fonts.google.com/specimen/Rammetto+One", - "enum": [ - "Rammetto One" - ] - }, - { - "title": "Ranchers", - "markdownDescription": "https://fonts.google.com/specimen/Ranchers", - "enum": [ - "Ranchers" - ] - }, - { - "title": "Rancho", - "markdownDescription": "https://fonts.google.com/specimen/Rancho", - "enum": [ - "Rancho" - ] - }, - { - "title": "Ranga", - "markdownDescription": "https://fonts.google.com/specimen/Ranga", - "enum": [ - "Ranga" - ] - }, - { - "title": "Rasa", - "markdownDescription": "https://fonts.google.com/specimen/Rasa", - "enum": [ - "Rasa" - ] - }, - { - "title": "Rationale", - "markdownDescription": "https://fonts.google.com/specimen/Rationale", - "enum": [ - "Rationale" - ] - }, - { - "title": "Ravi Prakash", - "markdownDescription": "https://fonts.google.com/specimen/Ravi+Prakash", - "enum": [ - "Ravi Prakash" - ] - }, - { - "title": "Recursive", - "markdownDescription": "https://fonts.google.com/specimen/Recursive", - "enum": [ - "Recursive" - ] - }, - { - "title": "Red Hat Display", - "markdownDescription": "https://fonts.google.com/specimen/Red+Hat+Display", - "enum": [ - "Red Hat Display" - ] - }, - { - "title": "Red Hat Text", - "markdownDescription": "https://fonts.google.com/specimen/Red+Hat+Text", - 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"enum": [ - "Rochester" - ] - }, - { - "title": "Rock Salt", - "markdownDescription": "https://fonts.google.com/specimen/Rock+Salt", - "enum": [ - "Rock Salt" - ] - }, - { - "title": "Rokkitt", - "markdownDescription": "https://fonts.google.com/specimen/Rokkitt", - "enum": [ - "Rokkitt" - ] - }, - { - "title": "Romanesco", - "markdownDescription": "https://fonts.google.com/specimen/Romanesco", - "enum": [ - "Romanesco" - ] - }, - { - "title": "Ropa Sans", - "markdownDescription": "https://fonts.google.com/specimen/Ropa+Sans", - "enum": [ - "Ropa Sans" - ] - }, - { - "title": "Rosario", - "markdownDescription": "https://fonts.google.com/specimen/Rosario", - "enum": [ - "Rosario" - ] - }, - { - "title": "Rosarivo", - "markdownDescription": "https://fonts.google.com/specimen/Rosarivo", - "enum": [ - "Rosarivo" - ] - }, - { - "title": "Rouge Script", - "markdownDescription": "https://fonts.google.com/specimen/Rouge+Script", - "enum": [ - "Rouge Script" - ] - }, - { - "title": "Rowdies", - 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"markdownDescription": "https://fonts.google.com/specimen/Zilla+Slab+Highlight", - "enum": [ - "Zilla Slab Highlight" - ] - } - ] -} \ No newline at end of file diff --git a/schema/assets/icons.json b/schema/assets/icons.json deleted file mode 100644 index 39fe4ab..0000000 --- a/schema/assets/icons.json +++ /dev/null @@ -1,9637 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Icon", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/reference/icons-emojis/#search", - "type": "string", - "enum": [ - "fontawesome/brands/42-group", - "fontawesome/brands/500px", - "fontawesome/brands/accessible-icon", - "fontawesome/brands/accusoft", - "fontawesome/brands/adn", - "fontawesome/brands/adversal", - "fontawesome/brands/affiliatetheme", - "fontawesome/brands/airbnb", - "fontawesome/brands/algolia", - "fontawesome/brands/alipay", - "fontawesome/brands/amazon-pay", - "fontawesome/brands/amazon", - "fontawesome/brands/amilia", - "fontawesome/brands/android", - 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"fontawesome/regular/face-grin-hearts", - "fontawesome/regular/face-grin-squint-tears", - "fontawesome/regular/face-grin-squint", - "fontawesome/regular/face-grin-stars", - "fontawesome/regular/face-grin-tears", - "fontawesome/regular/face-grin-tongue-squint", - "fontawesome/regular/face-grin-tongue-wink", - "fontawesome/regular/face-grin-tongue", - "fontawesome/regular/face-grin-wide", - "fontawesome/regular/face-grin-wink", - "fontawesome/regular/face-grin", - "fontawesome/regular/face-kiss-beam", - "fontawesome/regular/face-kiss-wink-heart", - "fontawesome/regular/face-kiss", - "fontawesome/regular/face-laugh-beam", - "fontawesome/regular/face-laugh-squint", - "fontawesome/regular/face-laugh-wink", - "fontawesome/regular/face-laugh", - "fontawesome/regular/face-meh-blank", - "fontawesome/regular/face-meh", - "fontawesome/regular/face-rolling-eyes", - "fontawesome/regular/face-sad-cry", - "fontawesome/regular/face-sad-tear", - "fontawesome/regular/face-smile-beam", - "fontawesome/regular/face-smile-wink", - "fontawesome/regular/face-smile", - "fontawesome/regular/face-surprise", - "fontawesome/regular/face-tired", - "fontawesome/regular/file-audio", - "fontawesome/regular/file-code", - "fontawesome/regular/file-excel", - "fontawesome/regular/file-image", - "fontawesome/regular/file-lines", - "fontawesome/regular/file-pdf", - "fontawesome/regular/file-powerpoint", - "fontawesome/regular/file-video", - "fontawesome/regular/file-word", - "fontawesome/regular/file-zipper", - "fontawesome/regular/file", - "fontawesome/regular/flag", - "fontawesome/regular/floppy-disk", - "fontawesome/regular/folder-closed", - "fontawesome/regular/folder-open", - "fontawesome/regular/folder", - "fontawesome/regular/font-awesome", - "fontawesome/regular/futbol", - "fontawesome/regular/gem", - "fontawesome/regular/hand-back-fist", - "fontawesome/regular/hand-lizard", - "fontawesome/regular/hand-peace", - "fontawesome/regular/hand-point-down", - "fontawesome/regular/hand-point-left", - "fontawesome/regular/hand-point-right", - "fontawesome/regular/hand-point-up", - "fontawesome/regular/hand-pointer", - "fontawesome/regular/hand-scissors", - "fontawesome/regular/hand-spock", - "fontawesome/regular/hand", - "fontawesome/regular/handshake", - "fontawesome/regular/hard-drive", - "fontawesome/regular/heart", - "fontawesome/regular/hospital", - "fontawesome/regular/hourglass-half", - "fontawesome/regular/hourglass", - "fontawesome/regular/id-badge", - "fontawesome/regular/id-card", - "fontawesome/regular/image", - "fontawesome/regular/images", - "fontawesome/regular/keyboard", - "fontawesome/regular/lemon", - "fontawesome/regular/life-ring", - "fontawesome/regular/lightbulb", - "fontawesome/regular/map", - "fontawesome/regular/message", - "fontawesome/regular/money-bill-1", - "fontawesome/regular/moon", - "fontawesome/regular/newspaper", - "fontawesome/regular/notdef", - "fontawesome/regular/note-sticky", - "fontawesome/regular/object-group", - "fontawesome/regular/object-ungroup", - "fontawesome/regular/paper-plane", - "fontawesome/regular/paste", - "fontawesome/regular/pen-to-square", - "fontawesome/regular/rectangle-list", - "fontawesome/regular/rectangle-xmark", - "fontawesome/regular/registered", - "fontawesome/regular/share-from-square", - "fontawesome/regular/snowflake", - "fontawesome/regular/square-caret-down", - "fontawesome/regular/square-caret-left", - "fontawesome/regular/square-caret-right", - "fontawesome/regular/square-caret-up", - "fontawesome/regular/square-check", - "fontawesome/regular/square-full", - "fontawesome/regular/square-minus", - "fontawesome/regular/square-plus", - "fontawesome/regular/square", - "fontawesome/regular/star-half-stroke", - "fontawesome/regular/star-half", - "fontawesome/regular/star", - "fontawesome/regular/sun", - "fontawesome/regular/thumbs-down", - "fontawesome/regular/thumbs-up", - "fontawesome/regular/trash-can", - "fontawesome/regular/user", - "fontawesome/regular/window-maximize", - "fontawesome/regular/window-minimize", - "fontawesome/regular/window-restore", - "fontawesome/solid/0", - "fontawesome/solid/1", - "fontawesome/solid/2", - "fontawesome/solid/3", - "fontawesome/solid/4", - "fontawesome/solid/5", - "fontawesome/solid/6", - "fontawesome/solid/7", - "fontawesome/solid/8", - "fontawesome/solid/9", - "fontawesome/solid/a", - "fontawesome/solid/address-book", - "fontawesome/solid/address-card", - "fontawesome/solid/align-center", - "fontawesome/solid/align-justify", - "fontawesome/solid/align-left", - "fontawesome/solid/align-right", - "fontawesome/solid/anchor-circle-check", - "fontawesome/solid/anchor-circle-exclamation", - "fontawesome/solid/anchor-circle-xmark", - "fontawesome/solid/anchor-lock", - "fontawesome/solid/anchor", - "fontawesome/solid/angle-down", - "fontawesome/solid/angle-left", - "fontawesome/solid/angle-right", - "fontawesome/solid/angle-up", - "fontawesome/solid/angles-down", - "fontawesome/solid/angles-left", - "fontawesome/solid/angles-right", - "fontawesome/solid/angles-up", - "fontawesome/solid/ankh", - "fontawesome/solid/apple-whole", - "fontawesome/solid/archway", - "fontawesome/solid/arrow-down-1-9", - "fontawesome/solid/arrow-down-9-1", - "fontawesome/solid/arrow-down-a-z", - "fontawesome/solid/arrow-down-long", - "fontawesome/solid/arrow-down-short-wide", - "fontawesome/solid/arrow-down-up-across-line", - "fontawesome/solid/arrow-down-up-lock", - "fontawesome/solid/arrow-down-wide-short", - "fontawesome/solid/arrow-down-z-a", - "fontawesome/solid/arrow-down", - "fontawesome/solid/arrow-left-long", - "fontawesome/solid/arrow-left", - "fontawesome/solid/arrow-pointer", - "fontawesome/solid/arrow-right-arrow-left", - "fontawesome/solid/arrow-right-from-bracket", - "fontawesome/solid/arrow-right-long", - "fontawesome/solid/arrow-right-to-bracket", - "fontawesome/solid/arrow-right-to-city", - "fontawesome/solid/arrow-right", - "fontawesome/solid/arrow-rotate-left", - "fontawesome/solid/arrow-rotate-right", - "fontawesome/solid/arrow-trend-down", - "fontawesome/solid/arrow-trend-up", - "fontawesome/solid/arrow-turn-down", - "fontawesome/solid/arrow-turn-up", - "fontawesome/solid/arrow-up-1-9", - "fontawesome/solid/arrow-up-9-1", - "fontawesome/solid/arrow-up-a-z", - "fontawesome/solid/arrow-up-from-bracket", - "fontawesome/solid/arrow-up-from-ground-water", - "fontawesome/solid/arrow-up-from-water-pump", - "fontawesome/solid/arrow-up-long", - "fontawesome/solid/arrow-up-right-dots", - "fontawesome/solid/arrow-up-right-from-square", - "fontawesome/solid/arrow-up-short-wide", - "fontawesome/solid/arrow-up-wide-short", - "fontawesome/solid/arrow-up-z-a", - "fontawesome/solid/arrow-up", - "fontawesome/solid/arrows-down-to-line", - "fontawesome/solid/arrows-down-to-people", - "fontawesome/solid/arrows-left-right-to-line", - "fontawesome/solid/arrows-left-right", - "fontawesome/solid/arrows-rotate", - "fontawesome/solid/arrows-spin", - "fontawesome/solid/arrows-split-up-and-left", - "fontawesome/solid/arrows-to-circle", - "fontawesome/solid/arrows-to-dot", - "fontawesome/solid/arrows-to-eye", - "fontawesome/solid/arrows-turn-right", - "fontawesome/solid/arrows-turn-to-dots", - "fontawesome/solid/arrows-up-down-left-right", - "fontawesome/solid/arrows-up-down", - "fontawesome/solid/arrows-up-to-line", - "fontawesome/solid/asterisk", - "fontawesome/solid/at", - "fontawesome/solid/atom", - "fontawesome/solid/audio-description", - "fontawesome/solid/austral-sign", - "fontawesome/solid/award", - "fontawesome/solid/b", - "fontawesome/solid/baby-carriage", - "fontawesome/solid/baby", - "fontawesome/solid/backward-fast", - "fontawesome/solid/backward-step", - "fontawesome/solid/backward", - "fontawesome/solid/bacon", - "fontawesome/solid/bacteria", - "fontawesome/solid/bacterium", - "fontawesome/solid/bag-shopping", - "fontawesome/solid/bahai", - "fontawesome/solid/baht-sign", - "fontawesome/solid/ban-smoking", - "fontawesome/solid/ban", - "fontawesome/solid/bandage", - "fontawesome/solid/barcode", - "fontawesome/solid/bars-progress", - "fontawesome/solid/bars-staggered", - "fontawesome/solid/bars", - "fontawesome/solid/baseball-bat-ball", - "fontawesome/solid/baseball", - "fontawesome/solid/basket-shopping", - "fontawesome/solid/basketball", - "fontawesome/solid/bath", - "fontawesome/solid/battery-empty", - "fontawesome/solid/battery-full", - "fontawesome/solid/battery-half", - "fontawesome/solid/battery-quarter", - "fontawesome/solid/battery-three-quarters", - "fontawesome/solid/bed-pulse", - "fontawesome/solid/bed", - "fontawesome/solid/beer-mug-empty", - "fontawesome/solid/bell-concierge", - "fontawesome/solid/bell-slash", - "fontawesome/solid/bell", - "fontawesome/solid/bezier-curve", - "fontawesome/solid/bicycle", - "fontawesome/solid/binoculars", - "fontawesome/solid/biohazard", - "fontawesome/solid/bitcoin-sign", - "fontawesome/solid/blender-phone", - "fontawesome/solid/blender", - "fontawesome/solid/blog", - "fontawesome/solid/bold", - "fontawesome/solid/bolt-lightning", - "fontawesome/solid/bolt", - "fontawesome/solid/bomb", - "fontawesome/solid/bone", - "fontawesome/solid/bong", - "fontawesome/solid/book-atlas", - "fontawesome/solid/book-bible", - "fontawesome/solid/book-bookmark", - "fontawesome/solid/book-journal-whills", - "fontawesome/solid/book-medical", - "fontawesome/solid/book-open-reader", - "fontawesome/solid/book-open", - "fontawesome/solid/book-quran", - "fontawesome/solid/book-skull", - "fontawesome/solid/book-tanakh", - "fontawesome/solid/book", - "fontawesome/solid/bookmark", - "fontawesome/solid/border-all", - "fontawesome/solid/border-none", - "fontawesome/solid/border-top-left", - "fontawesome/solid/bore-hole", - "fontawesome/solid/bottle-droplet", - "fontawesome/solid/bottle-water", - "fontawesome/solid/bowl-food", - "fontawesome/solid/bowl-rice", - "fontawesome/solid/bowling-ball", - "fontawesome/solid/box-archive", - "fontawesome/solid/box-open", - "fontawesome/solid/box-tissue", - "fontawesome/solid/box", - "fontawesome/solid/boxes-packing", - "fontawesome/solid/boxes-stacked", - "fontawesome/solid/braille", - "fontawesome/solid/brain", - "fontawesome/solid/brazilian-real-sign", - "fontawesome/solid/bread-slice", - "fontawesome/solid/bridge-circle-check", - "fontawesome/solid/bridge-circle-exclamation", - "fontawesome/solid/bridge-circle-xmark", - "fontawesome/solid/bridge-lock", - "fontawesome/solid/bridge-water", - "fontawesome/solid/bridge", - "fontawesome/solid/briefcase-medical", - "fontawesome/solid/briefcase", - "fontawesome/solid/broom-ball", - "fontawesome/solid/broom", - "fontawesome/solid/brush", - "fontawesome/solid/bucket", - "fontawesome/solid/bug-slash", - "fontawesome/solid/bug", - "fontawesome/solid/bugs", - "fontawesome/solid/building-circle-arrow-right", - "fontawesome/solid/building-circle-check", - "fontawesome/solid/building-circle-exclamation", - "fontawesome/solid/building-circle-xmark", - "fontawesome/solid/building-columns", - "fontawesome/solid/building-flag", - "fontawesome/solid/building-lock", - "fontawesome/solid/building-ngo", - "fontawesome/solid/building-shield", - "fontawesome/solid/building-un", - "fontawesome/solid/building-user", - "fontawesome/solid/building-wheat", - "fontawesome/solid/building", - "fontawesome/solid/bullhorn", - "fontawesome/solid/bullseye", - "fontawesome/solid/burger", - "fontawesome/solid/burst", - "fontawesome/solid/bus-simple", - "fontawesome/solid/bus", - "fontawesome/solid/business-time", - "fontawesome/solid/c", - "fontawesome/solid/cable-car", - "fontawesome/solid/cake-candles", - "fontawesome/solid/calculator", - "fontawesome/solid/calendar-check", - "fontawesome/solid/calendar-day", - "fontawesome/solid/calendar-days", - "fontawesome/solid/calendar-minus", - "fontawesome/solid/calendar-plus", - "fontawesome/solid/calendar-week", - "fontawesome/solid/calendar-xmark", - "fontawesome/solid/calendar", - "fontawesome/solid/camera-retro", - "fontawesome/solid/camera-rotate", - "fontawesome/solid/camera", - "fontawesome/solid/campground", - "fontawesome/solid/candy-cane", - "fontawesome/solid/cannabis", - "fontawesome/solid/capsules", - "fontawesome/solid/car-battery", - "fontawesome/solid/car-burst", - "fontawesome/solid/car-on", - "fontawesome/solid/car-rear", - "fontawesome/solid/car-side", - "fontawesome/solid/car-tunnel", - "fontawesome/solid/car", - "fontawesome/solid/caravan", - "fontawesome/solid/caret-down", - "fontawesome/solid/caret-left", - "fontawesome/solid/caret-right", - "fontawesome/solid/caret-up", - "fontawesome/solid/carrot", - "fontawesome/solid/cart-arrow-down", - "fontawesome/solid/cart-flatbed-suitcase", - "fontawesome/solid/cart-flatbed", - "fontawesome/solid/cart-plus", - "fontawesome/solid/cart-shopping", - "fontawesome/solid/cash-register", - "fontawesome/solid/cat", - "fontawesome/solid/cedi-sign", - "fontawesome/solid/cent-sign", - "fontawesome/solid/certificate", - "fontawesome/solid/chair", - "fontawesome/solid/chalkboard-user", - "fontawesome/solid/chalkboard", - "fontawesome/solid/champagne-glasses", - "fontawesome/solid/charging-station", - "fontawesome/solid/chart-area", - "fontawesome/solid/chart-bar", - "fontawesome/solid/chart-column", - "fontawesome/solid/chart-gantt", - "fontawesome/solid/chart-line", - "fontawesome/solid/chart-pie", - "fontawesome/solid/chart-simple", - "fontawesome/solid/check-double", - "fontawesome/solid/check-to-slot", - "fontawesome/solid/check", - "fontawesome/solid/cheese", - "fontawesome/solid/chess-bishop", - "fontawesome/solid/chess-board", - "fontawesome/solid/chess-king", - "fontawesome/solid/chess-knight", - "fontawesome/solid/chess-pawn", - "fontawesome/solid/chess-queen", - "fontawesome/solid/chess-rook", - "fontawesome/solid/chess", - "fontawesome/solid/chevron-down", - "fontawesome/solid/chevron-left", - "fontawesome/solid/chevron-right", - "fontawesome/solid/chevron-up", - "fontawesome/solid/child-dress", - "fontawesome/solid/child-reaching", - "fontawesome/solid/child-rifle", - "fontawesome/solid/child", - "fontawesome/solid/children", - "fontawesome/solid/church", - "fontawesome/solid/circle-arrow-down", - "fontawesome/solid/circle-arrow-left", - "fontawesome/solid/circle-arrow-right", - "fontawesome/solid/circle-arrow-up", - "fontawesome/solid/circle-check", - "fontawesome/solid/circle-chevron-down", - "fontawesome/solid/circle-chevron-left", - "fontawesome/solid/circle-chevron-right", - "fontawesome/solid/circle-chevron-up", - "fontawesome/solid/circle-dollar-to-slot", - "fontawesome/solid/circle-dot", - "fontawesome/solid/circle-down", - "fontawesome/solid/circle-exclamation", - "fontawesome/solid/circle-h", - "fontawesome/solid/circle-half-stroke", - "fontawesome/solid/circle-info", - "fontawesome/solid/circle-left", - "fontawesome/solid/circle-minus", - "fontawesome/solid/circle-nodes", - "fontawesome/solid/circle-notch", - "fontawesome/solid/circle-pause", - "fontawesome/solid/circle-play", - "fontawesome/solid/circle-plus", - "fontawesome/solid/circle-question", - "fontawesome/solid/circle-radiation", - "fontawesome/solid/circle-right", - "fontawesome/solid/circle-stop", - "fontawesome/solid/circle-up", - "fontawesome/solid/circle-user", - "fontawesome/solid/circle-xmark", - "fontawesome/solid/circle", - "fontawesome/solid/city", - "fontawesome/solid/clapperboard", - "fontawesome/solid/clipboard-check", - "fontawesome/solid/clipboard-list", - "fontawesome/solid/clipboard-question", - "fontawesome/solid/clipboard-user", - "fontawesome/solid/clipboard", - "fontawesome/solid/clock-rotate-left", - "fontawesome/solid/clock", - "fontawesome/solid/clone", - "fontawesome/solid/closed-captioning", - "fontawesome/solid/cloud-arrow-down", - "fontawesome/solid/cloud-arrow-up", - "fontawesome/solid/cloud-bolt", - "fontawesome/solid/cloud-meatball", - "fontawesome/solid/cloud-moon-rain", - "fontawesome/solid/cloud-moon", - "fontawesome/solid/cloud-rain", - "fontawesome/solid/cloud-showers-heavy", - "fontawesome/solid/cloud-showers-water", - "fontawesome/solid/cloud-sun-rain", - "fontawesome/solid/cloud-sun", - "fontawesome/solid/cloud", - "fontawesome/solid/clover", - "fontawesome/solid/code-branch", - "fontawesome/solid/code-commit", - "fontawesome/solid/code-compare", - "fontawesome/solid/code-fork", - "fontawesome/solid/code-merge", - "fontawesome/solid/code-pull-request", - "fontawesome/solid/code", - "fontawesome/solid/coins", - "fontawesome/solid/colon-sign", - "fontawesome/solid/comment-dollar", - "fontawesome/solid/comment-dots", - "fontawesome/solid/comment-medical", - "fontawesome/solid/comment-slash", - "fontawesome/solid/comment-sms", - "fontawesome/solid/comment", - "fontawesome/solid/comments-dollar", - "fontawesome/solid/comments", - "fontawesome/solid/compact-disc", - "fontawesome/solid/compass-drafting", - "fontawesome/solid/compass", - "fontawesome/solid/compress", - "fontawesome/solid/computer-mouse", - "fontawesome/solid/computer", - "fontawesome/solid/cookie-bite", - "fontawesome/solid/cookie", - "fontawesome/solid/copy", - "fontawesome/solid/copyright", - "fontawesome/solid/couch", - "fontawesome/solid/cow", - "fontawesome/solid/credit-card", - "fontawesome/solid/crop-simple", - "fontawesome/solid/crop", - "fontawesome/solid/cross", - "fontawesome/solid/crosshairs", - "fontawesome/solid/crow", - "fontawesome/solid/crown", - "fontawesome/solid/crutch", - "fontawesome/solid/cruzeiro-sign", - "fontawesome/solid/cube", - "fontawesome/solid/cubes-stacked", - "fontawesome/solid/cubes", - "fontawesome/solid/d", - "fontawesome/solid/database", - "fontawesome/solid/delete-left", - "fontawesome/solid/democrat", - "fontawesome/solid/desktop", - "fontawesome/solid/dharmachakra", - "fontawesome/solid/diagram-next", - "fontawesome/solid/diagram-predecessor", - "fontawesome/solid/diagram-project", - "fontawesome/solid/diagram-successor", - "fontawesome/solid/diamond-turn-right", - "fontawesome/solid/diamond", - "fontawesome/solid/dice-d20", - "fontawesome/solid/dice-d6", - "fontawesome/solid/dice-five", - "fontawesome/solid/dice-four", - "fontawesome/solid/dice-one", - "fontawesome/solid/dice-six", - "fontawesome/solid/dice-three", - "fontawesome/solid/dice-two", - "fontawesome/solid/dice", - "fontawesome/solid/disease", - "fontawesome/solid/display", - "fontawesome/solid/divide", - "fontawesome/solid/dna", - "fontawesome/solid/dog", - "fontawesome/solid/dollar-sign", - "fontawesome/solid/dolly", - "fontawesome/solid/dong-sign", - "fontawesome/solid/door-closed", - "fontawesome/solid/door-open", - "fontawesome/solid/dove", - "fontawesome/solid/down-left-and-up-right-to-center", - "fontawesome/solid/down-long", - "fontawesome/solid/download", - "fontawesome/solid/dragon", - "fontawesome/solid/draw-polygon", - "fontawesome/solid/droplet-slash", - "fontawesome/solid/droplet", - "fontawesome/solid/drum-steelpan", - "fontawesome/solid/drum", - "fontawesome/solid/drumstick-bite", - "fontawesome/solid/dumbbell", - "fontawesome/solid/dumpster-fire", - "fontawesome/solid/dumpster", - "fontawesome/solid/dungeon", - "fontawesome/solid/e", - "fontawesome/solid/ear-deaf", - "fontawesome/solid/ear-listen", - "fontawesome/solid/earth-africa", - "fontawesome/solid/earth-americas", - "fontawesome/solid/earth-asia", - "fontawesome/solid/earth-europe", - "fontawesome/solid/earth-oceania", - "fontawesome/solid/egg", - "fontawesome/solid/eject", - "fontawesome/solid/elevator", - "fontawesome/solid/ellipsis-vertical", - "fontawesome/solid/ellipsis", - "fontawesome/solid/envelope-circle-check", - "fontawesome/solid/envelope-open-text", - "fontawesome/solid/envelope-open", - "fontawesome/solid/envelope", - "fontawesome/solid/envelopes-bulk", - "fontawesome/solid/equals", - "fontawesome/solid/eraser", - "fontawesome/solid/ethernet", - "fontawesome/solid/euro-sign", - "fontawesome/solid/exclamation", - "fontawesome/solid/expand", - "fontawesome/solid/explosion", - "fontawesome/solid/eye-dropper", - "fontawesome/solid/eye-low-vision", - "fontawesome/solid/eye-slash", - "fontawesome/solid/eye", - "fontawesome/solid/f", - "fontawesome/solid/face-angry", - "fontawesome/solid/face-dizzy", - "fontawesome/solid/face-flushed", - "fontawesome/solid/face-frown-open", - "fontawesome/solid/face-frown", - "fontawesome/solid/face-grimace", - "fontawesome/solid/face-grin-beam-sweat", - "fontawesome/solid/face-grin-beam", - "fontawesome/solid/face-grin-hearts", - "fontawesome/solid/face-grin-squint-tears", - "fontawesome/solid/face-grin-squint", - "fontawesome/solid/face-grin-stars", - "fontawesome/solid/face-grin-tears", - "fontawesome/solid/face-grin-tongue-squint", - "fontawesome/solid/face-grin-tongue-wink", - "fontawesome/solid/face-grin-tongue", - "fontawesome/solid/face-grin-wide", - "fontawesome/solid/face-grin-wink", - "fontawesome/solid/face-grin", - "fontawesome/solid/face-kiss-beam", - "fontawesome/solid/face-kiss-wink-heart", - "fontawesome/solid/face-kiss", - "fontawesome/solid/face-laugh-beam", - "fontawesome/solid/face-laugh-squint", - "fontawesome/solid/face-laugh-wink", - "fontawesome/solid/face-laugh", - "fontawesome/solid/face-meh-blank", - "fontawesome/solid/face-meh", - "fontawesome/solid/face-rolling-eyes", - "fontawesome/solid/face-sad-cry", - "fontawesome/solid/face-sad-tear", - "fontawesome/solid/face-smile-beam", - "fontawesome/solid/face-smile-wink", - "fontawesome/solid/face-smile", - "fontawesome/solid/face-surprise", - "fontawesome/solid/face-tired", - "fontawesome/solid/fan", - "fontawesome/solid/faucet-drip", - "fontawesome/solid/faucet", - "fontawesome/solid/fax", - "fontawesome/solid/feather-pointed", - "fontawesome/solid/feather", - "fontawesome/solid/ferry", - "fontawesome/solid/file-arrow-down", - "fontawesome/solid/file-arrow-up", - "fontawesome/solid/file-audio", - "fontawesome/solid/file-circle-check", - "fontawesome/solid/file-circle-exclamation", - "fontawesome/solid/file-circle-minus", - "fontawesome/solid/file-circle-plus", - "fontawesome/solid/file-circle-question", - "fontawesome/solid/file-circle-xmark", - "fontawesome/solid/file-code", - "fontawesome/solid/file-contract", - "fontawesome/solid/file-csv", - "fontawesome/solid/file-excel", - "fontawesome/solid/file-export", - "fontawesome/solid/file-image", - "fontawesome/solid/file-import", - "fontawesome/solid/file-invoice-dollar", - "fontawesome/solid/file-invoice", - "fontawesome/solid/file-lines", - "fontawesome/solid/file-medical", - "fontawesome/solid/file-pdf", - "fontawesome/solid/file-pen", - "fontawesome/solid/file-powerpoint", - "fontawesome/solid/file-prescription", - "fontawesome/solid/file-shield", - "fontawesome/solid/file-signature", - "fontawesome/solid/file-video", - "fontawesome/solid/file-waveform", - "fontawesome/solid/file-word", - "fontawesome/solid/file-zipper", - "fontawesome/solid/file", - "fontawesome/solid/fill-drip", - "fontawesome/solid/fill", - "fontawesome/solid/film", - "fontawesome/solid/filter-circle-dollar", - "fontawesome/solid/filter-circle-xmark", - "fontawesome/solid/filter", - "fontawesome/solid/fingerprint", - "fontawesome/solid/fire-burner", - "fontawesome/solid/fire-extinguisher", - "fontawesome/solid/fire-flame-curved", - "fontawesome/solid/fire-flame-simple", - "fontawesome/solid/fire", - "fontawesome/solid/fish-fins", - "fontawesome/solid/fish", - "fontawesome/solid/flag-checkered", - "fontawesome/solid/flag-usa", - "fontawesome/solid/flag", - "fontawesome/solid/flask-vial", - "fontawesome/solid/flask", - "fontawesome/solid/floppy-disk", - "fontawesome/solid/florin-sign", - "fontawesome/solid/folder-closed", - "fontawesome/solid/folder-minus", - "fontawesome/solid/folder-open", - "fontawesome/solid/folder-plus", - "fontawesome/solid/folder-tree", - "fontawesome/solid/folder", - "fontawesome/solid/font-awesome", - "fontawesome/solid/font", - "fontawesome/solid/football", - "fontawesome/solid/forward-fast", - "fontawesome/solid/forward-step", - "fontawesome/solid/forward", - "fontawesome/solid/franc-sign", - "fontawesome/solid/frog", - "fontawesome/solid/futbol", - "fontawesome/solid/g", - "fontawesome/solid/gamepad", - "fontawesome/solid/gas-pump", - "fontawesome/solid/gauge-high", - "fontawesome/solid/gauge-simple-high", - "fontawesome/solid/gauge-simple", - "fontawesome/solid/gauge", - "fontawesome/solid/gavel", - "fontawesome/solid/gear", - "fontawesome/solid/gears", - "fontawesome/solid/gem", - "fontawesome/solid/genderless", - "fontawesome/solid/ghost", - "fontawesome/solid/gift", - "fontawesome/solid/gifts", - "fontawesome/solid/glass-water-droplet", - "fontawesome/solid/glass-water", - "fontawesome/solid/glasses", - "fontawesome/solid/globe", - "fontawesome/solid/golf-ball-tee", - "fontawesome/solid/gopuram", - "fontawesome/solid/graduation-cap", - "fontawesome/solid/greater-than-equal", - "fontawesome/solid/greater-than", - "fontawesome/solid/grip-lines-vertical", - "fontawesome/solid/grip-lines", - "fontawesome/solid/grip-vertical", - "fontawesome/solid/grip", - "fontawesome/solid/group-arrows-rotate", - "fontawesome/solid/guarani-sign", - "fontawesome/solid/guitar", - "fontawesome/solid/gun", - "fontawesome/solid/h", - "fontawesome/solid/hammer", - "fontawesome/solid/hamsa", - "fontawesome/solid/hand-back-fist", - "fontawesome/solid/hand-dots", - "fontawesome/solid/hand-fist", - "fontawesome/solid/hand-holding-dollar", - "fontawesome/solid/hand-holding-droplet", - "fontawesome/solid/hand-holding-hand", - "fontawesome/solid/hand-holding-heart", - "fontawesome/solid/hand-holding-medical", - "fontawesome/solid/hand-holding", - "fontawesome/solid/hand-lizard", - "fontawesome/solid/hand-middle-finger", - "fontawesome/solid/hand-peace", - "fontawesome/solid/hand-point-down", - "fontawesome/solid/hand-point-left", - "fontawesome/solid/hand-point-right", - "fontawesome/solid/hand-point-up", - "fontawesome/solid/hand-pointer", - "fontawesome/solid/hand-scissors", - "fontawesome/solid/hand-sparkles", - "fontawesome/solid/hand-spock", - "fontawesome/solid/hand", - "fontawesome/solid/handcuffs", - "fontawesome/solid/hands-asl-interpreting", - "fontawesome/solid/hands-bound", - "fontawesome/solid/hands-bubbles", - "fontawesome/solid/hands-clapping", - "fontawesome/solid/hands-holding-child", - "fontawesome/solid/hands-holding-circle", - "fontawesome/solid/hands-holding", - "fontawesome/solid/hands-praying", - "fontawesome/solid/hands", - "fontawesome/solid/handshake-angle", - "fontawesome/solid/handshake-simple-slash", - "fontawesome/solid/handshake-simple", - "fontawesome/solid/handshake-slash", - "fontawesome/solid/handshake", - "fontawesome/solid/hanukiah", - "fontawesome/solid/hard-drive", - "fontawesome/solid/hashtag", - "fontawesome/solid/hat-cowboy-side", - "fontawesome/solid/hat-cowboy", - "fontawesome/solid/hat-wizard", - "fontawesome/solid/head-side-cough-slash", - "fontawesome/solid/head-side-cough", - "fontawesome/solid/head-side-mask", - "fontawesome/solid/head-side-virus", - "fontawesome/solid/heading", - "fontawesome/solid/headphones-simple", - "fontawesome/solid/headphones", - "fontawesome/solid/headset", - "fontawesome/solid/heart-circle-bolt", - "fontawesome/solid/heart-circle-check", - "fontawesome/solid/heart-circle-exclamation", - "fontawesome/solid/heart-circle-minus", - "fontawesome/solid/heart-circle-plus", - "fontawesome/solid/heart-circle-xmark", - "fontawesome/solid/heart-crack", - "fontawesome/solid/heart-pulse", - "fontawesome/solid/heart", - "fontawesome/solid/helicopter-symbol", - "fontawesome/solid/helicopter", - "fontawesome/solid/helmet-safety", - "fontawesome/solid/helmet-un", - "fontawesome/solid/highlighter", - "fontawesome/solid/hill-avalanche", - "fontawesome/solid/hill-rockslide", - "fontawesome/solid/hippo", - "fontawesome/solid/hockey-puck", - "fontawesome/solid/holly-berry", - "fontawesome/solid/horse-head", - "fontawesome/solid/horse", - "fontawesome/solid/hospital-user", - "fontawesome/solid/hospital", - "fontawesome/solid/hot-tub-person", - "fontawesome/solid/hotdog", - "fontawesome/solid/hotel", - "fontawesome/solid/hourglass-end", - "fontawesome/solid/hourglass-half", - "fontawesome/solid/hourglass-start", - "fontawesome/solid/hourglass", - "fontawesome/solid/house-chimney-crack", - "fontawesome/solid/house-chimney-medical", - "fontawesome/solid/house-chimney-user", - "fontawesome/solid/house-chimney-window", - "fontawesome/solid/house-chimney", - "fontawesome/solid/house-circle-check", - "fontawesome/solid/house-circle-exclamation", - "fontawesome/solid/house-circle-xmark", - "fontawesome/solid/house-crack", - "fontawesome/solid/house-fire", - "fontawesome/solid/house-flag", - "fontawesome/solid/house-flood-water-circle-arrow-right", - "fontawesome/solid/house-flood-water", - "fontawesome/solid/house-laptop", - "fontawesome/solid/house-lock", - "fontawesome/solid/house-medical-circle-check", - "fontawesome/solid/house-medical-circle-exclamation", - "fontawesome/solid/house-medical-circle-xmark", - "fontawesome/solid/house-medical-flag", - "fontawesome/solid/house-medical", - "fontawesome/solid/house-signal", - "fontawesome/solid/house-tsunami", - "fontawesome/solid/house-user", - "fontawesome/solid/house", - "fontawesome/solid/hryvnia-sign", - "fontawesome/solid/hurricane", - "fontawesome/solid/i-cursor", - "fontawesome/solid/i", - "fontawesome/solid/ice-cream", - "fontawesome/solid/icicles", - "fontawesome/solid/icons", - "fontawesome/solid/id-badge", - "fontawesome/solid/id-card-clip", - "fontawesome/solid/id-card", - "fontawesome/solid/igloo", - "fontawesome/solid/image-portrait", - "fontawesome/solid/image", - "fontawesome/solid/images", - "fontawesome/solid/inbox", - "fontawesome/solid/indent", - "fontawesome/solid/indian-rupee-sign", - "fontawesome/solid/industry", - "fontawesome/solid/infinity", - "fontawesome/solid/info", - "fontawesome/solid/italic", - "fontawesome/solid/j", - "fontawesome/solid/jar-wheat", - "fontawesome/solid/jar", - "fontawesome/solid/jedi", - "fontawesome/solid/jet-fighter-up", - "fontawesome/solid/jet-fighter", - "fontawesome/solid/joint", - "fontawesome/solid/jug-detergent", - "fontawesome/solid/k", - "fontawesome/solid/kaaba", - "fontawesome/solid/key", - "fontawesome/solid/keyboard", - "fontawesome/solid/khanda", - "fontawesome/solid/kip-sign", - "fontawesome/solid/kit-medical", - "fontawesome/solid/kitchen-set", - "fontawesome/solid/kiwi-bird", - "fontawesome/solid/l", - "fontawesome/solid/land-mine-on", - "fontawesome/solid/landmark-dome", - "fontawesome/solid/landmark-flag", - "fontawesome/solid/landmark", - "fontawesome/solid/language", - "fontawesome/solid/laptop-code", - "fontawesome/solid/laptop-file", - "fontawesome/solid/laptop-medical", - "fontawesome/solid/laptop", - "fontawesome/solid/lari-sign", - "fontawesome/solid/layer-group", - "fontawesome/solid/leaf", - "fontawesome/solid/left-long", - "fontawesome/solid/left-right", - "fontawesome/solid/lemon", - "fontawesome/solid/less-than-equal", - "fontawesome/solid/less-than", - "fontawesome/solid/life-ring", - "fontawesome/solid/lightbulb", - "fontawesome/solid/lines-leaning", - "fontawesome/solid/link-slash", - "fontawesome/solid/link", - "fontawesome/solid/lira-sign", - "fontawesome/solid/list-check", - "fontawesome/solid/list-ol", - "fontawesome/solid/list-ul", - "fontawesome/solid/list", - "fontawesome/solid/litecoin-sign", - "fontawesome/solid/location-arrow", - "fontawesome/solid/location-crosshairs", - "fontawesome/solid/location-dot", - "fontawesome/solid/location-pin-lock", - "fontawesome/solid/location-pin", - "fontawesome/solid/lock-open", - "fontawesome/solid/lock", - "fontawesome/solid/locust", - "fontawesome/solid/lungs-virus", - "fontawesome/solid/lungs", - "fontawesome/solid/m", - "fontawesome/solid/magnet", - "fontawesome/solid/magnifying-glass-arrow-right", - "fontawesome/solid/magnifying-glass-chart", - "fontawesome/solid/magnifying-glass-dollar", - "fontawesome/solid/magnifying-glass-location", - "fontawesome/solid/magnifying-glass-minus", - "fontawesome/solid/magnifying-glass-plus", - "fontawesome/solid/magnifying-glass", - "fontawesome/solid/manat-sign", - "fontawesome/solid/map-location-dot", - "fontawesome/solid/map-location", - "fontawesome/solid/map-pin", - "fontawesome/solid/map", - "fontawesome/solid/marker", - "fontawesome/solid/mars-and-venus-burst", - "fontawesome/solid/mars-and-venus", - "fontawesome/solid/mars-double", - "fontawesome/solid/mars-stroke-right", - "fontawesome/solid/mars-stroke-up", - "fontawesome/solid/mars-stroke", - "fontawesome/solid/mars", - "fontawesome/solid/martini-glass-citrus", - "fontawesome/solid/martini-glass-empty", - "fontawesome/solid/martini-glass", - "fontawesome/solid/mask-face", - "fontawesome/solid/mask-ventilator", - "fontawesome/solid/mask", - "fontawesome/solid/masks-theater", - "fontawesome/solid/mattress-pillow", - "fontawesome/solid/maximize", - "fontawesome/solid/medal", - "fontawesome/solid/memory", - "fontawesome/solid/menorah", - "fontawesome/solid/mercury", - "fontawesome/solid/message", - "fontawesome/solid/meteor", - "fontawesome/solid/microchip", - "fontawesome/solid/microphone-lines-slash", - "fontawesome/solid/microphone-lines", - "fontawesome/solid/microphone-slash", - "fontawesome/solid/microphone", - "fontawesome/solid/microscope", - "fontawesome/solid/mill-sign", - "fontawesome/solid/minimize", - "fontawesome/solid/minus", - "fontawesome/solid/mitten", - "fontawesome/solid/mobile-button", - "fontawesome/solid/mobile-retro", - "fontawesome/solid/mobile-screen-button", - "fontawesome/solid/mobile-screen", - "fontawesome/solid/mobile", - "fontawesome/solid/money-bill-1-wave", - "fontawesome/solid/money-bill-1", - "fontawesome/solid/money-bill-transfer", - "fontawesome/solid/money-bill-trend-up", - "fontawesome/solid/money-bill-wave", - "fontawesome/solid/money-bill-wheat", - "fontawesome/solid/money-bill", - "fontawesome/solid/money-bills", - "fontawesome/solid/money-check-dollar", - "fontawesome/solid/money-check", - "fontawesome/solid/monument", - "fontawesome/solid/moon", - "fontawesome/solid/mortar-pestle", - "fontawesome/solid/mosque", - "fontawesome/solid/mosquito-net", - "fontawesome/solid/mosquito", - "fontawesome/solid/motorcycle", - "fontawesome/solid/mound", - "fontawesome/solid/mountain-city", - "fontawesome/solid/mountain-sun", - "fontawesome/solid/mountain", - "fontawesome/solid/mug-hot", - "fontawesome/solid/mug-saucer", - "fontawesome/solid/music", - "fontawesome/solid/n", - "fontawesome/solid/naira-sign", - "fontawesome/solid/network-wired", - "fontawesome/solid/neuter", - "fontawesome/solid/newspaper", - "fontawesome/solid/not-equal", - "fontawesome/solid/notdef", - "fontawesome/solid/note-sticky", - "fontawesome/solid/notes-medical", - "fontawesome/solid/o", - "fontawesome/solid/object-group", - "fontawesome/solid/object-ungroup", - "fontawesome/solid/oil-can", - "fontawesome/solid/oil-well", - "fontawesome/solid/om", - "fontawesome/solid/otter", - "fontawesome/solid/outdent", - "fontawesome/solid/p", - "fontawesome/solid/pager", - "fontawesome/solid/paint-roller", - "fontawesome/solid/paintbrush", - "fontawesome/solid/palette", - "fontawesome/solid/pallet", - "fontawesome/solid/panorama", - "fontawesome/solid/paper-plane", - "fontawesome/solid/paperclip", - "fontawesome/solid/parachute-box", - "fontawesome/solid/paragraph", - "fontawesome/solid/passport", - "fontawesome/solid/paste", - "fontawesome/solid/pause", - "fontawesome/solid/paw", - "fontawesome/solid/peace", - "fontawesome/solid/pen-clip", - "fontawesome/solid/pen-fancy", - "fontawesome/solid/pen-nib", - "fontawesome/solid/pen-ruler", - "fontawesome/solid/pen-to-square", - "fontawesome/solid/pen", - "fontawesome/solid/pencil", - "fontawesome/solid/people-arrows", - "fontawesome/solid/people-carry-box", - "fontawesome/solid/people-group", - "fontawesome/solid/people-line", - "fontawesome/solid/people-pulling", - "fontawesome/solid/people-robbery", - "fontawesome/solid/people-roof", - "fontawesome/solid/pepper-hot", - "fontawesome/solid/percent", - "fontawesome/solid/person-arrow-down-to-line", - "fontawesome/solid/person-arrow-up-from-line", - "fontawesome/solid/person-biking", - "fontawesome/solid/person-booth", - "fontawesome/solid/person-breastfeeding", - "fontawesome/solid/person-burst", - "fontawesome/solid/person-cane", - "fontawesome/solid/person-chalkboard", - "fontawesome/solid/person-circle-check", - "fontawesome/solid/person-circle-exclamation", - "fontawesome/solid/person-circle-minus", - "fontawesome/solid/person-circle-plus", - "fontawesome/solid/person-circle-question", - "fontawesome/solid/person-circle-xmark", - "fontawesome/solid/person-digging", - "fontawesome/solid/person-dots-from-line", - "fontawesome/solid/person-dress-burst", - "fontawesome/solid/person-dress", - "fontawesome/solid/person-drowning", - "fontawesome/solid/person-falling-burst", - "fontawesome/solid/person-falling", - "fontawesome/solid/person-half-dress", - "fontawesome/solid/person-harassing", - "fontawesome/solid/person-hiking", - "fontawesome/solid/person-military-pointing", - "fontawesome/solid/person-military-rifle", - "fontawesome/solid/person-military-to-person", - "fontawesome/solid/person-praying", - "fontawesome/solid/person-pregnant", - "fontawesome/solid/person-rays", - "fontawesome/solid/person-rifle", - "fontawesome/solid/person-running", - "fontawesome/solid/person-shelter", - "fontawesome/solid/person-skating", - "fontawesome/solid/person-skiing-nordic", - "fontawesome/solid/person-skiing", - "fontawesome/solid/person-snowboarding", - "fontawesome/solid/person-swimming", - "fontawesome/solid/person-through-window", - "fontawesome/solid/person-walking-arrow-loop-left", - "fontawesome/solid/person-walking-arrow-right", - "fontawesome/solid/person-walking-dashed-line-arrow-right", - "fontawesome/solid/person-walking-luggage", - "fontawesome/solid/person-walking-with-cane", - "fontawesome/solid/person-walking", - "fontawesome/solid/person", - "fontawesome/solid/peseta-sign", - "fontawesome/solid/peso-sign", - "fontawesome/solid/phone-flip", - "fontawesome/solid/phone-slash", - "fontawesome/solid/phone-volume", - "fontawesome/solid/phone", - "fontawesome/solid/photo-film", - "fontawesome/solid/piggy-bank", - "fontawesome/solid/pills", - "fontawesome/solid/pizza-slice", - "fontawesome/solid/place-of-worship", - "fontawesome/solid/plane-arrival", - "fontawesome/solid/plane-circle-check", - "fontawesome/solid/plane-circle-exclamation", - "fontawesome/solid/plane-circle-xmark", - "fontawesome/solid/plane-departure", - "fontawesome/solid/plane-lock", - "fontawesome/solid/plane-slash", - "fontawesome/solid/plane-up", - "fontawesome/solid/plane", - "fontawesome/solid/plant-wilt", - "fontawesome/solid/plate-wheat", - "fontawesome/solid/play", - "fontawesome/solid/plug-circle-bolt", - "fontawesome/solid/plug-circle-check", - "fontawesome/solid/plug-circle-exclamation", - "fontawesome/solid/plug-circle-minus", - "fontawesome/solid/plug-circle-plus", - "fontawesome/solid/plug-circle-xmark", - "fontawesome/solid/plug", - "fontawesome/solid/plus-minus", - "fontawesome/solid/plus", - "fontawesome/solid/podcast", - "fontawesome/solid/poo-storm", - "fontawesome/solid/poo", - "fontawesome/solid/poop", - "fontawesome/solid/power-off", - "fontawesome/solid/prescription-bottle-medical", - "fontawesome/solid/prescription-bottle", - "fontawesome/solid/prescription", - "fontawesome/solid/print", - "fontawesome/solid/pump-medical", - "fontawesome/solid/pump-soap", - "fontawesome/solid/puzzle-piece", - "fontawesome/solid/q", - "fontawesome/solid/qrcode", - "fontawesome/solid/question", - "fontawesome/solid/quote-left", - "fontawesome/solid/quote-right", - "fontawesome/solid/r", - "fontawesome/solid/radiation", - "fontawesome/solid/radio", - "fontawesome/solid/rainbow", - "fontawesome/solid/ranking-star", - "fontawesome/solid/receipt", - "fontawesome/solid/record-vinyl", - "fontawesome/solid/rectangle-ad", - "fontawesome/solid/rectangle-list", - "fontawesome/solid/rectangle-xmark", - "fontawesome/solid/recycle", - "fontawesome/solid/registered", - "fontawesome/solid/repeat", - "fontawesome/solid/reply-all", - "fontawesome/solid/reply", - "fontawesome/solid/republican", - "fontawesome/solid/restroom", - "fontawesome/solid/retweet", - "fontawesome/solid/ribbon", - "fontawesome/solid/right-from-bracket", - "fontawesome/solid/right-left", - "fontawesome/solid/right-long", - "fontawesome/solid/right-to-bracket", - "fontawesome/solid/ring", - "fontawesome/solid/road-barrier", - "fontawesome/solid/road-bridge", - "fontawesome/solid/road-circle-check", - "fontawesome/solid/road-circle-exclamation", - "fontawesome/solid/road-circle-xmark", - "fontawesome/solid/road-lock", - "fontawesome/solid/road-spikes", - "fontawesome/solid/road", - "fontawesome/solid/robot", - "fontawesome/solid/rocket", - "fontawesome/solid/rotate-left", - "fontawesome/solid/rotate-right", - "fontawesome/solid/rotate", - "fontawesome/solid/route", - "fontawesome/solid/rss", - "fontawesome/solid/ruble-sign", - "fontawesome/solid/rug", - "fontawesome/solid/ruler-combined", - "fontawesome/solid/ruler-horizontal", - "fontawesome/solid/ruler-vertical", - "fontawesome/solid/ruler", - "fontawesome/solid/rupee-sign", - "fontawesome/solid/rupiah-sign", - "fontawesome/solid/s", - "fontawesome/solid/sack-dollar", - "fontawesome/solid/sack-xmark", - "fontawesome/solid/sailboat", - "fontawesome/solid/satellite-dish", - "fontawesome/solid/satellite", - "fontawesome/solid/scale-balanced", - "fontawesome/solid/scale-unbalanced-flip", - "fontawesome/solid/scale-unbalanced", - "fontawesome/solid/school-circle-check", - "fontawesome/solid/school-circle-exclamation", - "fontawesome/solid/school-circle-xmark", - "fontawesome/solid/school-flag", - "fontawesome/solid/school-lock", - "fontawesome/solid/school", - "fontawesome/solid/scissors", - "fontawesome/solid/screwdriver-wrench", - "fontawesome/solid/screwdriver", - "fontawesome/solid/scroll-torah", - "fontawesome/solid/scroll", - "fontawesome/solid/sd-card", - "fontawesome/solid/section", - "fontawesome/solid/seedling", - "fontawesome/solid/server", - "fontawesome/solid/shapes", - "fontawesome/solid/share-from-square", - "fontawesome/solid/share-nodes", - "fontawesome/solid/share", - "fontawesome/solid/sheet-plastic", - "fontawesome/solid/shekel-sign", - "fontawesome/solid/shield-cat", - "fontawesome/solid/shield-dog", - "fontawesome/solid/shield-halved", - "fontawesome/solid/shield-heart", - "fontawesome/solid/shield-virus", - "fontawesome/solid/shield", - "fontawesome/solid/ship", - "fontawesome/solid/shirt", - "fontawesome/solid/shoe-prints", - "fontawesome/solid/shop-lock", - "fontawesome/solid/shop-slash", - "fontawesome/solid/shop", - "fontawesome/solid/shower", - "fontawesome/solid/shrimp", - "fontawesome/solid/shuffle", - "fontawesome/solid/shuttle-space", - "fontawesome/solid/sign-hanging", - "fontawesome/solid/signal", - "fontawesome/solid/signature", - "fontawesome/solid/signs-post", - "fontawesome/solid/sim-card", - "fontawesome/solid/sink", - "fontawesome/solid/sitemap", - "fontawesome/solid/skull-crossbones", - "fontawesome/solid/skull", - "fontawesome/solid/slash", - "fontawesome/solid/sleigh", - "fontawesome/solid/sliders", - "fontawesome/solid/smog", - "fontawesome/solid/smoking", - "fontawesome/solid/snowflake", - "fontawesome/solid/snowman", - "fontawesome/solid/snowplow", - "fontawesome/solid/soap", - "fontawesome/solid/socks", - "fontawesome/solid/solar-panel", - "fontawesome/solid/sort-down", - "fontawesome/solid/sort-up", - "fontawesome/solid/sort", - "fontawesome/solid/spa", - "fontawesome/solid/spaghetti-monster-flying", - "fontawesome/solid/spell-check", - "fontawesome/solid/spider", - "fontawesome/solid/spinner", - "fontawesome/solid/splotch", - "fontawesome/solid/spoon", - "fontawesome/solid/spray-can-sparkles", - "fontawesome/solid/spray-can", - "fontawesome/solid/square-arrow-up-right", - "fontawesome/solid/square-caret-down", - "fontawesome/solid/square-caret-left", - "fontawesome/solid/square-caret-right", - "fontawesome/solid/square-caret-up", - "fontawesome/solid/square-check", - "fontawesome/solid/square-envelope", - "fontawesome/solid/square-full", - "fontawesome/solid/square-h", - "fontawesome/solid/square-minus", - "fontawesome/solid/square-nfi", - "fontawesome/solid/square-parking", - "fontawesome/solid/square-pen", - "fontawesome/solid/square-person-confined", - "fontawesome/solid/square-phone-flip", - "fontawesome/solid/square-phone", - "fontawesome/solid/square-plus", - "fontawesome/solid/square-poll-horizontal", - "fontawesome/solid/square-poll-vertical", - "fontawesome/solid/square-root-variable", - "fontawesome/solid/square-rss", - "fontawesome/solid/square-share-nodes", - "fontawesome/solid/square-up-right", - "fontawesome/solid/square-virus", - "fontawesome/solid/square-xmark", - "fontawesome/solid/square", - "fontawesome/solid/staff-snake", - "fontawesome/solid/stairs", - "fontawesome/solid/stamp", - "fontawesome/solid/stapler", - "fontawesome/solid/star-and-crescent", - "fontawesome/solid/star-half-stroke", - "fontawesome/solid/star-half", - "fontawesome/solid/star-of-david", - "fontawesome/solid/star-of-life", - "fontawesome/solid/star", - "fontawesome/solid/sterling-sign", - "fontawesome/solid/stethoscope", - "fontawesome/solid/stop", - "fontawesome/solid/stopwatch-20", - "fontawesome/solid/stopwatch", - "fontawesome/solid/store-slash", - "fontawesome/solid/store", - "fontawesome/solid/street-view", - "fontawesome/solid/strikethrough", - "fontawesome/solid/stroopwafel", - "fontawesome/solid/subscript", - "fontawesome/solid/suitcase-medical", - "fontawesome/solid/suitcase-rolling", - "fontawesome/solid/suitcase", - "fontawesome/solid/sun-plant-wilt", - "fontawesome/solid/sun", - "fontawesome/solid/superscript", - "fontawesome/solid/swatchbook", - "fontawesome/solid/synagogue", - "fontawesome/solid/syringe", - "fontawesome/solid/t", - "fontawesome/solid/table-cells-large", - "fontawesome/solid/table-cells", - "fontawesome/solid/table-columns", - "fontawesome/solid/table-list", - "fontawesome/solid/table-tennis-paddle-ball", - "fontawesome/solid/table", - "fontawesome/solid/tablet-button", - "fontawesome/solid/tablet-screen-button", - "fontawesome/solid/tablet", - "fontawesome/solid/tablets", - "fontawesome/solid/tachograph-digital", - "fontawesome/solid/tag", - "fontawesome/solid/tags", - "fontawesome/solid/tape", - "fontawesome/solid/tarp-droplet", - "fontawesome/solid/tarp", - "fontawesome/solid/taxi", - "fontawesome/solid/teeth-open", - "fontawesome/solid/teeth", - "fontawesome/solid/temperature-arrow-down", - "fontawesome/solid/temperature-arrow-up", - "fontawesome/solid/temperature-empty", - "fontawesome/solid/temperature-full", - "fontawesome/solid/temperature-half", - "fontawesome/solid/temperature-high", - "fontawesome/solid/temperature-low", - "fontawesome/solid/temperature-quarter", - "fontawesome/solid/temperature-three-quarters", - "fontawesome/solid/tenge-sign", - "fontawesome/solid/tent-arrow-down-to-line", - "fontawesome/solid/tent-arrow-left-right", - "fontawesome/solid/tent-arrow-turn-left", - "fontawesome/solid/tent-arrows-down", - "fontawesome/solid/tent", - "fontawesome/solid/tents", - "fontawesome/solid/terminal", - "fontawesome/solid/text-height", - "fontawesome/solid/text-slash", - "fontawesome/solid/text-width", - "fontawesome/solid/thermometer", - "fontawesome/solid/thumbs-down", - "fontawesome/solid/thumbs-up", - "fontawesome/solid/thumbtack", - "fontawesome/solid/ticket-simple", - "fontawesome/solid/ticket", - "fontawesome/solid/timeline", - "fontawesome/solid/toggle-off", - "fontawesome/solid/toggle-on", - "fontawesome/solid/toilet-paper-slash", - "fontawesome/solid/toilet-paper", - "fontawesome/solid/toilet-portable", - "fontawesome/solid/toilet", - "fontawesome/solid/toilets-portable", - "fontawesome/solid/toolbox", - "fontawesome/solid/tooth", - "fontawesome/solid/torii-gate", - "fontawesome/solid/tornado", - "fontawesome/solid/tower-broadcast", - "fontawesome/solid/tower-cell", - "fontawesome/solid/tower-observation", - "fontawesome/solid/tractor", - "fontawesome/solid/trademark", - "fontawesome/solid/traffic-light", - "fontawesome/solid/trailer", - "fontawesome/solid/train-subway", - "fontawesome/solid/train-tram", - "fontawesome/solid/train", - "fontawesome/solid/transgender", - "fontawesome/solid/trash-arrow-up", - "fontawesome/solid/trash-can-arrow-up", - "fontawesome/solid/trash-can", - "fontawesome/solid/trash", - "fontawesome/solid/tree-city", - "fontawesome/solid/tree", - "fontawesome/solid/triangle-exclamation", - "fontawesome/solid/trophy", - "fontawesome/solid/trowel-bricks", - "fontawesome/solid/trowel", - "fontawesome/solid/truck-arrow-right", - "fontawesome/solid/truck-droplet", - "fontawesome/solid/truck-fast", - "fontawesome/solid/truck-field-un", - "fontawesome/solid/truck-field", - "fontawesome/solid/truck-front", - "fontawesome/solid/truck-medical", - "fontawesome/solid/truck-monster", - "fontawesome/solid/truck-moving", - "fontawesome/solid/truck-pickup", - "fontawesome/solid/truck-plane", - "fontawesome/solid/truck-ramp-box", - "fontawesome/solid/truck", - "fontawesome/solid/tty", - "fontawesome/solid/turkish-lira-sign", - "fontawesome/solid/turn-down", - "fontawesome/solid/turn-up", - "fontawesome/solid/tv", - "fontawesome/solid/u", - "fontawesome/solid/umbrella-beach", - "fontawesome/solid/umbrella", - "fontawesome/solid/underline", - "fontawesome/solid/universal-access", - "fontawesome/solid/unlock-keyhole", - "fontawesome/solid/unlock", - "fontawesome/solid/up-down-left-right", - "fontawesome/solid/up-down", - "fontawesome/solid/up-long", - "fontawesome/solid/up-right-and-down-left-from-center", - "fontawesome/solid/up-right-from-square", - "fontawesome/solid/upload", - "fontawesome/solid/user-astronaut", - "fontawesome/solid/user-check", - "fontawesome/solid/user-clock", - "fontawesome/solid/user-doctor", - "fontawesome/solid/user-gear", - "fontawesome/solid/user-graduate", - "fontawesome/solid/user-group", - "fontawesome/solid/user-injured", - "fontawesome/solid/user-large-slash", - "fontawesome/solid/user-large", - "fontawesome/solid/user-lock", - "fontawesome/solid/user-minus", - "fontawesome/solid/user-ninja", - "fontawesome/solid/user-nurse", - "fontawesome/solid/user-pen", - "fontawesome/solid/user-plus", - "fontawesome/solid/user-secret", - "fontawesome/solid/user-shield", - "fontawesome/solid/user-slash", - "fontawesome/solid/user-tag", - "fontawesome/solid/user-tie", - "fontawesome/solid/user-xmark", - "fontawesome/solid/user", - "fontawesome/solid/users-between-lines", - "fontawesome/solid/users-gear", - "fontawesome/solid/users-line", - "fontawesome/solid/users-rays", - "fontawesome/solid/users-rectangle", - "fontawesome/solid/users-slash", - "fontawesome/solid/users-viewfinder", - "fontawesome/solid/users", - "fontawesome/solid/utensils", - "fontawesome/solid/v", - "fontawesome/solid/van-shuttle", - "fontawesome/solid/vault", - "fontawesome/solid/vector-square", - "fontawesome/solid/venus-double", - "fontawesome/solid/venus-mars", - "fontawesome/solid/venus", - "fontawesome/solid/vest-patches", - "fontawesome/solid/vest", - "fontawesome/solid/vial-circle-check", - "fontawesome/solid/vial-virus", - "fontawesome/solid/vial", - "fontawesome/solid/vials", - "fontawesome/solid/video-slash", - "fontawesome/solid/video", - "fontawesome/solid/vihara", - "fontawesome/solid/virus-covid-slash", - "fontawesome/solid/virus-covid", - "fontawesome/solid/virus-slash", - "fontawesome/solid/virus", - "fontawesome/solid/viruses", - "fontawesome/solid/voicemail", - "fontawesome/solid/volcano", - "fontawesome/solid/volleyball", - "fontawesome/solid/volume-high", - "fontawesome/solid/volume-low", - "fontawesome/solid/volume-off", - "fontawesome/solid/volume-xmark", - "fontawesome/solid/vr-cardboard", - "fontawesome/solid/w", - "fontawesome/solid/walkie-talkie", - "fontawesome/solid/wallet", - "fontawesome/solid/wand-magic-sparkles", - "fontawesome/solid/wand-magic", - "fontawesome/solid/wand-sparkles", - "fontawesome/solid/warehouse", - "fontawesome/solid/water-ladder", - "fontawesome/solid/water", - "fontawesome/solid/wave-square", - "fontawesome/solid/weight-hanging", - "fontawesome/solid/weight-scale", - "fontawesome/solid/wheat-awn-circle-exclamation", - "fontawesome/solid/wheat-awn", - "fontawesome/solid/wheelchair-move", - "fontawesome/solid/wheelchair", - "fontawesome/solid/whiskey-glass", - "fontawesome/solid/wifi", - "fontawesome/solid/wind", - "fontawesome/solid/window-maximize", - "fontawesome/solid/window-minimize", - "fontawesome/solid/window-restore", - "fontawesome/solid/wine-bottle", - "fontawesome/solid/wine-glass-empty", - "fontawesome/solid/wine-glass", - "fontawesome/solid/won-sign", - "fontawesome/solid/worm", - "fontawesome/solid/wrench", - "fontawesome/solid/x-ray", - "fontawesome/solid/x", - "fontawesome/solid/xmark", - "fontawesome/solid/xmarks-lines", - "fontawesome/solid/y", - "fontawesome/solid/yen-sign", - "fontawesome/solid/yin-yang", - "fontawesome/solid/z", - "logo", - "material/ab-testing", - "material/abacus", - "material/abjad-arabic", - "material/abjad-hebrew", - "material/abugida-devanagari", - "material/abugida-thai", - "material/access-point-check", - "material/access-point-minus", - "material/access-point-network-off", - "material/access-point-network", - "material/access-point-off", - "material/access-point-plus", - "material/access-point-remove", - "material/access-point", - "material/account-alert-outline", - "material/account-alert", - "material/account-arrow-down-outline", - "material/account-arrow-down", - "material/account-arrow-left-outline", - "material/account-arrow-left", - "material/account-arrow-right-outline", - "material/account-arrow-right", - "material/account-arrow-up-outline", - "material/account-arrow-up", - "material/account-badge-outline", - "material/account-badge", - "material/account-box-multiple-outline", - "material/account-box-multiple", - "material/account-box-outline", - "material/account-box", - "material/account-cancel-outline", - "material/account-cancel", - "material/account-card-outline", - "material/account-card", - "material/account-cash-outline", - "material/account-cash", - "material/account-check-outline", - "material/account-check", - "material/account-child-circle", - "material/account-child-outline", - "material/account-child", - "material/account-circle-outline", - "material/account-circle", - "material/account-clock-outline", - "material/account-clock", - "material/account-cog-outline", - "material/account-cog", - "material/account-convert-outline", - "material/account-convert", - "material/account-cowboy-hat-outline", - "material/account-cowboy-hat", - "material/account-credit-card-outline", - "material/account-credit-card", - "material/account-details-outline", - "material/account-details", - "material/account-edit-outline", - "material/account-edit", - "material/account-eye-outline", - "material/account-eye", - "material/account-filter-outline", - "material/account-filter", - "material/account-group-outline", - "material/account-group", - "material/account-hard-hat-outline", - "material/account-hard-hat", - "material/account-heart-outline", - "material/account-heart", - "material/account-injury-outline", - "material/account-injury", - "material/account-key-outline", - "material/account-key", - "material/account-lock-open-outline", - "material/account-lock-open", - "material/account-lock-outline", - "material/account-lock", - "material/account-minus-outline", - "material/account-minus", - "material/account-multiple-check-outline", - "material/account-multiple-check", - "material/account-multiple-minus-outline", - "material/account-multiple-minus", - "material/account-multiple-outline", - "material/account-multiple-plus-outline", - "material/account-multiple-plus", - "material/account-multiple-remove-outline", - "material/account-multiple-remove", - "material/account-multiple", - "material/account-music-outline", - "material/account-music", - "material/account-network-off-outline", - "material/account-network-off", - "material/account-network-outline", - "material/account-network", - "material/account-off-outline", - "material/account-off", - "material/account-outline", - "material/account-plus-outline", - "material/account-plus", - "material/account-question-outline", - "material/account-question", - "material/account-reactivate-outline", - "material/account-reactivate", - "material/account-remove-outline", - "material/account-remove", - "material/account-school-outline", - "material/account-school", - "material/account-search-outline", - "material/account-search", - "material/account-settings-outline", - "material/account-settings", - "material/account-star-outline", - "material/account-star", - "material/account-supervisor-circle-outline", - "material/account-supervisor-circle", - "material/account-supervisor-outline", - "material/account-supervisor", - "material/account-switch-outline", - "material/account-switch", - "material/account-sync-outline", - "material/account-sync", - "material/account-tie-hat-outline", - "material/account-tie-hat", - "material/account-tie-outline", - "material/account-tie-voice-off-outline", - "material/account-tie-voice-off", - "material/account-tie-voice-outline", - "material/account-tie-voice", - "material/account-tie-woman", - "material/account-tie", - "material/account-voice-off", - "material/account-voice", - "material/account-wrench-outline", - "material/account-wrench", - "material/account", - "material/adjust", - "material/advertisements-off", - "material/advertisements", - "material/air-conditioner", - "material/air-filter", - "material/air-horn", - "material/air-humidifier-off", - "material/air-humidifier", - "material/air-purifier-off", - "material/air-purifier", - "material/airbag", - "material/airballoon-outline", - "material/airballoon", - "material/airplane-alert", - "material/airplane-check", - "material/airplane-clock", - "material/airplane-cog", - "material/airplane-edit", - "material/airplane-landing", - "material/airplane-marker", - "material/airplane-minus", - "material/airplane-off", - "material/airplane-plus", - "material/airplane-remove", - "material/airplane-search", - "material/airplane-settings", - "material/airplane-takeoff", - "material/airplane", - "material/airport", - "material/alarm-bell", - "material/alarm-check", - "material/alarm-light-off-outline", - "material/alarm-light-off", - "material/alarm-light-outline", - "material/alarm-light", - "material/alarm-multiple", - "material/alarm-note-off", - "material/alarm-note", - "material/alarm-off", - "material/alarm-panel-outline", - "material/alarm-panel", - "material/alarm-plus", - "material/alarm-snooze", - "material/alarm", - "material/album", - "material/alert-box-outline", - "material/alert-box", - "material/alert-circle-check-outline", - "material/alert-circle-check", - "material/alert-circle-outline", - "material/alert-circle", - "material/alert-decagram-outline", - "material/alert-decagram", - "material/alert-minus-outline", - "material/alert-minus", - "material/alert-octagon-outline", - "material/alert-octagon", - "material/alert-octagram-outline", - "material/alert-octagram", - "material/alert-outline", - "material/alert-plus-outline", - "material/alert-plus", - "material/alert-remove-outline", - "material/alert-remove", - "material/alert-rhombus-outline", - "material/alert-rhombus", - "material/alert", - "material/alien-outline", - "material/alien", - "material/align-horizontal-center", - "material/align-horizontal-distribute", - "material/align-horizontal-left", - "material/align-horizontal-right", - "material/align-vertical-bottom", - "material/align-vertical-center", - "material/align-vertical-distribute", - "material/align-vertical-top", - "material/all-inclusive-box-outline", - "material/all-inclusive-box", - "material/all-inclusive", - "material/allergy", - "material/alpha-a-box-outline", - "material/alpha-a-box", - "material/alpha-a-circle-outline", - "material/alpha-a-circle", - "material/alpha-a", - "material/alpha-b-box-outline", - "material/alpha-b-box", - "material/alpha-b-circle-outline", - "material/alpha-b-circle", - "material/alpha-b", - "material/alpha-c-box-outline", - "material/alpha-c-box", - "material/alpha-c-circle-outline", - "material/alpha-c-circle", - "material/alpha-c", - "material/alpha-d-box-outline", - "material/alpha-d-box", - "material/alpha-d-circle-outline", - "material/alpha-d-circle", - "material/alpha-d", - "material/alpha-e-box-outline", - "material/alpha-e-box", - "material/alpha-e-circle-outline", - "material/alpha-e-circle", - "material/alpha-e", - "material/alpha-f-box-outline", - "material/alpha-f-box", - "material/alpha-f-circle-outline", - "material/alpha-f-circle", - "material/alpha-f", - "material/alpha-g-box-outline", - "material/alpha-g-box", - "material/alpha-g-circle-outline", - "material/alpha-g-circle", - "material/alpha-g", - "material/alpha-h-box-outline", - "material/alpha-h-box", - "material/alpha-h-circle-outline", - "material/alpha-h-circle", - "material/alpha-h", - "material/alpha-i-box-outline", - "material/alpha-i-box", - "material/alpha-i-circle-outline", - "material/alpha-i-circle", - "material/alpha-i", - "material/alpha-j-box-outline", - "material/alpha-j-box", - "material/alpha-j-circle-outline", - "material/alpha-j-circle", - "material/alpha-j", - "material/alpha-k-box-outline", - "material/alpha-k-box", - "material/alpha-k-circle-outline", - "material/alpha-k-circle", - "material/alpha-k", - "material/alpha-l-box-outline", - "material/alpha-l-box", - "material/alpha-l-circle-outline", - "material/alpha-l-circle", - "material/alpha-l", - "material/alpha-m-box-outline", - "material/alpha-m-box", - "material/alpha-m-circle-outline", - "material/alpha-m-circle", - "material/alpha-m", - "material/alpha-n-box-outline", - "material/alpha-n-box", - "material/alpha-n-circle-outline", - "material/alpha-n-circle", - "material/alpha-n", - "material/alpha-o-box-outline", - "material/alpha-o-box", - "material/alpha-o-circle-outline", - "material/alpha-o-circle", - "material/alpha-o", - "material/alpha-p-box-outline", - "material/alpha-p-box", - "material/alpha-p-circle-outline", - "material/alpha-p-circle", - "material/alpha-p", - "material/alpha-q-box-outline", - "material/alpha-q-box", - "material/alpha-q-circle-outline", - "material/alpha-q-circle", - "material/alpha-q", - "material/alpha-r-box-outline", - "material/alpha-r-box", - "material/alpha-r-circle-outline", - "material/alpha-r-circle", - "material/alpha-r", - "material/alpha-s-box-outline", - "material/alpha-s-box", - "material/alpha-s-circle-outline", - "material/alpha-s-circle", - "material/alpha-s", - "material/alpha-t-box-outline", - "material/alpha-t-box", - "material/alpha-t-circle-outline", - "material/alpha-t-circle", - "material/alpha-t", - "material/alpha-u-box-outline", - "material/alpha-u-box", - "material/alpha-u-circle-outline", - "material/alpha-u-circle", - "material/alpha-u", - "material/alpha-v-box-outline", - "material/alpha-v-box", - "material/alpha-v-circle-outline", - "material/alpha-v-circle", - "material/alpha-v", - "material/alpha-w-box-outline", - "material/alpha-w-box", - "material/alpha-w-circle-outline", - "material/alpha-w-circle", - "material/alpha-w", - "material/alpha-x-box-outline", - "material/alpha-x-box", - "material/alpha-x-circle-outline", - "material/alpha-x-circle", - "material/alpha-x", - "material/alpha-y-box-outline", - "material/alpha-y-box", - "material/alpha-y-circle-outline", - "material/alpha-y-circle", - "material/alpha-y", - "material/alpha-z-box-outline", - "material/alpha-z-box", - "material/alpha-z-circle-outline", - "material/alpha-z-circle", - "material/alpha-z", - "material/alpha", - "material/alphabet-aurebesh", - "material/alphabet-cyrillic", - "material/alphabet-greek", - "material/alphabet-latin", - "material/alphabet-piqad", - "material/alphabet-tengwar", - "material/alphabetical-off", - "material/alphabetical-variant-off", - "material/alphabetical-variant", - "material/alphabetical", - "material/altimeter", - "material/ambulance", - "material/ammunition", - "material/ampersand", - "material/amplifier-off", - "material/amplifier", - "material/anchor", - "material/android-studio", - "material/android", - "material/angle-acute", - "material/angle-obtuse", - "material/angle-right", - "material/angular", - "material/angularjs", - "material/animation-outline", - "material/animation-play-outline", - "material/animation-play", - "material/animation", - "material/ansible", - "material/antenna", - "material/anvil", - "material/apache-kafka", - "material/api-off", - "material/api", - "material/apple-finder", - "material/apple-icloud", - "material/apple-ios", - "material/apple-keyboard-caps", - "material/apple-keyboard-command", - "material/apple-keyboard-control", - "material/apple-keyboard-option", - "material/apple-keyboard-shift", - "material/apple-safari", - "material/apple", - "material/application-array-outline", - "material/application-array", - "material/application-braces-outline", - "material/application-braces", - "material/application-brackets-outline", - "material/application-brackets", - "material/application-cog-outline", - "material/application-cog", - "material/application-edit-outline", - "material/application-edit", - "material/application-export", - "material/application-import", - "material/application-outline", - "material/application-parentheses-outline", - "material/application-parentheses", - "material/application-settings-outline", - "material/application-settings", - "material/application-variable-outline", - "material/application-variable", - "material/application", - "material/approximately-equal-box", - "material/approximately-equal", - "material/apps-box", - "material/apps", - "material/arch", - "material/archive-alert-outline", - "material/archive-alert", - "material/archive-arrow-down-outline", - "material/archive-arrow-down", - "material/archive-arrow-up-outline", - "material/archive-arrow-up", - "material/archive-cancel-outline", - "material/archive-cancel", - "material/archive-check-outline", - "material/archive-check", - "material/archive-clock-outline", - "material/archive-clock", - "material/archive-cog-outline", - "material/archive-cog", - "material/archive-edit-outline", - "material/archive-edit", - "material/archive-eye-outline", - "material/archive-eye", - "material/archive-lock-open-outline", - "material/archive-lock-open", - "material/archive-lock-outline", - "material/archive-lock", - "material/archive-marker-outline", - "material/archive-marker", - "material/archive-minus-outline", - "material/archive-minus", - "material/archive-music-outline", - "material/archive-music", - "material/archive-off-outline", - "material/archive-off", - "material/archive-outline", - "material/archive-plus-outline", - "material/archive-plus", - "material/archive-refresh-outline", - "material/archive-refresh", - "material/archive-remove-outline", - "material/archive-remove", - "material/archive-search-outline", - "material/archive-search", - "material/archive-settings-outline", - "material/archive-settings", - "material/archive-star-outline", - "material/archive-star", - "material/archive-sync-outline", - "material/archive-sync", - "material/archive", - "material/arm-flex-outline", - "material/arm-flex", - "material/arrange-bring-forward", - "material/arrange-bring-to-front", - "material/arrange-send-backward", - "material/arrange-send-to-back", - "material/arrow-all", - "material/arrow-bottom-left-bold-box-outline", - "material/arrow-bottom-left-bold-box", - "material/arrow-bottom-left-bold-outline", - "material/arrow-bottom-left-thick", - "material/arrow-bottom-left-thin-circle-outline", - "material/arrow-bottom-left-thin", - "material/arrow-bottom-left", - "material/arrow-bottom-right-bold-box-outline", - "material/arrow-bottom-right-bold-box", - "material/arrow-bottom-right-bold-outline", - "material/arrow-bottom-right-thick", - "material/arrow-bottom-right-thin-circle-outline", - "material/arrow-bottom-right-thin", - "material/arrow-bottom-right", - "material/arrow-collapse-all", - "material/arrow-collapse-down", - "material/arrow-collapse-horizontal", - "material/arrow-collapse-left", - "material/arrow-collapse-right", - "material/arrow-collapse-up", - "material/arrow-collapse-vertical", - "material/arrow-collapse", - "material/arrow-decision-auto-outline", - "material/arrow-decision-auto", - "material/arrow-decision-outline", - "material/arrow-decision", - "material/arrow-down-bold-box-outline", - "material/arrow-down-bold-box", - "material/arrow-down-bold-circle-outline", - "material/arrow-down-bold-circle", - "material/arrow-down-bold-hexagon-outline", - "material/arrow-down-bold-outline", - "material/arrow-down-bold", - "material/arrow-down-box", - "material/arrow-down-circle-outline", - "material/arrow-down-circle", - "material/arrow-down-drop-circle-outline", - "material/arrow-down-drop-circle", - "material/arrow-down-left-bold", - "material/arrow-down-left", - "material/arrow-down-right-bold", - "material/arrow-down-right", - "material/arrow-down-thick", - "material/arrow-down-thin-circle-outline", - "material/arrow-down-thin", - "material/arrow-down", - "material/arrow-expand-all", - "material/arrow-expand-down", - "material/arrow-expand-horizontal", - "material/arrow-expand-left", - "material/arrow-expand-right", - "material/arrow-expand-up", - "material/arrow-expand-vertical", - "material/arrow-expand", - "material/arrow-horizontal-lock", - "material/arrow-left-bold-box-outline", - "material/arrow-left-bold-box", - "material/arrow-left-bold-circle-outline", - "material/arrow-left-bold-circle", - "material/arrow-left-bold-hexagon-outline", - "material/arrow-left-bold-outline", - "material/arrow-left-bold", - "material/arrow-left-bottom-bold", - "material/arrow-left-bottom", - "material/arrow-left-box", - "material/arrow-left-circle-outline", - "material/arrow-left-circle", - "material/arrow-left-drop-circle-outline", - "material/arrow-left-drop-circle", - "material/arrow-left-right-bold-outline", - "material/arrow-left-right-bold", - "material/arrow-left-right", - "material/arrow-left-thick", - "material/arrow-left-thin-circle-outline", - "material/arrow-left-thin", - "material/arrow-left-top-bold", - "material/arrow-left-top", - "material/arrow-left", - "material/arrow-projectile-multiple", - "material/arrow-projectile", - "material/arrow-right-bold-box-outline", - "material/arrow-right-bold-box", - "material/arrow-right-bold-circle-outline", - "material/arrow-right-bold-circle", - "material/arrow-right-bold-hexagon-outline", - "material/arrow-right-bold-outline", - "material/arrow-right-bold", - "material/arrow-right-bottom-bold", - "material/arrow-right-bottom", - "material/arrow-right-box", - "material/arrow-right-circle-outline", - "material/arrow-right-circle", - "material/arrow-right-drop-circle-outline", - "material/arrow-right-drop-circle", - "material/arrow-right-thick", - "material/arrow-right-thin-circle-outline", - "material/arrow-right-thin", - "material/arrow-right-top-bold", - "material/arrow-right-top", - "material/arrow-right", - "material/arrow-split-horizontal", - "material/arrow-split-vertical", - "material/arrow-top-left-bold-box-outline", - "material/arrow-top-left-bold-box", - "material/arrow-top-left-bold-outline", - "material/arrow-top-left-bottom-right-bold", - "material/arrow-top-left-bottom-right", - "material/arrow-top-left-thick", - "material/arrow-top-left-thin-circle-outline", - "material/arrow-top-left-thin", - "material/arrow-top-left", - "material/arrow-top-right-bold-box-outline", - "material/arrow-top-right-bold-box", - "material/arrow-top-right-bold-outline", - "material/arrow-top-right-bottom-left-bold", - "material/arrow-top-right-bottom-left", - "material/arrow-top-right-thick", - "material/arrow-top-right-thin-circle-outline", - "material/arrow-top-right-thin", - "material/arrow-top-right", - "material/arrow-u-down-left-bold", - "material/arrow-u-down-left", - "material/arrow-u-down-right-bold", - "material/arrow-u-down-right", - "material/arrow-u-left-bottom-bold", - "material/arrow-u-left-bottom", - "material/arrow-u-left-top-bold", - "material/arrow-u-left-top", - "material/arrow-u-right-bottom-bold", - "material/arrow-u-right-bottom", - "material/arrow-u-right-top-bold", - "material/arrow-u-right-top", - "material/arrow-u-up-left-bold", - "material/arrow-u-up-left", - "material/arrow-u-up-right-bold", - "material/arrow-u-up-right", - "material/arrow-up-bold-box-outline", - "material/arrow-up-bold-box", - "material/arrow-up-bold-circle-outline", - "material/arrow-up-bold-circle", - "material/arrow-up-bold-hexagon-outline", - "material/arrow-up-bold-outline", - "material/arrow-up-bold", - "material/arrow-up-box", - "material/arrow-up-circle-outline", - "material/arrow-up-circle", - "material/arrow-up-down-bold-outline", - "material/arrow-up-down-bold", - "material/arrow-up-down", - "material/arrow-up-drop-circle-outline", - "material/arrow-up-drop-circle", - "material/arrow-up-left-bold", - "material/arrow-up-left", - "material/arrow-up-right-bold", - "material/arrow-up-right", - "material/arrow-up-thick", - "material/arrow-up-thin-circle-outline", - "material/arrow-up-thin", - "material/arrow-up", - "material/arrow-vertical-lock", - "material/artboard", - "material/artstation", - "material/aspect-ratio", - "material/assistant", - "material/asterisk-circle-outline", - "material/asterisk", - "material/at", - "material/atlassian", - "material/atm", - "material/atom-variant", - "material/atom", - "material/attachment-check", - "material/attachment-lock", - "material/attachment-minus", - "material/attachment-off", - "material/attachment-plus", - "material/attachment-remove", - "material/attachment", - "material/atv", - "material/audio-input-rca", - "material/audio-input-stereo-minijack", - "material/audio-input-xlr", - "material/audio-video-off", - "material/audio-video", - "material/augmented-reality", - "material/auto-download", - "material/auto-fix", - "material/auto-upload", - "material/autorenew-off", - "material/autorenew", - "material/av-timer", - "material/awning-outline", - "material/awning", - "material/aws", - "material/axe-battle", - "material/axe", - "material/axis-arrow-info", - "material/axis-arrow-lock", - "material/axis-arrow", - "material/axis-lock", - "material/axis-x-arrow-lock", - "material/axis-x-arrow", - "material/axis-x-rotate-clockwise", - "material/axis-x-rotate-counterclockwise", - "material/axis-x-y-arrow-lock", - "material/axis-y-arrow-lock", - "material/axis-y-arrow", - "material/axis-y-rotate-clockwise", - "material/axis-y-rotate-counterclockwise", - "material/axis-z-arrow-lock", - "material/axis-z-arrow", - "material/axis-z-rotate-clockwise", - "material/axis-z-rotate-counterclockwise", - "material/axis", - "material/babel", - "material/baby-bottle-outline", - "material/baby-bottle", - "material/baby-buggy-off", - "material/baby-buggy", - "material/baby-carriage-off", - "material/baby-carriage", - "material/baby-face-outline", - "material/baby-face", - "material/baby", - "material/backburger", - "material/backspace-outline", - "material/backspace-reverse-outline", - "material/backspace-reverse", - "material/backspace", - "material/backup-restore", - "material/bacteria-outline", - "material/bacteria", - "material/badge-account-alert-outline", - "material/badge-account-alert", - "material/badge-account-horizontal-outline", - "material/badge-account-horizontal", - "material/badge-account-outline", - "material/badge-account", - "material/badminton", - "material/bag-carry-on-check", - "material/bag-carry-on-off", - "material/bag-carry-on", - "material/bag-checked", - "material/bag-personal-off-outline", - "material/bag-personal-off", - "material/bag-personal-outline", - "material/bag-personal-tag-outline", - "material/bag-personal-tag", - "material/bag-personal", - "material/bag-suitcase-off-outline", - "material/bag-suitcase-off", - "material/bag-suitcase-outline", - "material/bag-suitcase", - "material/baguette", - "material/balcony", - "material/balloon", - "material/ballot-outline", - "material/ballot-recount-outline", - "material/ballot-recount", - "material/ballot", - "material/bandage", - "material/bank-check", - "material/bank-minus", - "material/bank-off-outline", - "material/bank-off", - "material/bank-outline", - "material/bank-plus", - "material/bank-remove", - "material/bank-transfer-in", - "material/bank-transfer-out", - "material/bank-transfer", - "material/bank", - "material/barcode-off", - "material/barcode-scan", - "material/barcode", - "material/barley-off", - "material/barley", - "material/barn", - "material/barrel-outline", - "material/barrel", - "material/baseball-bat", - "material/baseball-diamond-outline", - "material/baseball-diamond", - "material/baseball", - "material/bash", - "material/basket-check-outline", - "material/basket-check", - "material/basket-fill", - "material/basket-minus-outline", - "material/basket-minus", - "material/basket-off-outline", - "material/basket-off", - "material/basket-outline", - "material/basket-plus-outline", - "material/basket-plus", - "material/basket-remove-outline", - "material/basket-remove", - "material/basket-unfill", - "material/basket", - "material/basketball-hoop-outline", - "material/basketball-hoop", - "material/basketball", - "material/bat", - "material/bathtub-outline", - "material/bathtub", - "material/battery-10-bluetooth", - "material/battery-10", - "material/battery-20-bluetooth", - "material/battery-20", - "material/battery-30-bluetooth", - "material/battery-30", - "material/battery-40-bluetooth", - "material/battery-40", - "material/battery-50-bluetooth", - "material/battery-50", - "material/battery-60-bluetooth", - "material/battery-60", - "material/battery-70-bluetooth", - "material/battery-70", - "material/battery-80-bluetooth", - "material/battery-80", - "material/battery-90-bluetooth", - "material/battery-90", - "material/battery-alert-bluetooth", - "material/battery-alert-variant-outline", - "material/battery-alert-variant", - "material/battery-alert", - "material/battery-arrow-down-outline", - "material/battery-arrow-down", - "material/battery-arrow-up-outline", - "material/battery-arrow-up", - "material/battery-bluetooth-variant", - "material/battery-bluetooth", - "material/battery-charging-10", - "material/battery-charging-100", - "material/battery-charging-20", - "material/battery-charging-30", - "material/battery-charging-40", - "material/battery-charging-50", - "material/battery-charging-60", - "material/battery-charging-70", - "material/battery-charging-80", - "material/battery-charging-90", - "material/battery-charging-high", - "material/battery-charging-low", - "material/battery-charging-medium", - "material/battery-charging-outline", - "material/battery-charging-wireless-10", - "material/battery-charging-wireless-20", - "material/battery-charging-wireless-30", - "material/battery-charging-wireless-40", - "material/battery-charging-wireless-50", - "material/battery-charging-wireless-60", - "material/battery-charging-wireless-70", - "material/battery-charging-wireless-80", - "material/battery-charging-wireless-90", - "material/battery-charging-wireless-alert", - "material/battery-charging-wireless-outline", - "material/battery-charging-wireless", - "material/battery-charging", - "material/battery-check-outline", - "material/battery-check", - "material/battery-clock-outline", - "material/battery-clock", - "material/battery-heart-outline", - "material/battery-heart-variant", - "material/battery-heart", - "material/battery-high", - "material/battery-lock-open", - "material/battery-lock", - "material/battery-low", - "material/battery-medium", - "material/battery-minus-outline", - "material/battery-minus-variant", - "material/battery-minus", - "material/battery-negative", - "material/battery-off-outline", - "material/battery-off", - "material/battery-outline", - "material/battery-plus-outline", - "material/battery-plus-variant", - "material/battery-plus", - "material/battery-positive", - "material/battery-remove-outline", - "material/battery-remove", - "material/battery-sync-outline", - "material/battery-sync", - "material/battery-unknown-bluetooth", - "material/battery-unknown", - "material/battery", - "material/beach", - "material/beaker-alert-outline", - "material/beaker-alert", - "material/beaker-check-outline", - "material/beaker-check", - "material/beaker-minus-outline", - "material/beaker-minus", - "material/beaker-outline", - "material/beaker-plus-outline", - "material/beaker-plus", - "material/beaker-question-outline", - "material/beaker-question", - "material/beaker-remove-outline", - "material/beaker-remove", - "material/beaker", - "material/bed-clock", - "material/bed-double-outline", - "material/bed-double", - "material/bed-empty", - "material/bed-king-outline", - "material/bed-king", - "material/bed-outline", - "material/bed-queen-outline", - "material/bed-queen", - "material/bed-single-outline", - "material/bed-single", - "material/bed", - "material/bee-flower", - "material/bee", - "material/beehive-off-outline", - "material/beehive-outline", - "material/beekeeper", - "material/beer-outline", - "material/beer", - "material/bell-alert-outline", - "material/bell-alert", - "material/bell-badge-outline", - "material/bell-badge", - "material/bell-cancel-outline", - "material/bell-cancel", - "material/bell-check-outline", - "material/bell-check", - "material/bell-circle-outline", - "material/bell-circle", - "material/bell-cog-outline", - "material/bell-cog", - "material/bell-minus-outline", - "material/bell-minus", - "material/bell-off-outline", - "material/bell-off", - "material/bell-outline", - "material/bell-plus-outline", - "material/bell-plus", - "material/bell-remove-outline", - "material/bell-remove", - "material/bell-ring-outline", - "material/bell-ring", - "material/bell-sleep-outline", - "material/bell-sleep", - "material/bell", - "material/beta", - "material/betamax", - "material/biathlon", - "material/bicycle-basket", - "material/bicycle-cargo", - "material/bicycle-electric", - "material/bicycle-penny-farthing", - "material/bicycle", - "material/bike-fast", - "material/bike", - "material/billboard", - "material/billiards-rack", - "material/billiards", - "material/binoculars", - "material/bio", - "material/biohazard", - "material/bird", - "material/bitbucket", - "material/bitcoin", - "material/black-mesa", - "material/blender-outline", - "material/blender-software", - "material/blender", - "material/blinds-horizontal-closed", - "material/blinds-horizontal", - "material/blinds-open", - "material/blinds-vertical-closed", - "material/blinds-vertical", - "material/blinds", - "material/block-helper", - "material/blood-bag", - "material/bluetooth-audio", - "material/bluetooth-connect", - "material/bluetooth-off", - "material/bluetooth-settings", - "material/bluetooth-transfer", - "material/bluetooth", - "material/blur-linear", - "material/blur-off", - "material/blur-radial", - "material/blur", - "material/bolt", - "material/bomb-off", - "material/bomb", - "material/bone-off", - "material/bone", - "material/book-account-outline", - "material/book-account", - "material/book-alert-outline", - "material/book-alert", - "material/book-alphabet", - "material/book-arrow-down-outline", - "material/book-arrow-down", - "material/book-arrow-left-outline", - "material/book-arrow-left", - "material/book-arrow-right-outline", - "material/book-arrow-right", - "material/book-arrow-up-outline", - "material/book-arrow-up", - "material/book-cancel-outline", - "material/book-cancel", - "material/book-check-outline", - "material/book-check", - "material/book-clock-outline", - "material/book-clock", - "material/book-cog-outline", - "material/book-cog", - "material/book-cross", - "material/book-edit-outline", - "material/book-edit", - "material/book-education-outline", - "material/book-education", - "material/book-heart-outline", - "material/book-heart", - "material/book-information-variant", - "material/book-lock-open-outline", - "material/book-lock-open", - "material/book-lock-outline", - "material/book-lock", - "material/book-marker-outline", - "material/book-marker", - "material/book-minus-multiple-outline", - "material/book-minus-multiple", - "material/book-minus-outline", - "material/book-minus", - "material/book-multiple-outline", - "material/book-multiple", - "material/book-music-outline", - "material/book-music", - "material/book-off-outline", - "material/book-off", - "material/book-open-blank-variant", - "material/book-open-outline", - "material/book-open-page-variant-outline", - "material/book-open-page-variant", - "material/book-open-variant", - "material/book-open", - "material/book-outline", - "material/book-play-outline", - "material/book-play", - "material/book-plus-multiple-outline", - "material/book-plus-multiple", - "material/book-plus-outline", - "material/book-plus", - "material/book-refresh-outline", - "material/book-refresh", - "material/book-remove-multiple-outline", - "material/book-remove-multiple", - "material/book-remove-outline", - "material/book-remove", - "material/book-search-outline", - "material/book-search", - "material/book-settings-outline", - "material/book-settings", - "material/book-sync-outline", - "material/book-sync", - "material/book-variant", - "material/book", - "material/bookmark-box-multiple-outline", - "material/bookmark-box-multiple", - "material/bookmark-box-outline", - "material/bookmark-box", - "material/bookmark-check-outline", - "material/bookmark-check", - "material/bookmark-minus-outline", - "material/bookmark-minus", - "material/bookmark-multiple-outline", - "material/bookmark-multiple", - "material/bookmark-music-outline", - "material/bookmark-music", - "material/bookmark-off-outline", - "material/bookmark-off", - "material/bookmark-outline", - "material/bookmark-plus-outline", - "material/bookmark-plus", - "material/bookmark-remove-outline", - "material/bookmark-remove", - "material/bookmark", - "material/bookshelf", - "material/boom-gate-alert-outline", - "material/boom-gate-alert", - "material/boom-gate-arrow-down-outline", - "material/boom-gate-arrow-down", - "material/boom-gate-arrow-up-outline", - "material/boom-gate-arrow-up", - "material/boom-gate-outline", - "material/boom-gate-up-outline", - "material/boom-gate-up", - "material/boom-gate", - "material/boombox", - "material/boomerang", - "material/bootstrap", - "material/border-all-variant", - "material/border-all", - "material/border-bottom-variant", - "material/border-bottom", - "material/border-color", - "material/border-horizontal", - "material/border-inside", - "material/border-left-variant", - "material/border-left", - "material/border-none-variant", - "material/border-none", - "material/border-outside", - "material/border-radius", - "material/border-right-variant", - "material/border-right", - "material/border-style", - "material/border-top-variant", - "material/border-top", - "material/border-vertical", - "material/bottle-soda-classic-outline", - "material/bottle-soda-classic", - "material/bottle-soda-outline", - "material/bottle-soda", - "material/bottle-tonic-outline", - "material/bottle-tonic-plus-outline", - "material/bottle-tonic-plus", - "material/bottle-tonic-skull-outline", - "material/bottle-tonic-skull", - "material/bottle-tonic", - "material/bottle-wine-outline", - "material/bottle-wine", - "material/bow-arrow", - "material/bow-tie", - "material/bowl-mix-outline", - "material/bowl-mix", - "material/bowl-outline", - "material/bowl", - "material/bowling", - "material/box-cutter-off", - "material/box-cutter", - "material/box-shadow", - "material/box", - "material/boxing-glove", - "material/braille", - "material/brain", - "material/bread-slice-outline", - "material/bread-slice", - "material/bridge", - "material/briefcase-account-outline", - "material/briefcase-account", - "material/briefcase-arrow-left-right-outline", - "material/briefcase-arrow-left-right", - "material/briefcase-arrow-up-down-outline", - "material/briefcase-arrow-up-down", - "material/briefcase-check-outline", - "material/briefcase-check", - "material/briefcase-clock-outline", - "material/briefcase-clock", - "material/briefcase-download-outline", - "material/briefcase-download", - "material/briefcase-edit-outline", - "material/briefcase-edit", - "material/briefcase-eye-outline", - "material/briefcase-eye", - "material/briefcase-minus-outline", - "material/briefcase-minus", - "material/briefcase-off-outline", - "material/briefcase-off", - "material/briefcase-outline", - "material/briefcase-plus-outline", - "material/briefcase-plus", - "material/briefcase-remove-outline", - "material/briefcase-remove", - "material/briefcase-search-outline", - "material/briefcase-search", - "material/briefcase-upload-outline", - "material/briefcase-upload", - "material/briefcase-variant-off-outline", - "material/briefcase-variant-off", - "material/briefcase-variant-outline", - "material/briefcase-variant", - "material/briefcase", - "material/brightness-1", - "material/brightness-2", - "material/brightness-3", - "material/brightness-4", - "material/brightness-5", - "material/brightness-6", - "material/brightness-7", - "material/brightness-auto", - "material/brightness-percent", - "material/broadcast-off", - "material/broadcast", - "material/broom", - "material/brush-off", - "material/brush-outline", - "material/brush-variant", - "material/brush", - "material/bucket-outline", - "material/bucket", - "material/buffet", - "material/bug-check-outline", - "material/bug-check", - "material/bug-outline", - "material/bug-pause-outline", - "material/bug-pause", - "material/bug-play-outline", - "material/bug-play", - "material/bug-stop-outline", - "material/bug-stop", - "material/bug", - "material/bugle", - "material/bulkhead-light", - "material/bulldozer", - "material/bullet", - "material/bulletin-board", - "material/bullhorn-outline", - "material/bullhorn-variant-outline", - "material/bullhorn-variant", - "material/bullhorn", - "material/bullseye-arrow", - "material/bullseye", - "material/bulma", - "material/bunk-bed-outline", - "material/bunk-bed", - "material/bus-alert", - "material/bus-articulated-end", - "material/bus-articulated-front", - "material/bus-clock", - "material/bus-double-decker", - "material/bus-electric", - "material/bus-marker", - "material/bus-multiple", - "material/bus-school", - "material/bus-side", - "material/bus-stop-covered", - "material/bus-stop-uncovered", - "material/bus-stop", - "material/bus", - "material/butterfly-outline", - "material/butterfly", - "material/button-cursor", - "material/button-pointer", - "material/cabin-a-frame", - "material/cable-data", - "material/cached", - "material/cactus", - "material/cake-layered", - "material/cake-variant-outline", - "material/cake-variant", - "material/cake", - "material/calculator-variant-outline", - "material/calculator-variant", - "material/calculator", - "material/calendar-account-outline", - "material/calendar-account", - "material/calendar-alert-outline", - "material/calendar-alert", - "material/calendar-arrow-left", - "material/calendar-arrow-right", - "material/calendar-badge-outline", - "material/calendar-badge", - "material/calendar-blank-multiple", - "material/calendar-blank-outline", - "material/calendar-blank", - "material/calendar-check-outline", - "material/calendar-check", - "material/calendar-clock-outline", - "material/calendar-clock", - "material/calendar-collapse-horizontal-outline", - "material/calendar-collapse-horizontal", - "material/calendar-cursor-outline", - "material/calendar-cursor", - "material/calendar-edit-outline", - "material/calendar-edit", - "material/calendar-end-outline", - "material/calendar-end", - "material/calendar-expand-horizontal-outline", - "material/calendar-expand-horizontal", - "material/calendar-export-outline", - "material/calendar-export", - "material/calendar-filter-outline", - "material/calendar-filter", - "material/calendar-heart-outline", - "material/calendar-heart", - "material/calendar-import-outline", - "material/calendar-import", - "material/calendar-lock-open-outline", - "material/calendar-lock-open", - "material/calendar-lock-outline", - "material/calendar-lock", - "material/calendar-minus-outline", - "material/calendar-minus", - "material/calendar-month-outline", - "material/calendar-month", - "material/calendar-multiple-check", - "material/calendar-multiple", - "material/calendar-multiselect-outline", - "material/calendar-multiselect", - "material/calendar-outline", - "material/calendar-plus-outline", - "material/calendar-plus", - "material/calendar-question-outline", - "material/calendar-question", - "material/calendar-range-outline", - "material/calendar-range", - "material/calendar-refresh-outline", - "material/calendar-refresh", - "material/calendar-remove-outline", - "material/calendar-remove", - "material/calendar-search-outline", - "material/calendar-search", - "material/calendar-star-outline", - "material/calendar-star", - "material/calendar-start-outline", - "material/calendar-start", - "material/calendar-sync-outline", - "material/calendar-sync", - "material/calendar-text-outline", - "material/calendar-text", - "material/calendar-today-outline", - "material/calendar-today", - "material/calendar-week-begin-outline", - "material/calendar-week-begin", - "material/calendar-week-outline", - "material/calendar-week", - "material/calendar-weekend-outline", - "material/calendar-weekend", - "material/calendar", - "material/call-made", - "material/call-merge", - "material/call-missed", - "material/call-received", - "material/call-split", - "material/camcorder-off", - "material/camcorder", - "material/camera-account", - "material/camera-burst", - "material/camera-control", - "material/camera-document-off", - "material/camera-document", - "material/camera-enhance-outline", - "material/camera-enhance", - "material/camera-flip-outline", - "material/camera-flip", - "material/camera-front-variant", - "material/camera-front", - "material/camera-gopro", - "material/camera-image", - "material/camera-iris", - "material/camera-lock-outline", - "material/camera-lock", - "material/camera-marker-outline", - "material/camera-marker", - "material/camera-metering-center", - "material/camera-metering-matrix", - "material/camera-metering-partial", - "material/camera-metering-spot", - "material/camera-off-outline", - "material/camera-off", - "material/camera-outline", - "material/camera-party-mode", - "material/camera-plus-outline", - "material/camera-plus", - "material/camera-rear-variant", - "material/camera-rear", - "material/camera-retake-outline", - "material/camera-retake", - "material/camera-switch-outline", - "material/camera-switch", - "material/camera-timer", - "material/camera-wireless-outline", - "material/camera-wireless", - "material/camera", - "material/campfire", - "material/cancel", - "material/candelabra-fire", - "material/candelabra", - "material/candle", - "material/candy-off-outline", - "material/candy-off", - "material/candy-outline", - "material/candy", - "material/candycane", - "material/cannabis-off", - "material/cannabis", - "material/caps-lock", - "material/car-2-plus", - "material/car-3-plus", - "material/car-arrow-left", - "material/car-arrow-right", - "material/car-back", - "material/car-battery", - "material/car-brake-abs", - "material/car-brake-alert", - "material/car-brake-fluid-level", - "material/car-brake-hold", - "material/car-brake-low-pressure", - "material/car-brake-parking", - "material/car-brake-retarder", - "material/car-brake-temperature", - "material/car-brake-worn-linings", - "material/car-child-seat", - "material/car-clock", - "material/car-clutch", - "material/car-cog", - "material/car-connected", - "material/car-convertible", - "material/car-coolant-level", - "material/car-cruise-control", - "material/car-defrost-front", - "material/car-defrost-rear", - "material/car-door-lock", - "material/car-door", - "material/car-electric-outline", - "material/car-electric", - "material/car-emergency", - "material/car-esp", - "material/car-estate", - "material/car-hatchback", - "material/car-info", - "material/car-key", - "material/car-lifted-pickup", - "material/car-light-alert", - "material/car-light-dimmed", - "material/car-light-fog", - "material/car-light-high", - "material/car-limousine", - "material/car-multiple", - "material/car-off", - "material/car-outline", - "material/car-parking-lights", - "material/car-pickup", - "material/car-search-outline", - "material/car-search", - "material/car-seat-cooler", - "material/car-seat-heater", - "material/car-seat", - "material/car-select", - "material/car-settings", - "material/car-shift-pattern", - "material/car-side", - "material/car-speed-limiter", - "material/car-sports", - "material/car-tire-alert", - "material/car-traction-control", - "material/car-turbocharger", - "material/car-wash", - "material/car-windshield-outline", - "material/car-windshield", - "material/car-wireless", - "material/car-wrench", - "material/car", - "material/carabiner", - "material/caravan", - "material/card-account-details-outline", - "material/card-account-details-star-outline", - "material/card-account-details-star", - "material/card-account-details", - "material/card-account-mail-outline", - "material/card-account-mail", - "material/card-account-phone-outline", - "material/card-account-phone", - "material/card-bulleted-off-outline", - "material/card-bulleted-off", - "material/card-bulleted-outline", - "material/card-bulleted-settings-outline", - "material/card-bulleted-settings", - "material/card-bulleted", - "material/card-minus-outline", - "material/card-minus", - "material/card-multiple-outline", - "material/card-multiple", - "material/card-off-outline", - "material/card-off", - "material/card-outline", - "material/card-plus-outline", - "material/card-plus", - "material/card-remove-outline", - "material/card-remove", - "material/card-search-outline", - "material/card-search", - "material/card-text-outline", - "material/card-text", - "material/card", - "material/cards-club-outline", - "material/cards-club", - "material/cards-diamond-outline", - "material/cards-diamond", - "material/cards-heart-outline", - "material/cards-heart", - "material/cards-outline", - "material/cards-playing-club-multiple-outline", - "material/cards-playing-club-multiple", - "material/cards-playing-club-outline", - "material/cards-playing-club", - "material/cards-playing-diamond-multiple-outline", - "material/cards-playing-diamond-multiple", - "material/cards-playing-diamond-outline", - "material/cards-playing-diamond", - "material/cards-playing-heart-multiple-outline", - "material/cards-playing-heart-multiple", - "material/cards-playing-heart-outline", - "material/cards-playing-heart", - "material/cards-playing-outline", - "material/cards-playing-spade-multiple-outline", - "material/cards-playing-spade-multiple", - "material/cards-playing-spade-outline", - "material/cards-playing-spade", - "material/cards-playing", - "material/cards-spade-outline", - "material/cards-spade", - "material/cards-variant", - "material/cards", - "material/carrot", - "material/cart-arrow-down", - "material/cart-arrow-right", - "material/cart-arrow-up", - "material/cart-check", - "material/cart-heart", - "material/cart-minus", - "material/cart-off", - "material/cart-outline", - "material/cart-percent", - "material/cart-plus", - "material/cart-remove", - "material/cart-variant", - "material/cart", - "material/case-sensitive-alt", - "material/cash-100", - "material/cash-check", - "material/cash-clock", - "material/cash-fast", - "material/cash-lock-open", - "material/cash-lock", - "material/cash-marker", - "material/cash-minus", - "material/cash-multiple", - "material/cash-plus", - "material/cash-refund", - "material/cash-register", - "material/cash-remove", - "material/cash-sync", - "material/cash", - "material/cassette", - "material/cast-audio-variant", - "material/cast-audio", - "material/cast-connected", - "material/cast-education", - "material/cast-off", - "material/cast-variant", - "material/cast", - "material/castle", - "material/cat", - "material/cctv-off", - "material/cctv", - "material/ceiling-fan-light", - "material/ceiling-fan", - "material/ceiling-light-multiple-outline", - "material/ceiling-light-multiple", - "material/ceiling-light-outline", - "material/ceiling-light", - "material/cellphone-arrow-down-variant", - "material/cellphone-arrow-down", - "material/cellphone-basic", - "material/cellphone-charging", - "material/cellphone-check", - "material/cellphone-cog", - "material/cellphone-dock", - "material/cellphone-information", - "material/cellphone-key", - "material/cellphone-link-off", - "material/cellphone-link", - "material/cellphone-lock", - "material/cellphone-marker", - "material/cellphone-message-off", - "material/cellphone-message", - "material/cellphone-nfc-off", - "material/cellphone-nfc", - "material/cellphone-off", - "material/cellphone-play", - "material/cellphone-remove", - "material/cellphone-screenshot", - "material/cellphone-settings", - "material/cellphone-sound", - "material/cellphone-text", - "material/cellphone-wireless", - "material/cellphone", - "material/centos", - "material/certificate-outline", - "material/certificate", - "material/chair-rolling", - "material/chair-school", - "material/chandelier", - "material/charity", - "material/chart-arc", - "material/chart-areaspline-variant", - "material/chart-areaspline", - "material/chart-bar-stacked", - "material/chart-bar", - "material/chart-bell-curve-cumulative", - "material/chart-bell-curve", - "material/chart-box-outline", - "material/chart-box-plus-outline", - "material/chart-box", - "material/chart-bubble", - "material/chart-donut-variant", - "material/chart-donut", - "material/chart-gantt", - "material/chart-histogram", - "material/chart-line-stacked", - "material/chart-line-variant", - "material/chart-line", - "material/chart-multiline", - "material/chart-multiple", - "material/chart-pie", - "material/chart-ppf", - "material/chart-sankey-variant", - "material/chart-sankey", - "material/chart-scatter-plot-hexbin", - "material/chart-scatter-plot", - "material/chart-timeline-variant-shimmer", - "material/chart-timeline-variant", - "material/chart-timeline", - "material/chart-tree", - "material/chart-waterfall", - "material/chat-alert-outline", - "material/chat-alert", - "material/chat-minus-outline", - "material/chat-minus", - "material/chat-outline", - "material/chat-plus-outline", - "material/chat-plus", - "material/chat-processing-outline", - "material/chat-processing", - "material/chat-question-outline", - "material/chat-question", - "material/chat-remove-outline", - "material/chat-remove", - "material/chat-sleep-outline", - "material/chat-sleep", - "material/chat", - "material/check-all", - "material/check-bold", - "material/check-circle-outline", - "material/check-circle", - "material/check-decagram-outline", - "material/check-decagram", - "material/check-network-outline", - "material/check-network", - "material/check-outline", - "material/check-underline-circle-outline", - "material/check-underline-circle", - "material/check-underline", - "material/check", - "material/checkbook", - "material/checkbox-blank-badge-outline", - "material/checkbox-blank-badge", - "material/checkbox-blank-circle-outline", - "material/checkbox-blank-circle", - "material/checkbox-blank-off-outline", - "material/checkbox-blank-off", - "material/checkbox-blank-outline", - "material/checkbox-blank", - "material/checkbox-intermediate-variant", - "material/checkbox-intermediate", - "material/checkbox-marked-circle-outline", - "material/checkbox-marked-circle-plus-outline", - "material/checkbox-marked-circle", - "material/checkbox-marked-outline", - "material/checkbox-marked", - "material/checkbox-multiple-blank-circle-outline", - "material/checkbox-multiple-blank-circle", - "material/checkbox-multiple-blank-outline", - "material/checkbox-multiple-blank", - "material/checkbox-multiple-marked-circle-outline", - "material/checkbox-multiple-marked-circle", - "material/checkbox-multiple-marked-outline", - "material/checkbox-multiple-marked", - "material/checkbox-multiple-outline", - "material/checkbox-outline", - "material/checkerboard-minus", - "material/checkerboard-plus", - "material/checkerboard-remove", - "material/checkerboard", - "material/cheese-off", - "material/cheese", - "material/chef-hat", - "material/chemical-weapon", - "material/chess-bishop", - "material/chess-king", - "material/chess-knight", - "material/chess-pawn", - "material/chess-queen", - "material/chess-rook", - "material/chevron-double-down", - "material/chevron-double-left", - "material/chevron-double-right", - "material/chevron-double-up", - "material/chevron-down-box-outline", - "material/chevron-down-box", - "material/chevron-down-circle-outline", - "material/chevron-down-circle", - "material/chevron-down", - "material/chevron-left-box-outline", - "material/chevron-left-box", - "material/chevron-left-circle-outline", - "material/chevron-left-circle", - "material/chevron-left", - "material/chevron-right-box-outline", - "material/chevron-right-box", - "material/chevron-right-circle-outline", - "material/chevron-right-circle", - "material/chevron-right", - "material/chevron-triple-down", - "material/chevron-triple-left", - "material/chevron-triple-right", - "material/chevron-triple-up", - "material/chevron-up-box-outline", - "material/chevron-up-box", - "material/chevron-up-circle-outline", - "material/chevron-up-circle", - "material/chevron-up", - "material/chili-alert-outline", - "material/chili-alert", - "material/chili-hot-outline", - "material/chili-hot", - "material/chili-medium-outline", - "material/chili-medium", - "material/chili-mild-outline", - "material/chili-mild", - "material/chili-off-outline", - "material/chili-off", - "material/chip", - "material/church-outline", - "material/church", - "material/cigar-off", - "material/cigar", - "material/circle-box-outline", - "material/circle-box", - "material/circle-double", - "material/circle-edit-outline", - "material/circle-expand", - "material/circle-half-full", - "material/circle-half", - "material/circle-medium", - "material/circle-multiple-outline", - "material/circle-multiple", - "material/circle-off-outline", - "material/circle-opacity", - "material/circle-outline", - "material/circle-slice-1", - "material/circle-slice-2", - "material/circle-slice-3", - "material/circle-slice-4", - "material/circle-slice-5", - "material/circle-slice-6", - "material/circle-slice-7", - "material/circle-slice-8", - "material/circle-small", - "material/circle", - "material/circular-saw", - "material/city-variant-outline", - "material/city-variant", - "material/city", - "material/clipboard-account-outline", - "material/clipboard-account", - "material/clipboard-alert-outline", - "material/clipboard-alert", - "material/clipboard-arrow-down-outline", - "material/clipboard-arrow-down", - "material/clipboard-arrow-left-outline", - "material/clipboard-arrow-left", - "material/clipboard-arrow-right-outline", - "material/clipboard-arrow-right", - "material/clipboard-arrow-up-outline", - "material/clipboard-arrow-up", - "material/clipboard-check-multiple-outline", - "material/clipboard-check-multiple", - "material/clipboard-check-outline", - "material/clipboard-check", - "material/clipboard-clock-outline", - "material/clipboard-clock", - "material/clipboard-edit-outline", - "material/clipboard-edit", - "material/clipboard-file-outline", - "material/clipboard-file", - "material/clipboard-flow-outline", - "material/clipboard-flow", - "material/clipboard-list-outline", - "material/clipboard-list", - "material/clipboard-minus-outline", - "material/clipboard-minus", - "material/clipboard-multiple-outline", - "material/clipboard-multiple", - "material/clipboard-off-outline", - "material/clipboard-off", - "material/clipboard-outline", - "material/clipboard-play-multiple-outline", - "material/clipboard-play-multiple", - "material/clipboard-play-outline", - "material/clipboard-play", - "material/clipboard-plus-outline", - "material/clipboard-plus", - "material/clipboard-pulse-outline", - "material/clipboard-pulse", - "material/clipboard-remove-outline", - "material/clipboard-remove", - "material/clipboard-search-outline", - "material/clipboard-search", - "material/clipboard-text-clock-outline", - "material/clipboard-text-clock", - "material/clipboard-text-multiple-outline", - "material/clipboard-text-multiple", - "material/clipboard-text-off-outline", - "material/clipboard-text-off", - "material/clipboard-text-outline", - "material/clipboard-text-play-outline", - "material/clipboard-text-play", - "material/clipboard-text-search-outline", - "material/clipboard-text-search", - "material/clipboard-text", - "material/clipboard", - "material/clippy", - "material/clock-alert-outline", - "material/clock-alert", - "material/clock-check-outline", - "material/clock-check", - "material/clock-digital", - "material/clock-edit-outline", - "material/clock-edit", - "material/clock-end", - "material/clock-fast", - "material/clock-in", - "material/clock-minus-outline", - "material/clock-minus", - "material/clock-out", - "material/clock-outline", - "material/clock-plus-outline", - "material/clock-plus", - "material/clock-remove-outline", - "material/clock-remove", - "material/clock-start", - "material/clock-time-eight-outline", - "material/clock-time-eight", - "material/clock-time-eleven-outline", - "material/clock-time-eleven", - "material/clock-time-five-outline", - "material/clock-time-five", - "material/clock-time-four-outline", - "material/clock-time-four", - "material/clock-time-nine-outline", - "material/clock-time-nine", - "material/clock-time-one-outline", - "material/clock-time-one", - "material/clock-time-seven-outline", - "material/clock-time-seven", - "material/clock-time-six-outline", - "material/clock-time-six", - "material/clock-time-ten-outline", - "material/clock-time-ten", - "material/clock-time-three-outline", - "material/clock-time-three", - "material/clock-time-twelve-outline", - "material/clock-time-twelve", - "material/clock-time-two-outline", - "material/clock-time-two", - "material/clock", - "material/close-box-multiple-outline", - "material/close-box-multiple", - "material/close-box-outline", - "material/close-box", - "material/close-circle-multiple-outline", - "material/close-circle-multiple", - "material/close-circle-outline", - "material/close-circle", - "material/close-network-outline", - "material/close-network", - "material/close-octagon-outline", - "material/close-octagon", - "material/close-outline", - "material/close-thick", - "material/close", - "material/closed-caption-outline", - "material/closed-caption", - "material/cloud-alert", - "material/cloud-braces", - "material/cloud-check-outline", - "material/cloud-check", - "material/cloud-circle", - "material/cloud-download-outline", - "material/cloud-download", - "material/cloud-lock-outline", - "material/cloud-lock", - "material/cloud-off-outline", - "material/cloud-outline", - "material/cloud-percent-outline", - "material/cloud-percent", - "material/cloud-print-outline", - "material/cloud-print", - "material/cloud-question", - "material/cloud-refresh", - "material/cloud-search-outline", - "material/cloud-search", - "material/cloud-sync-outline", - "material/cloud-sync", - "material/cloud-tags", - "material/cloud-upload-outline", - "material/cloud-upload", - "material/cloud", - "material/clouds", - "material/clover", - "material/coach-lamp-variant", - "material/coach-lamp", - "material/coat-rack", - "material/code-array", - "material/code-braces-box", - "material/code-braces", - "material/code-brackets", - "material/code-equal", - "material/code-greater-than-or-equal", - "material/code-greater-than", - "material/code-json", - "material/code-less-than-or-equal", - "material/code-less-than", - "material/code-not-equal-variant", - "material/code-not-equal", - "material/code-parentheses-box", - "material/code-parentheses", - "material/code-string", - "material/code-tags-check", - "material/code-tags", - "material/codepen", - "material/coffee-maker-check-outline", - "material/coffee-maker-check", - "material/coffee-maker-outline", - "material/coffee-maker", - "material/coffee-off-outline", - "material/coffee-off", - "material/coffee-outline", - "material/coffee-to-go-outline", - "material/coffee-to-go", - "material/coffee", - "material/coffin", - "material/cog-box", - "material/cog-clockwise", - "material/cog-counterclockwise", - "material/cog-off-outline", - "material/cog-off", - "material/cog-outline", - "material/cog-pause-outline", - "material/cog-pause", - "material/cog-play-outline", - "material/cog-play", - "material/cog-refresh-outline", - "material/cog-refresh", - "material/cog-stop-outline", - "material/cog-stop", - "material/cog-sync-outline", - "material/cog-sync", - "material/cog-transfer-outline", - "material/cog-transfer", - "material/cog", - "material/cogs", - "material/collage", - "material/collapse-all-outline", - "material/collapse-all", - "material/color-helper", - "material/comma-box-outline", - "material/comma-box", - "material/comma-circle-outline", - "material/comma-circle", - "material/comma", - "material/comment-account-outline", - "material/comment-account", - "material/comment-alert-outline", - "material/comment-alert", - "material/comment-arrow-left-outline", - "material/comment-arrow-left", - "material/comment-arrow-right-outline", - "material/comment-arrow-right", - "material/comment-bookmark-outline", - "material/comment-bookmark", - "material/comment-check-outline", - "material/comment-check", - "material/comment-edit-outline", - "material/comment-edit", - "material/comment-eye-outline", - "material/comment-eye", - "material/comment-flash-outline", - "material/comment-flash", - "material/comment-minus-outline", - "material/comment-minus", - "material/comment-multiple-outline", - "material/comment-multiple", - "material/comment-off-outline", - "material/comment-off", - "material/comment-outline", - "material/comment-plus-outline", - "material/comment-plus", - "material/comment-processing-outline", - "material/comment-processing", - "material/comment-question-outline", - "material/comment-question", - "material/comment-quote-outline", - "material/comment-quote", - "material/comment-remove-outline", - "material/comment-remove", - "material/comment-search-outline", - "material/comment-search", - "material/comment-text-multiple-outline", - "material/comment-text-multiple", - "material/comment-text-outline", - "material/comment-text", - "material/comment", - "material/compare-horizontal", - "material/compare-remove", - "material/compare-vertical", - "material/compare", - "material/compass-off-outline", - "material/compass-off", - "material/compass-outline", - "material/compass-rose", - "material/compass", - "material/compost", - "material/cone-off", - "material/cone", - "material/connection", - "material/console-line", - "material/console-network-outline", - "material/console-network", - "material/console", - "material/consolidate", - "material/contactless-payment-circle-outline", - "material/contactless-payment-circle", - "material/contactless-payment", - "material/contacts-outline", - "material/contacts", - "material/contain-end", - "material/contain-start", - "material/contain", - "material/content-copy", - "material/content-cut", - "material/content-duplicate", - "material/content-paste", - "material/content-save-alert-outline", - "material/content-save-alert", - "material/content-save-all-outline", - "material/content-save-all", - "material/content-save-check-outline", - "material/content-save-check", - "material/content-save-cog-outline", - "material/content-save-cog", - "material/content-save-edit-outline", - "material/content-save-edit", - "material/content-save-minus-outline", - "material/content-save-minus", - "material/content-save-move-outline", - "material/content-save-move", - "material/content-save-off-outline", - "material/content-save-off", - "material/content-save-outline", - "material/content-save-plus-outline", - "material/content-save-plus", - "material/content-save-settings-outline", - "material/content-save-settings", - "material/content-save", - "material/contrast-box", - "material/contrast-circle", - "material/contrast", - "material/controller-classic-outline", - "material/controller-classic", - "material/controller-off", - "material/controller", - "material/cookie-alert-outline", - "material/cookie-alert", - "material/cookie-check-outline", - "material/cookie-check", - "material/cookie-clock-outline", - "material/cookie-clock", - "material/cookie-cog-outline", - "material/cookie-cog", - "material/cookie-edit-outline", - "material/cookie-edit", - "material/cookie-lock-outline", - "material/cookie-lock", - "material/cookie-minus-outline", - "material/cookie-minus", - "material/cookie-off-outline", - "material/cookie-off", - "material/cookie-outline", - "material/cookie-plus-outline", - "material/cookie-plus", - "material/cookie-refresh-outline", - "material/cookie-refresh", - "material/cookie-remove-outline", - "material/cookie-remove", - "material/cookie-settings-outline", - "material/cookie-settings", - "material/cookie", - "material/coolant-temperature", - "material/copyleft", - "material/copyright", - "material/cordova", - "material/corn-off", - "material/corn", - "material/cosine-wave", - "material/counter", - "material/countertop-outline", - "material/countertop", - "material/cow-off", - "material/cow", - "material/cpu-32-bit", - "material/cpu-64-bit", - "material/cradle-outline", - "material/cradle", - "material/crane", - "material/creation", - "material/creative-commons", - "material/credit-card-check-outline", - "material/credit-card-check", - "material/credit-card-chip-outline", - "material/credit-card-chip", - "material/credit-card-clock-outline", - "material/credit-card-clock", - "material/credit-card-edit-outline", - "material/credit-card-edit", - "material/credit-card-fast-outline", - "material/credit-card-fast", - "material/credit-card-lock-outline", - "material/credit-card-lock", - "material/credit-card-marker-outline", - "material/credit-card-marker", - "material/credit-card-minus-outline", - "material/credit-card-minus", - "material/credit-card-multiple-outline", - "material/credit-card-multiple", - "material/credit-card-off-outline", - "material/credit-card-off", - "material/credit-card-outline", - "material/credit-card-plus-outline", - "material/credit-card-plus", - "material/credit-card-refresh-outline", - "material/credit-card-refresh", - "material/credit-card-refund-outline", - "material/credit-card-refund", - "material/credit-card-remove-outline", - "material/credit-card-remove", - "material/credit-card-scan-outline", - "material/credit-card-scan", - "material/credit-card-search-outline", - "material/credit-card-search", - "material/credit-card-settings-outline", - "material/credit-card-settings", - "material/credit-card-sync-outline", - "material/credit-card-sync", - "material/credit-card-wireless-off-outline", - "material/credit-card-wireless-off", - "material/credit-card-wireless-outline", - "material/credit-card-wireless", - "material/credit-card", - "material/cricket", - "material/crop-free", - "material/crop-landscape", - "material/crop-portrait", - "material/crop-rotate", - "material/crop-square", - "material/crop", - "material/cross-bolnisi", - "material/cross-celtic", - "material/cross-outline", - "material/cross", - "material/crosshairs-gps", - "material/crosshairs-off", - "material/crosshairs-question", - "material/crosshairs", - "material/crowd", - "material/crown-circle-outline", - "material/crown-circle", - "material/crown-outline", - "material/crown", - "material/cryengine", - "material/crystal-ball", - "material/cube-off-outline", - "material/cube-off", - "material/cube-outline", - "material/cube-scan", - "material/cube-send", - "material/cube-unfolded", - "material/cube", - "material/cup-off-outline", - "material/cup-off", - "material/cup-outline", - "material/cup-water", - "material/cup", - "material/cupboard-outline", - "material/cupboard", - "material/cupcake", - "material/curling", - "material/currency-bdt", - "material/currency-brl", - "material/currency-btc", - "material/currency-cny", - "material/currency-eth", - "material/currency-eur-off", - "material/currency-eur", - "material/currency-fra", - "material/currency-gbp", - "material/currency-ils", - "material/currency-inr", - "material/currency-jpy", - "material/currency-krw", - "material/currency-kzt", - "material/currency-mnt", - "material/currency-ngn", - "material/currency-php", - "material/currency-rial", - "material/currency-rub", - "material/currency-rupee", - "material/currency-sign", - "material/currency-try", - "material/currency-twd", - "material/currency-uah", - "material/currency-usd-off", - "material/currency-usd", - "material/current-ac", - "material/current-dc", - "material/cursor-default-click-outline", - "material/cursor-default-click", - "material/cursor-default-gesture-outline", - "material/cursor-default-gesture", - "material/cursor-default-outline", - "material/cursor-default", - "material/cursor-move", - "material/cursor-pointer", - "material/cursor-text", - "material/curtains-closed", - "material/curtains", - "material/cylinder-off", - "material/cylinder", - "material/dance-ballroom", - "material/dance-pole", - "material/data-matrix-edit", - "material/data-matrix-minus", - "material/data-matrix-plus", - "material/data-matrix-remove", - "material/data-matrix-scan", - "material/data-matrix", - "material/database-alert-outline", - "material/database-alert", - "material/database-arrow-down-outline", - "material/database-arrow-down", - "material/database-arrow-left-outline", - "material/database-arrow-left", - "material/database-arrow-right-outline", - "material/database-arrow-right", - "material/database-arrow-up-outline", - "material/database-arrow-up", - "material/database-check-outline", - "material/database-check", - "material/database-clock-outline", - "material/database-clock", - "material/database-cog-outline", - "material/database-cog", - "material/database-edit-outline", - "material/database-edit", - "material/database-export-outline", - "material/database-export", - "material/database-eye-off-outline", - "material/database-eye-off", - "material/database-eye-outline", - "material/database-eye", - "material/database-import-outline", - "material/database-import", - "material/database-lock-outline", - "material/database-lock", - "material/database-marker-outline", - "material/database-marker", - "material/database-minus-outline", - "material/database-minus", - "material/database-off-outline", - "material/database-off", - "material/database-outline", - "material/database-plus-outline", - "material/database-plus", - "material/database-refresh-outline", - "material/database-refresh", - "material/database-remove-outline", - "material/database-remove", - "material/database-search-outline", - "material/database-search", - "material/database-settings-outline", - "material/database-settings", - "material/database-sync-outline", - "material/database-sync", - "material/database", - "material/death-star-variant", - "material/death-star", - "material/deathly-hallows", - "material/debian", - "material/debug-step-into", - "material/debug-step-out", - "material/debug-step-over", - "material/decagram-outline", - "material/decagram", - "material/decimal-comma-decrease", - "material/decimal-comma-increase", - "material/decimal-comma", - "material/decimal-decrease", - "material/decimal-increase", - "material/decimal", - "material/delete-alert-outline", - "material/delete-alert", - "material/delete-circle-outline", - "material/delete-circle", - "material/delete-clock-outline", - "material/delete-clock", - "material/delete-empty-outline", - "material/delete-empty", - "material/delete-forever-outline", - "material/delete-forever", - "material/delete-off-outline", - "material/delete-off", - "material/delete-outline", - "material/delete-restore", - "material/delete-sweep-outline", - "material/delete-sweep", - "material/delete-variant", - "material/delete", - "material/delta", - "material/desk-lamp-off", - "material/desk-lamp-on", - "material/desk-lamp", - "material/desk", - "material/deskphone", - "material/desktop-classic", - "material/desktop-tower-monitor", - "material/desktop-tower", - "material/details", - "material/dev-to", - "material/developer-board", - "material/deviantart", - "material/devices", - "material/dharmachakra", - "material/diabetes", - "material/dialpad", - "material/diameter-outline", - "material/diameter-variant", - "material/diameter", - "material/diamond-outline", - "material/diamond-stone", - "material/diamond", - "material/dice-1-outline", - "material/dice-1", - "material/dice-2-outline", - "material/dice-2", - "material/dice-3-outline", - "material/dice-3", - "material/dice-4-outline", - "material/dice-4", - "material/dice-5-outline", - "material/dice-5", - "material/dice-6-outline", - "material/dice-6", - "material/dice-d10-outline", - "material/dice-d10", - "material/dice-d12-outline", - "material/dice-d12", - "material/dice-d20-outline", - "material/dice-d20", - "material/dice-d4-outline", - "material/dice-d4", - "material/dice-d6-outline", - "material/dice-d6", - "material/dice-d8-outline", - "material/dice-d8", - "material/dice-multiple-outline", - "material/dice-multiple", - "material/digital-ocean", - "material/dip-switch", - "material/directions-fork", - "material/directions", - "material/disc-alert", - "material/disc-player", - "material/disc", - "material/dishwasher-alert", - "material/dishwasher-off", - "material/dishwasher", - "material/disqus", - "material/distribute-horizontal-center", - "material/distribute-horizontal-left", - "material/distribute-horizontal-right", - "material/distribute-vertical-bottom", - "material/distribute-vertical-center", - "material/distribute-vertical-top", - "material/diversify", - "material/diving-flippers", - "material/diving-helmet", - "material/diving-scuba-flag", - "material/diving-scuba-mask", - "material/diving-scuba-tank-multiple", - "material/diving-scuba-tank", - "material/diving-scuba", - "material/diving-snorkel", - "material/diving", - "material/division-box", - "material/division", - "material/dlna", - "material/dna", - "material/dns-outline", - "material/dns", - "material/dock-bottom", - "material/dock-left", - "material/dock-right", - "material/dock-top", - "material/dock-window", - "material/docker", - "material/doctor", - "material/dog-service", - "material/dog-side-off", - "material/dog-side", - "material/dog", - "material/dolby", - "material/dolly", - "material/dolphin", - "material/domain-off", - "material/domain-plus", - "material/domain-remove", - "material/domain", - "material/dome-light", - "material/domino-mask", - "material/donkey", - "material/door-closed-lock", - "material/door-closed", - "material/door-open", - "material/door-sliding-lock", - "material/door-sliding-open", - "material/door-sliding", - "material/door", - "material/doorbell-video", - "material/doorbell", - "material/dot-net", - "material/dots-circle", - "material/dots-grid", - "material/dots-hexagon", - "material/dots-horizontal-circle-outline", - "material/dots-horizontal-circle", - "material/dots-horizontal", - "material/dots-square", - "material/dots-triangle", - "material/dots-vertical-circle-outline", - "material/dots-vertical-circle", - "material/dots-vertical", - "material/download-box-outline", - "material/download-box", - "material/download-circle-outline", - "material/download-circle", - "material/download-lock-outline", - "material/download-lock", - "material/download-multiple", - "material/download-network-outline", - "material/download-network", - "material/download-off-outline", - "material/download-off", - "material/download-outline", - "material/download", - "material/drag-horizontal-variant", - "material/drag-horizontal", - "material/drag-variant", - "material/drag-vertical-variant", - "material/drag-vertical", - "material/drag", - "material/drama-masks", - "material/draw-pen", - "material/draw", - "material/drawing-box", - "material/drawing", - "material/dresser-outline", - "material/dresser", - "material/drone", - "material/dropbox", - "material/drupal", - "material/duck", - "material/dumbbell", - "material/dump-truck", - "material/ear-hearing-loop", - "material/ear-hearing-off", - "material/ear-hearing", - "material/earbuds-off-outline", - "material/earbuds-off", - "material/earbuds-outline", - "material/earbuds", - "material/earth-arrow-right", - "material/earth-box-minus", - "material/earth-box-off", - "material/earth-box-plus", - "material/earth-box-remove", - "material/earth-box", - "material/earth-minus", - "material/earth-off", - "material/earth-plus", - "material/earth-remove", - "material/earth", - "material/egg-easter", - "material/egg-fried", - "material/egg-off-outline", - "material/egg-off", - "material/egg-outline", - "material/egg", - "material/eiffel-tower", - "material/eight-track", - "material/eject-circle-outline", - "material/eject-circle", - "material/eject-outline", - "material/eject", - "material/electric-switch-closed", - "material/electric-switch", - "material/electron-framework", - "material/elephant", - "material/elevation-decline", - "material/elevation-rise", - "material/elevator-down", - "material/elevator-passenger-off-outline", - "material/elevator-passenger-off", - "material/elevator-passenger-outline", - "material/elevator-passenger", - "material/elevator-up", - "material/elevator", - "material/ellipse-outline", - "material/ellipse", - "material/email-alert-outline", - "material/email-alert", - "material/email-arrow-left-outline", - "material/email-arrow-left", - "material/email-arrow-right-outline", - "material/email-arrow-right", - "material/email-box", - "material/email-check-outline", - "material/email-check", - "material/email-edit-outline", - "material/email-edit", - "material/email-fast-outline", - "material/email-fast", - "material/email-lock-outline", - "material/email-lock", - "material/email-mark-as-unread", - "material/email-minus-outline", - "material/email-minus", - "material/email-multiple-outline", - "material/email-multiple", - "material/email-newsletter", - "material/email-off-outline", - "material/email-off", - "material/email-open-multiple-outline", - "material/email-open-multiple", - "material/email-open-outline", - "material/email-open", - "material/email-outline", - "material/email-plus-outline", - "material/email-plus", - "material/email-remove-outline", - "material/email-remove", - "material/email-seal-outline", - "material/email-seal", - "material/email-search-outline", - "material/email-search", - "material/email-sync-outline", - "material/email-sync", - "material/email-variant", - "material/email", - "material/ember", - "material/emby", - "material/emoticon-angry-outline", - "material/emoticon-angry", - "material/emoticon-confused-outline", - "material/emoticon-confused", - "material/emoticon-cool-outline", - "material/emoticon-cool", - "material/emoticon-cry-outline", - "material/emoticon-cry", - "material/emoticon-dead-outline", - "material/emoticon-dead", - "material/emoticon-devil-outline", - "material/emoticon-devil", - "material/emoticon-excited-outline", - "material/emoticon-excited", - "material/emoticon-frown-outline", - "material/emoticon-frown", - "material/emoticon-happy-outline", - "material/emoticon-happy", - "material/emoticon-kiss-outline", - "material/emoticon-kiss", - "material/emoticon-lol-outline", - "material/emoticon-lol", - "material/emoticon-neutral-outline", - "material/emoticon-neutral", - "material/emoticon-outline", - "material/emoticon-poop-outline", - "material/emoticon-poop", - "material/emoticon-sad-outline", - "material/emoticon-sad", - "material/emoticon-sick-outline", - "material/emoticon-sick", - "material/emoticon-tongue-outline", - "material/emoticon-tongue", - "material/emoticon-wink-outline", - "material/emoticon-wink", - "material/emoticon", - "material/engine-off-outline", - "material/engine-off", - "material/engine-outline", - "material/engine", - "material/epsilon", - "material/equal-box", - "material/equal", - "material/equalizer-outline", - "material/equalizer", - "material/eraser-variant", - "material/eraser", - "material/escalator-box", - "material/escalator-down", - "material/escalator-up", - "material/escalator", - "material/eslint", - "material/et", - "material/ethereum", - "material/ethernet-cable-off", - "material/ethernet-cable", - "material/ethernet", - "material/ev-plug-ccs1", - "material/ev-plug-ccs2", - "material/ev-plug-chademo", - "material/ev-plug-tesla", - "material/ev-plug-type1", - "material/ev-plug-type2", - "material/ev-station", - "material/evernote", - "material/excavator", - "material/exclamation-thick", - "material/exclamation", - "material/exit-run", - "material/exit-to-app", - "material/expand-all-outline", - "material/expand-all", - "material/expansion-card-variant", - "material/expansion-card", - "material/exponent-box", - "material/exponent", - "material/export-variant", - "material/export", - "material/eye-arrow-left-outline", - "material/eye-arrow-left", - "material/eye-arrow-right-outline", - "material/eye-arrow-right", - "material/eye-check-outline", - "material/eye-check", - "material/eye-circle-outline", - "material/eye-circle", - "material/eye-minus-outline", - "material/eye-minus", - "material/eye-off-outline", - "material/eye-off", - "material/eye-outline", - "material/eye-plus-outline", - "material/eye-plus", - "material/eye-refresh-outline", - "material/eye-refresh", - "material/eye-remove-outline", - "material/eye-remove", - "material/eye-settings-outline", - "material/eye-settings", - "material/eye", - "material/eyedropper-minus", - "material/eyedropper-off", - "material/eyedropper-plus", - "material/eyedropper-remove", - "material/eyedropper-variant", - "material/eyedropper", - "material/face-agent", - "material/face-man-outline", - "material/face-man-profile", - "material/face-man-shimmer-outline", - "material/face-man-shimmer", - "material/face-man", - "material/face-mask-outline", - "material/face-mask", - "material/face-recognition", - "material/face-woman-outline", - "material/face-woman-profile", - "material/face-woman-shimmer-outline", - "material/face-woman-shimmer", - "material/face-woman", - "material/facebook-gaming", - "material/facebook-messenger", - "material/facebook-workplace", - "material/facebook", - "material/factory", - "material/family-tree", - "material/fan-alert", - "material/fan-auto", - "material/fan-chevron-down", - "material/fan-chevron-up", - "material/fan-clock", - "material/fan-minus", - "material/fan-off", - "material/fan-plus", - "material/fan-remove", - "material/fan-speed-1", - "material/fan-speed-2", - "material/fan-speed-3", - "material/fan", - "material/fast-forward-10", - "material/fast-forward-15", - "material/fast-forward-30", - "material/fast-forward-45", - "material/fast-forward-5", - "material/fast-forward-60", - "material/fast-forward-outline", - "material/fast-forward", - "material/faucet-variant", - "material/faucet", - "material/fax", - "material/feather", - "material/feature-search-outline", - "material/feature-search", - "material/fedora", - "material/fence-electric", - "material/fence", - "material/fencing", - "material/ferris-wheel", - "material/ferry", - "material/file-account-outline", - "material/file-account", - "material/file-alert-outline", - "material/file-alert", - "material/file-arrow-left-right-outline", - "material/file-arrow-left-right", - "material/file-arrow-up-down-outline", - "material/file-arrow-up-down", - "material/file-cabinet", - "material/file-cad-box", - "material/file-cad", - "material/file-cancel-outline", - "material/file-cancel", - "material/file-certificate-outline", - "material/file-certificate", - "material/file-chart-check-outline", - "material/file-chart-check", - "material/file-chart-outline", - "material/file-chart", - "material/file-check-outline", - "material/file-check", - "material/file-clock-outline", - "material/file-clock", - "material/file-cloud-outline", - "material/file-cloud", - "material/file-code-outline", - "material/file-code", - "material/file-cog-outline", - "material/file-cog", - "material/file-compare", - "material/file-delimited-outline", - "material/file-delimited", - "material/file-document-alert-outline", - "material/file-document-alert", - "material/file-document-check-outline", - "material/file-document-check", - "material/file-document-edit-outline", - "material/file-document-edit", - "material/file-document-minus-outline", - "material/file-document-minus", - "material/file-document-multiple-outline", - "material/file-document-multiple", - "material/file-document-outline", - "material/file-document-plus-outline", - "material/file-document-plus", - "material/file-document-remove-outline", - "material/file-document-remove", - "material/file-document", - "material/file-download-outline", - "material/file-download", - "material/file-edit-outline", - "material/file-edit", - "material/file-excel-box-outline", - "material/file-excel-box", - "material/file-excel-outline", - "material/file-excel", - "material/file-export-outline", - "material/file-export", - "material/file-eye-outline", - "material/file-eye", - "material/file-find-outline", - "material/file-find", - "material/file-gif-box", - "material/file-hidden", - "material/file-image-marker-outline", - "material/file-image-marker", - "material/file-image-minus-outline", - "material/file-image-minus", - "material/file-image-outline", - "material/file-image-plus-outline", - "material/file-image-plus", - "material/file-image-remove-outline", - "material/file-image-remove", - "material/file-image", - "material/file-import-outline", - "material/file-import", - "material/file-jpg-box", - "material/file-key-outline", - "material/file-key", - "material/file-link-outline", - "material/file-link", - "material/file-lock-open-outline", - "material/file-lock-open", - "material/file-lock-outline", - "material/file-lock", - "material/file-marker-outline", - "material/file-marker", - "material/file-minus-outline", - "material/file-minus", - "material/file-move-outline", - "material/file-move", - "material/file-multiple-outline", - "material/file-multiple", - "material/file-music-outline", - "material/file-music", - "material/file-outline", - "material/file-pdf-box", - "material/file-percent-outline", - "material/file-percent", - "material/file-phone-outline", - "material/file-phone", - "material/file-plus-outline", - "material/file-plus", - "material/file-png-box", - "material/file-powerpoint-box-outline", - "material/file-powerpoint-box", - "material/file-powerpoint-outline", - "material/file-powerpoint", - "material/file-presentation-box", - "material/file-question-outline", - "material/file-question", - "material/file-refresh-outline", - "material/file-refresh", - "material/file-remove-outline", - "material/file-remove", - "material/file-replace-outline", - "material/file-replace", - "material/file-restore-outline", - "material/file-restore", - "material/file-rotate-left-outline", - "material/file-rotate-left", - "material/file-rotate-right-outline", - "material/file-rotate-right", - "material/file-search-outline", - "material/file-search", - "material/file-send-outline", - "material/file-send", - "material/file-settings-outline", - "material/file-settings", - "material/file-sign", - "material/file-star-outline", - "material/file-star", - "material/file-swap-outline", - "material/file-swap", - "material/file-sync-outline", - "material/file-sync", - "material/file-table-box-multiple-outline", - "material/file-table-box-multiple", - "material/file-table-box-outline", - "material/file-table-box", - "material/file-table-outline", - "material/file-table", - "material/file-tree-outline", - "material/file-tree", - "material/file-undo-outline", - "material/file-undo", - "material/file-upload-outline", - "material/file-upload", - "material/file-video-outline", - "material/file-video", - "material/file-word-box-outline", - "material/file-word-box", - "material/file-word-outline", - "material/file-word", - "material/file-xml-box", - "material/file", - "material/film", - "material/filmstrip-box-multiple", - "material/filmstrip-box", - "material/filmstrip-off", - "material/filmstrip", - "material/filter-check-outline", - "material/filter-check", - "material/filter-cog-outline", - "material/filter-cog", - "material/filter-menu-outline", - "material/filter-menu", - "material/filter-minus-outline", - "material/filter-minus", - "material/filter-multiple-outline", - "material/filter-multiple", - "material/filter-off-outline", - "material/filter-off", - "material/filter-outline", - "material/filter-plus-outline", - "material/filter-plus", - "material/filter-remove-outline", - "material/filter-remove", - "material/filter-settings-outline", - "material/filter-settings", - "material/filter-variant-minus", - "material/filter-variant-plus", - "material/filter-variant-remove", - "material/filter-variant", - "material/filter", - "material/finance", - "material/find-replace", - "material/fingerprint-off", - "material/fingerprint", - "material/fire-alert", - "material/fire-circle", - "material/fire-extinguisher", - "material/fire-hydrant-alert", - "material/fire-hydrant-off", - "material/fire-hydrant", - "material/fire-off", - "material/fire-truck", - "material/fire", - "material/firebase", - "material/firefox", - "material/fireplace-off", - "material/fireplace", - "material/firewire", - "material/firework-off", - "material/firework", - "material/fish-off", - "material/fish", - "material/fishbowl-outline", - "material/fishbowl", - "material/fit-to-page-outline", - "material/fit-to-page", - "material/fit-to-screen-outline", - "material/fit-to-screen", - "material/flag-checkered", - "material/flag-minus-outline", - "material/flag-minus", - "material/flag-off-outline", - "material/flag-off", - "material/flag-outline", - "material/flag-plus-outline", - "material/flag-plus", - "material/flag-remove-outline", - "material/flag-remove", - "material/flag-triangle", - "material/flag-variant-minus-outline", - "material/flag-variant-minus", - "material/flag-variant-off-outline", - "material/flag-variant-off", - "material/flag-variant-outline", - "material/flag-variant-plus-outline", - "material/flag-variant-plus", - "material/flag-variant-remove-outline", - "material/flag-variant-remove", - "material/flag-variant", - "material/flag", - "material/flare", - "material/flash-alert-outline", - "material/flash-alert", - "material/flash-auto", - "material/flash-off-outline", - "material/flash-off", - "material/flash-outline", - "material/flash-red-eye", - "material/flash-triangle-outline", - "material/flash-triangle", - "material/flash", - "material/flashlight-off", - "material/flashlight", - "material/flask-empty-minus-outline", - "material/flask-empty-minus", - "material/flask-empty-off-outline", - "material/flask-empty-off", - "material/flask-empty-outline", - "material/flask-empty-plus-outline", - "material/flask-empty-plus", - "material/flask-empty-remove-outline", - "material/flask-empty-remove", - "material/flask-empty", - "material/flask-minus-outline", - "material/flask-minus", - "material/flask-off-outline", - "material/flask-off", - "material/flask-outline", - "material/flask-plus-outline", - "material/flask-plus", - "material/flask-remove-outline", - "material/flask-remove", - "material/flask-round-bottom-empty-outline", - "material/flask-round-bottom-empty", - "material/flask-round-bottom-outline", - "material/flask-round-bottom", - "material/flask", - "material/fleur-de-lis", - "material/flip-horizontal", - "material/flip-to-back", - "material/flip-to-front", - "material/flip-vertical", - "material/floor-lamp-dual-outline", - "material/floor-lamp-dual", - "material/floor-lamp-outline", - "material/floor-lamp-torchiere-outline", - "material/floor-lamp-torchiere-variant-outline", - "material/floor-lamp-torchiere-variant", - "material/floor-lamp-torchiere", - "material/floor-lamp", - "material/floor-plan", - "material/floppy-variant", - "material/floppy", - "material/flower-outline", - "material/flower-pollen-outline", - "material/flower-pollen", - "material/flower-poppy", - "material/flower-tulip-outline", - "material/flower-tulip", - "material/flower", - "material/focus-auto", - "material/focus-field-horizontal", - "material/focus-field-vertical", - "material/focus-field", - "material/folder-account-outline", - "material/folder-account", - "material/folder-alert-outline", - "material/folder-alert", - "material/folder-arrow-down-outline", - "material/folder-arrow-down", - "material/folder-arrow-left-outline", - "material/folder-arrow-left-right-outline", - "material/folder-arrow-left-right", - "material/folder-arrow-left", - "material/folder-arrow-right-outline", - "material/folder-arrow-right", - "material/folder-arrow-up-down-outline", - "material/folder-arrow-up-down", - "material/folder-arrow-up-outline", - "material/folder-arrow-up", - "material/folder-cancel-outline", - "material/folder-cancel", - "material/folder-check-outline", - "material/folder-check", - "material/folder-clock-outline", - "material/folder-clock", - "material/folder-cog-outline", - "material/folder-cog", - "material/folder-download-outline", - "material/folder-download", - "material/folder-edit-outline", - "material/folder-edit", - "material/folder-eye-outline", - "material/folder-eye", - "material/folder-file-outline", - "material/folder-file", - "material/folder-google-drive", - "material/folder-heart-outline", - "material/folder-heart", - "material/folder-hidden", - "material/folder-home-outline", - "material/folder-home", - "material/folder-image", - "material/folder-information-outline", - "material/folder-information", - "material/folder-key-network-outline", - "material/folder-key-network", - "material/folder-key-outline", - "material/folder-key", - "material/folder-lock-open-outline", - "material/folder-lock-open", - "material/folder-lock-outline", - "material/folder-lock", - "material/folder-marker-outline", - "material/folder-marker", - "material/folder-minus-outline", - "material/folder-minus", - "material/folder-move-outline", - "material/folder-move", - "material/folder-multiple-image", - "material/folder-multiple-outline", - "material/folder-multiple-plus-outline", - "material/folder-multiple-plus", - "material/folder-multiple", - "material/folder-music-outline", - "material/folder-music", - "material/folder-network-outline", - "material/folder-network", - "material/folder-off-outline", - "material/folder-off", - "material/folder-open-outline", - "material/folder-open", - "material/folder-outline", - "material/folder-play-outline", - "material/folder-play", - "material/folder-plus-outline", - "material/folder-plus", - "material/folder-pound-outline", - "material/folder-pound", - "material/folder-question-outline", - "material/folder-question", - "material/folder-refresh-outline", - "material/folder-refresh", - "material/folder-remove-outline", - "material/folder-remove", - "material/folder-search-outline", - "material/folder-search", - "material/folder-settings-outline", - "material/folder-settings", - "material/folder-star-multiple-outline", - "material/folder-star-multiple", - "material/folder-star-outline", - "material/folder-star", - "material/folder-swap-outline", - "material/folder-swap", - "material/folder-sync-outline", - "material/folder-sync", - "material/folder-table-outline", - "material/folder-table", - "material/folder-text-outline", - "material/folder-text", - "material/folder-upload-outline", - "material/folder-upload", - "material/folder-wrench-outline", - "material/folder-wrench", - "material/folder-zip-outline", - "material/folder-zip", - "material/folder", - "material/font-awesome", - "material/food-apple-outline", - "material/food-apple", - "material/food-croissant", - "material/food-drumstick-off-outline", - "material/food-drumstick-off", - "material/food-drumstick-outline", - "material/food-drumstick", - "material/food-fork-drink", - "material/food-halal", - "material/food-hot-dog", - "material/food-kosher", - "material/food-off-outline", - "material/food-off", - "material/food-outline", - "material/food-steak-off", - "material/food-steak", - "material/food-takeout-box-outline", - "material/food-takeout-box", - "material/food-turkey", - "material/food-variant-off", - "material/food-variant", - "material/food", - "material/foot-print", - "material/football-australian", - "material/football-helmet", - "material/football", - "material/forest", - "material/forklift", - "material/form-dropdown", - "material/form-select", - "material/form-textarea", - "material/form-textbox-lock", - "material/form-textbox-password", - "material/form-textbox", - "material/format-align-bottom", - "material/format-align-center", - "material/format-align-justify", - "material/format-align-left", - "material/format-align-middle", - "material/format-align-right", - "material/format-align-top", - "material/format-annotation-minus", - "material/format-annotation-plus", - "material/format-bold", - "material/format-clear", - "material/format-color-fill", - "material/format-color-highlight", - "material/format-color-marker-cancel", - "material/format-color-text", - "material/format-columns", - "material/format-float-center", - "material/format-float-left", - "material/format-float-none", - "material/format-float-right", - "material/format-font-size-decrease", - "material/format-font-size-increase", - "material/format-font", - "material/format-header-1", - "material/format-header-2", - "material/format-header-3", - "material/format-header-4", - "material/format-header-5", - "material/format-header-6", - "material/format-header-decrease", - "material/format-header-equal", - "material/format-header-increase", - "material/format-header-pound", - "material/format-horizontal-align-center", - "material/format-horizontal-align-left", - "material/format-horizontal-align-right", - "material/format-indent-decrease", - "material/format-indent-increase", - "material/format-italic", - "material/format-letter-case-lower", - "material/format-letter-case-upper", - "material/format-letter-case", - "material/format-letter-ends-with", - "material/format-letter-matches", - "material/format-letter-spacing-variant", - "material/format-letter-spacing", - "material/format-letter-starts-with", - "material/format-line-height", - "material/format-line-spacing", - "material/format-line-style", - "material/format-line-weight", - "material/format-list-bulleted-square", - "material/format-list-bulleted-triangle", - "material/format-list-bulleted-type", - "material/format-list-bulleted", - "material/format-list-checkbox", - "material/format-list-checks", - "material/format-list-group-plus", - "material/format-list-group", - "material/format-list-numbered-rtl", - "material/format-list-numbered", - "material/format-list-text", - "material/format-overline", - "material/format-page-break", - "material/format-page-split", - "material/format-paint", - "material/format-paragraph-spacing", - "material/format-paragraph", - "material/format-pilcrow-arrow-left", - "material/format-pilcrow-arrow-right", - "material/format-pilcrow", - "material/format-quote-close-outline", - "material/format-quote-close", - "material/format-quote-open-outline", - "material/format-quote-open", - "material/format-rotate-90", - "material/format-section", - "material/format-size", - "material/format-strikethrough-variant", - "material/format-strikethrough", - "material/format-subscript", - "material/format-superscript", - "material/format-text-rotation-angle-down", - "material/format-text-rotation-angle-up", - "material/format-text-rotation-down-vertical", - "material/format-text-rotation-down", - "material/format-text-rotation-none", - "material/format-text-rotation-up", - "material/format-text-rotation-vertical", - "material/format-text-variant-outline", - "material/format-text-variant", - "material/format-text-wrapping-clip", - "material/format-text-wrapping-overflow", - "material/format-text-wrapping-wrap", - "material/format-text", - "material/format-textbox", - "material/format-title", - "material/format-underline-wavy", - "material/format-underline", - "material/format-vertical-align-bottom", - "material/format-vertical-align-center", - "material/format-vertical-align-top", - "material/format-wrap-inline", - "material/format-wrap-square", - "material/format-wrap-tight", - "material/format-wrap-top-bottom", - "material/forum-minus-outline", - "material/forum-minus", - "material/forum-outline", - "material/forum-plus-outline", - "material/forum-plus", - "material/forum-remove-outline", - "material/forum-remove", - "material/forum", - "material/forward", - "material/forwardburger", - "material/fountain-pen-tip", - "material/fountain-pen", - "material/fountain", - "material/fraction-one-half", - "material/freebsd", - "material/french-fries", - "material/frequently-asked-questions", - "material/fridge-alert-outline", - "material/fridge-alert", - "material/fridge-bottom", - "material/fridge-industrial-alert-outline", - "material/fridge-industrial-alert", - "material/fridge-industrial-off-outline", - "material/fridge-industrial-off", - "material/fridge-industrial-outline", - "material/fridge-industrial", - "material/fridge-off-outline", - "material/fridge-off", - "material/fridge-outline", - "material/fridge-top", - "material/fridge-variant-alert-outline", - "material/fridge-variant-alert", - "material/fridge-variant-off-outline", - "material/fridge-variant-off", - "material/fridge-variant-outline", - "material/fridge-variant", - "material/fridge", - "material/fruit-cherries-off", - "material/fruit-cherries", - "material/fruit-citrus-off", - "material/fruit-citrus", - "material/fruit-grapes-outline", - "material/fruit-grapes", - "material/fruit-pear", - "material/fruit-pineapple", - "material/fruit-watermelon", - "material/fuel-cell", - "material/fuel", - "material/fullscreen-exit", - "material/fullscreen", - "material/function-variant", - "material/function", - "material/furigana-horizontal", - "material/furigana-vertical", - "material/fuse-alert", - "material/fuse-blade", - "material/fuse-off", - "material/fuse", - "material/gamepad-circle-down", - "material/gamepad-circle-left", - "material/gamepad-circle-outline", - "material/gamepad-circle-right", - "material/gamepad-circle-up", - "material/gamepad-circle", - "material/gamepad-down", - "material/gamepad-left", - "material/gamepad-outline", - "material/gamepad-right", - "material/gamepad-round-down", - "material/gamepad-round-left", - "material/gamepad-round-outline", - "material/gamepad-round-right", - "material/gamepad-round-up", - "material/gamepad-round", - "material/gamepad-square-outline", - "material/gamepad-square", - "material/gamepad-up", - "material/gamepad-variant-outline", - "material/gamepad-variant", - "material/gamepad", - "material/gamma", - "material/gantry-crane", - "material/garage-alert-variant", - "material/garage-alert", - "material/garage-lock", - "material/garage-open-variant", - "material/garage-open", - "material/garage-variant-lock", - "material/garage-variant", - "material/garage", - "material/gas-burner", - "material/gas-cylinder", - "material/gas-station-off-outline", - "material/gas-station-off", - "material/gas-station-outline", - "material/gas-station", - "material/gate-alert", - "material/gate-and", - "material/gate-arrow-left", - "material/gate-arrow-right", - "material/gate-buffer", - "material/gate-nand", - "material/gate-nor", - "material/gate-not", - "material/gate-open", - "material/gate-or", - "material/gate-xnor", - "material/gate-xor", - "material/gate", - "material/gatsby", - "material/gauge-empty", - "material/gauge-full", - "material/gauge-low", - "material/gauge", - "material/gavel", - "material/gender-female", - "material/gender-male-female-variant", - "material/gender-male-female", - "material/gender-male", - "material/gender-non-binary", - "material/gender-transgender", - "material/gentoo", - "material/gesture-double-tap", - "material/gesture-pinch", - "material/gesture-spread", - "material/gesture-swipe-down", - "material/gesture-swipe-horizontal", - "material/gesture-swipe-left", - "material/gesture-swipe-right", - "material/gesture-swipe-up", - "material/gesture-swipe-vertical", - "material/gesture-swipe", - "material/gesture-tap-box", - "material/gesture-tap-button", - "material/gesture-tap-hold", - "material/gesture-tap", - "material/gesture-two-double-tap", - "material/gesture-two-tap", - "material/gesture", - "material/ghost-off-outline", - "material/ghost-off", - "material/ghost-outline", - "material/ghost", - "material/gift-off-outline", - "material/gift-off", - "material/gift-open-outline", - "material/gift-open", - "material/gift-outline", - "material/gift", - "material/git", - "material/github", - "material/gitlab", - "material/glass-cocktail-off", - "material/glass-cocktail", - "material/glass-flute", - "material/glass-fragile", - "material/glass-mug-off", - "material/glass-mug-variant-off", - "material/glass-mug-variant", - "material/glass-mug", - "material/glass-pint-outline", - "material/glass-stange", - "material/glass-tulip", - "material/glass-wine", - "material/glasses", - "material/globe-light-outline", - "material/globe-light", - "material/globe-model", - "material/gmail", - "material/gnome", - "material/go-kart-track", - "material/go-kart", - "material/gog", - "material/gold", - "material/golf-cart", - "material/golf-tee", - "material/golf", - "material/gondola", - "material/goodreads", - "material/google-ads", - "material/google-analytics", - "material/google-assistant", - "material/google-cardboard", - "material/google-chrome", - "material/google-circles-communities", - "material/google-circles-extended", - "material/google-circles-group", - "material/google-circles", - "material/google-classroom", - "material/google-cloud", - "material/google-downasaur", - "material/google-drive", - "material/google-earth", - "material/google-fit", - "material/google-glass", - "material/google-hangouts", - "material/google-keep", - "material/google-lens", - "material/google-maps", - "material/google-my-business", - "material/google-nearby", - "material/google-play", - "material/google-plus", - "material/google-podcast", - "material/google-spreadsheet", - "material/google-street-view", - "material/google-translate", - "material/google", - "material/gradient-horizontal", - "material/gradient-vertical", - "material/grain", - "material/graph-outline", - "material/graph", - "material/graphql", - "material/grass", - "material/grave-stone", - "material/grease-pencil", - "material/greater-than-or-equal", - "material/greater-than", - "material/greenhouse", - "material/grid-large", - "material/grid-off", - "material/grid", - "material/grill-outline", - "material/grill", - "material/group", - "material/guitar-acoustic", - "material/guitar-electric", - "material/guitar-pick-outline", - "material/guitar-pick", - "material/guy-fawkes-mask", - "material/gymnastics", - "material/hail", - "material/hair-dryer-outline", - "material/hair-dryer", - "material/halloween", - "material/hamburger-check", - "material/hamburger-minus", - "material/hamburger-off", - "material/hamburger-plus", - "material/hamburger-remove", - "material/hamburger", - "material/hammer-screwdriver", - "material/hammer-sickle", - "material/hammer-wrench", - "material/hammer", - "material/hand-back-left-off-outline", - "material/hand-back-left-off", - "material/hand-back-left-outline", - "material/hand-back-left", - "material/hand-back-right-off-outline", - "material/hand-back-right-off", - "material/hand-back-right-outline", - "material/hand-back-right", - "material/hand-clap-off", - "material/hand-clap", - "material/hand-coin-outline", - "material/hand-coin", - "material/hand-cycle", - "material/hand-extended-outline", - "material/hand-extended", - "material/hand-front-left-outline", - "material/hand-front-left", - "material/hand-front-right-outline", - "material/hand-front-right", - "material/hand-heart-outline", - "material/hand-heart", - "material/hand-okay", - "material/hand-peace-variant", - "material/hand-peace", - "material/hand-pointing-down", - "material/hand-pointing-left", - "material/hand-pointing-right", - "material/hand-pointing-up", - "material/hand-saw", - "material/hand-wash-outline", - "material/hand-wash", - "material/hand-water", - "material/hand-wave-outline", - "material/hand-wave", - "material/handball", - "material/handcuffs", - "material/hands-pray", - "material/handshake-outline", - "material/handshake", - "material/hanger", - "material/hard-hat", - "material/harddisk-plus", - "material/harddisk-remove", - "material/harddisk", - "material/hat-fedora", - "material/hazard-lights", - "material/hdmi-port", - "material/hdr-off", - "material/hdr", - "material/head-alert-outline", - "material/head-alert", - "material/head-check-outline", - "material/head-check", - "material/head-cog-outline", - "material/head-cog", - "material/head-dots-horizontal-outline", - "material/head-dots-horizontal", - "material/head-flash-outline", - "material/head-flash", - "material/head-heart-outline", - "material/head-heart", - "material/head-lightbulb-outline", - "material/head-lightbulb", - "material/head-minus-outline", - "material/head-minus", - "material/head-outline", - "material/head-plus-outline", - "material/head-plus", - "material/head-question-outline", - "material/head-question", - "material/head-remove-outline", - "material/head-remove", - "material/head-snowflake-outline", - "material/head-snowflake", - "material/head-sync-outline", - "material/head-sync", - "material/head", - "material/headphones-bluetooth", - "material/headphones-box", - "material/headphones-off", - "material/headphones-settings", - "material/headphones", - "material/headset-dock", - "material/headset-off", - "material/headset", - "material/heart-box-outline", - "material/heart-box", - "material/heart-broken-outline", - "material/heart-broken", - "material/heart-circle-outline", - "material/heart-circle", - "material/heart-cog-outline", - "material/heart-cog", - "material/heart-flash", - "material/heart-half-full", - "material/heart-half-outline", - "material/heart-half", - "material/heart-minus-outline", - "material/heart-minus", - "material/heart-multiple-outline", - "material/heart-multiple", - "material/heart-off-outline", - "material/heart-off", - "material/heart-outline", - "material/heart-plus-outline", - "material/heart-plus", - "material/heart-pulse", - "material/heart-remove-outline", - "material/heart-remove", - "material/heart-settings-outline", - "material/heart-settings", - "material/heart", - "material/heat-pump-outline", - "material/heat-pump", - "material/heat-wave", - "material/heating-coil", - "material/helicopter", - "material/help-box", - "material/help-circle-outline", - "material/help-circle", - "material/help-network-outline", - "material/help-network", - "material/help-rhombus-outline", - "material/help-rhombus", - "material/help", - "material/hexadecimal", - "material/hexagon-multiple-outline", - "material/hexagon-multiple", - "material/hexagon-outline", - "material/hexagon-slice-1", - "material/hexagon-slice-2", - "material/hexagon-slice-3", - "material/hexagon-slice-4", - "material/hexagon-slice-5", - "material/hexagon-slice-6", - "material/hexagon", - "material/hexagram-outline", - "material/hexagram", - "material/high-definition-box", - "material/high-definition", - "material/highway", - "material/hiking", - "material/history", - "material/hockey-puck", - "material/hockey-sticks", - "material/hololens", - "material/home-account", - "material/home-alert-outline", - "material/home-alert", - "material/home-analytics", - "material/home-assistant", - "material/home-automation", - "material/home-battery-outline", - "material/home-battery", - "material/home-circle-outline", - "material/home-circle", - "material/home-city-outline", - "material/home-city", - "material/home-clock-outline", - "material/home-clock", - "material/home-edit-outline", - "material/home-edit", - "material/home-export-outline", - "material/home-flood", - "material/home-floor-0", - "material/home-floor-1", - "material/home-floor-2", - "material/home-floor-3", - "material/home-floor-a", - "material/home-floor-b", - "material/home-floor-g", - "material/home-floor-l", - "material/home-floor-negative-1", - "material/home-group-minus", - "material/home-group-plus", - "material/home-group-remove", - "material/home-group", - "material/home-heart", - "material/home-import-outline", - "material/home-lightbulb-outline", - "material/home-lightbulb", - "material/home-lightning-bolt-outline", - "material/home-lightning-bolt", - "material/home-lock-open", - "material/home-lock", - "material/home-map-marker", - "material/home-minus-outline", - "material/home-minus", - "material/home-modern", - "material/home-off-outline", - "material/home-off", - "material/home-outline", - "material/home-plus-outline", - "material/home-plus", - "material/home-remove-outline", - "material/home-remove", - "material/home-roof", - "material/home-search-outline", - "material/home-search", - "material/home-silo-outline", - "material/home-silo", - "material/home-switch-outline", - "material/home-switch", - "material/home-thermometer-outline", - "material/home-thermometer", - "material/home-variant-outline", - "material/home-variant", - "material/home", - "material/hook-off", - "material/hook", - "material/hoop-house", - "material/hops", - "material/horizontal-rotate-clockwise", - "material/horizontal-rotate-counterclockwise", - "material/horse-human", - "material/horse-variant-fast", - "material/horse-variant", - "material/horse", - "material/horseshoe", - "material/hospital-box-outline", - "material/hospital-box", - "material/hospital-building", - "material/hospital-marker", - "material/hospital", - "material/hot-tub", - "material/hours-24", - "material/hubspot", - "material/hulu", - "material/human-baby-changing-table", - "material/human-cane", - "material/human-capacity-decrease", - "material/human-capacity-increase", - "material/human-child", - "material/human-dolly", - "material/human-edit", - "material/human-female-boy", - "material/human-female-dance", - "material/human-female-female", - "material/human-female-girl", - "material/human-female", - "material/human-greeting-proximity", - "material/human-greeting-variant", - "material/human-greeting", - "material/human-handsdown", - "material/human-handsup", - "material/human-male-board-poll", - "material/human-male-board", - "material/human-male-boy", - "material/human-male-child", - "material/human-male-female-child", - "material/human-male-female", - "material/human-male-girl", - "material/human-male-height-variant", - "material/human-male-height", - "material/human-male-male", - "material/human-male", - "material/human-non-binary", - "material/human-pregnant", - "material/human-queue", - "material/human-scooter", - "material/human-walker", - "material/human-wheelchair", - "material/human-white-cane", - "material/human", - "material/humble-bundle", - "material/hvac-off", - "material/hvac", - "material/hydraulic-oil-level", - "material/hydraulic-oil-temperature", - "material/hydro-power", - "material/hydrogen-station", - "material/ice-cream-off", - "material/ice-cream", - "material/ice-pop", - "material/id-card", - "material/identifier", - "material/ideogram-cjk-variant", - "material/ideogram-cjk", - "material/image-album", - "material/image-area-close", - "material/image-area", - "material/image-auto-adjust", - "material/image-broken-variant", - "material/image-broken", - "material/image-check-outline", - "material/image-check", - "material/image-edit-outline", - "material/image-edit", - "material/image-filter-black-white", - "material/image-filter-center-focus-strong-outline", - "material/image-filter-center-focus-strong", - "material/image-filter-center-focus-weak", - "material/image-filter-center-focus", - "material/image-filter-drama", - "material/image-filter-frames", - "material/image-filter-hdr", - "material/image-filter-none", - "material/image-filter-tilt-shift", - "material/image-filter-vintage", - "material/image-frame", - "material/image-lock-outline", - "material/image-lock", - "material/image-marker-outline", - "material/image-marker", - "material/image-minus-outline", - "material/image-minus", - "material/image-move", - "material/image-multiple-outline", - "material/image-multiple", - "material/image-off-outline", - "material/image-off", - "material/image-outline", - "material/image-plus-outline", - "material/image-plus", - "material/image-refresh-outline", - "material/image-refresh", - "material/image-remove-outline", - "material/image-remove", - "material/image-search-outline", - "material/image-search", - "material/image-size-select-actual", - "material/image-size-select-large", - "material/image-size-select-small", - "material/image-sync-outline", - "material/image-sync", - "material/image-text", - "material/image", - "material/import", - "material/inbox-arrow-down-outline", - "material/inbox-arrow-down", - "material/inbox-arrow-up-outline", - "material/inbox-arrow-up", - "material/inbox-full-outline", - "material/inbox-full", - "material/inbox-multiple-outline", - "material/inbox-multiple", - "material/inbox-outline", - "material/inbox-remove-outline", - "material/inbox-remove", - "material/inbox", - "material/incognito-circle-off", - "material/incognito-circle", - "material/incognito-off", - "material/incognito", - "material/induction", - "material/infinity", - "material/information-off-outline", - "material/information-off", - "material/information-outline", - "material/information-variant", - "material/information", - "material/instagram", - "material/instrument-triangle", - "material/integrated-circuit-chip", - "material/invert-colors-off", - "material/invert-colors", - "material/iobroker", - "material/ip-network-outline", - "material/ip-network", - "material/ip-outline", - "material/ip", - "material/ipod", - "material/iron-board", - "material/iron-outline", - "material/iron", - "material/island", - "material/iv-bag", - "material/jabber", - "material/jeepney", - "material/jellyfish-outline", - "material/jellyfish", - "material/jira", - "material/jquery", - "material/jsfiddle", - "material/jump-rope", - "material/kabaddi", - "material/kangaroo", - "material/karate", - "material/kayaking", - "material/keg", - "material/kettle-alert-outline", - "material/kettle-alert", - "material/kettle-off-outline", - "material/kettle-off", - "material/kettle-outline", - "material/kettle-pour-over", - "material/kettle-steam-outline", - "material/kettle-steam", - "material/kettle", - "material/kettlebell", - "material/key-alert-outline", - "material/key-alert", - "material/key-arrow-right", - "material/key-chain-variant", - "material/key-chain", - "material/key-change", - "material/key-link", - "material/key-minus", - "material/key-outline", - "material/key-plus", - "material/key-remove", - "material/key-star", - "material/key-variant", - "material/key-wireless", - "material/key", - "material/keyboard-backspace", - "material/keyboard-caps", - "material/keyboard-close", - "material/keyboard-esc", - "material/keyboard-f1", - "material/keyboard-f10", - "material/keyboard-f11", - "material/keyboard-f12", - "material/keyboard-f2", - "material/keyboard-f3", - "material/keyboard-f4", - "material/keyboard-f5", - "material/keyboard-f6", - "material/keyboard-f7", - "material/keyboard-f8", - "material/keyboard-f9", - "material/keyboard-off-outline", - "material/keyboard-off", - "material/keyboard-outline", - "material/keyboard-return", - "material/keyboard-settings-outline", - "material/keyboard-settings", - "material/keyboard-space", - "material/keyboard-tab-reverse", - "material/keyboard-tab", - "material/keyboard-variant", - "material/keyboard", - "material/khanda", - "material/kickstarter", - "material/kite-outline", - "material/kite", - "material/kitesurfing", - "material/klingon", - "material/knife-military", - "material/knife", - "material/knob", - "material/koala", - "material/kodi", - "material/kubernetes", - "material/label-multiple-outline", - "material/label-multiple", - "material/label-off-outline", - "material/label-off", - "material/label-outline", - "material/label-percent-outline", - "material/label-percent", - "material/label-variant-outline", - "material/label-variant", - "material/label", - "material/ladder", - "material/ladybug", - "material/lambda", - "material/lamp-outline", - "material/lamp", - "material/lamps-outline", - "material/lamps", - "material/lan-check", - "material/lan-connect", - "material/lan-disconnect", - "material/lan-pending", - "material/lan", - "material/land-fields", - "material/land-plots-circle-variant", - "material/land-plots-circle", - "material/land-plots", - "material/land-rows-horizontal", - "material/land-rows-vertical", - "material/landslide-outline", - "material/landslide", - "material/language-c", - "material/language-cpp", - "material/language-csharp", - "material/language-css3", - "material/language-fortran", - "material/language-go", - "material/language-haskell", - "material/language-html5", - "material/language-java", - "material/language-javascript", - "material/language-kotlin", - "material/language-lua", - "material/language-markdown-outline", - "material/language-markdown", - "material/language-php", - "material/language-python", - "material/language-r", - "material/language-ruby-on-rails", - "material/language-ruby", - "material/language-rust", - "material/language-swift", - "material/language-typescript", - "material/language-xaml", - "material/laptop-account", - "material/laptop-off", - "material/laptop", - "material/laravel", - "material/laser-pointer", - "material/lasso", - "material/lastpass", - "material/latitude", - "material/launch", - "material/lava-lamp", - "material/layers-edit", - "material/layers-minus", - "material/layers-off-outline", - "material/layers-off", - "material/layers-outline", - "material/layers-plus", - "material/layers-remove", - "material/layers-search-outline", - "material/layers-search", - "material/layers-triple-outline", - "material/layers-triple", - "material/layers", - "material/lead-pencil", - "material/leaf-circle-outline", - "material/leaf-circle", - "material/leaf-maple-off", - "material/leaf-maple", - "material/leaf-off", - "material/leaf", - "material/leak-off", - "material/leak", - "material/lectern", - "material/led-off", - "material/led-on", - "material/led-outline", - "material/led-strip-variant-off", - "material/led-strip-variant", - "material/led-strip", - "material/led-variant-off", - "material/led-variant-on", - "material/led-variant-outline", - "material/leek", - "material/less-than-or-equal", - "material/less-than", - "material/library-outline", - "material/library-shelves", - "material/library", - "material/license", - "material/lifebuoy", - "material/light-flood-down", - "material/light-flood-up", - "material/light-recessed", - "material/light-switch-off", - "material/light-switch", - "material/lightbulb-alert-outline", - "material/lightbulb-alert", - "material/lightbulb-auto-outline", - "material/lightbulb-auto", - "material/lightbulb-cfl-off", - "material/lightbulb-cfl-spiral-off", - "material/lightbulb-cfl-spiral", - "material/lightbulb-cfl", - "material/lightbulb-fluorescent-tube-outline", - "material/lightbulb-fluorescent-tube", - "material/lightbulb-group-off-outline", - "material/lightbulb-group-off", - "material/lightbulb-group-outline", - "material/lightbulb-group", - "material/lightbulb-multiple-off-outline", - "material/lightbulb-multiple-off", - "material/lightbulb-multiple-outline", - "material/lightbulb-multiple", - "material/lightbulb-night-outline", - "material/lightbulb-night", - "material/lightbulb-off-outline", - "material/lightbulb-off", - "material/lightbulb-on-10", - "material/lightbulb-on-20", - "material/lightbulb-on-30", - "material/lightbulb-on-40", - "material/lightbulb-on-50", - "material/lightbulb-on-60", - "material/lightbulb-on-70", - "material/lightbulb-on-80", - "material/lightbulb-on-90", - "material/lightbulb-on-outline", - "material/lightbulb-on", - "material/lightbulb-outline", - "material/lightbulb-question-outline", - "material/lightbulb-question", - "material/lightbulb-spot-off", - "material/lightbulb-spot", - "material/lightbulb-variant-outline", - "material/lightbulb-variant", - "material/lightbulb", - "material/lighthouse-on", - "material/lighthouse", - "material/lightning-bolt-circle", - "material/lightning-bolt-outline", - "material/lightning-bolt", - "material/line-scan", - "material/lingerie", - "material/link-box-outline", - "material/link-box-variant-outline", - "material/link-box-variant", - "material/link-box", - "material/link-lock", - "material/link-off", - "material/link-plus", - "material/link-variant-minus", - "material/link-variant-off", - "material/link-variant-plus", - "material/link-variant-remove", - "material/link-variant", - "material/link", - "material/linkedin", - "material/linux-mint", - "material/linux", - "material/lipstick", - "material/liquid-spot", - "material/liquor", - "material/list-box-outline", - "material/list-box", - "material/list-status", - "material/litecoin", - "material/loading", - "material/location-enter", - "material/location-exit", - "material/lock-alert-outline", - "material/lock-alert", - "material/lock-check-outline", - "material/lock-check", - "material/lock-clock", - "material/lock-minus-outline", - "material/lock-minus", - "material/lock-off-outline", - "material/lock-off", - "material/lock-open-alert-outline", - "material/lock-open-alert", - "material/lock-open-check-outline", - "material/lock-open-check", - "material/lock-open-minus-outline", - "material/lock-open-minus", - "material/lock-open-outline", - "material/lock-open-plus-outline", - "material/lock-open-plus", - "material/lock-open-remove-outline", - "material/lock-open-remove", - "material/lock-open-variant-outline", - "material/lock-open-variant", - "material/lock-open", - "material/lock-outline", - "material/lock-pattern", - "material/lock-plus-outline", - "material/lock-plus", - "material/lock-question", - "material/lock-remove-outline", - "material/lock-remove", - "material/lock-reset", - "material/lock-smart", - "material/lock", - "material/locker-multiple", - "material/locker", - "material/login-variant", - "material/login", - "material/logout-variant", - "material/logout", - "material/longitude", - "material/looks", - "material/lotion-outline", - "material/lotion-plus-outline", - "material/lotion-plus", - "material/lotion", - "material/loupe", - "material/lumx", - "material/lungs", - "material/mace", - "material/magazine-pistol", - "material/magazine-rifle", - "material/magic-staff", - "material/magnet-on", - "material/magnet", - "material/magnify-close", - "material/magnify-expand", - "material/magnify-minus-cursor", - "material/magnify-minus-outline", - "material/magnify-minus", - "material/magnify-plus-cursor", - "material/magnify-plus-outline", - "material/magnify-plus", - "material/magnify-remove-cursor", - "material/magnify-remove-outline", - "material/magnify-scan", - "material/magnify", - "material/mail", - "material/mailbox-open-outline", - "material/mailbox-open-up-outline", - "material/mailbox-open-up", - "material/mailbox-open", - "material/mailbox-outline", - "material/mailbox-up-outline", - "material/mailbox-up", - "material/mailbox", - "material/manjaro", - "material/map-check-outline", - "material/map-check", - "material/map-clock-outline", - "material/map-clock", - "material/map-legend", - "material/map-marker-account-outline", - "material/map-marker-account", - "material/map-marker-alert-outline", - "material/map-marker-alert", - "material/map-marker-check-outline", - "material/map-marker-check", - "material/map-marker-circle", - "material/map-marker-distance", - "material/map-marker-down", - "material/map-marker-left-outline", - "material/map-marker-left", - "material/map-marker-minus-outline", - "material/map-marker-minus", - "material/map-marker-multiple-outline", - "material/map-marker-multiple", - "material/map-marker-off-outline", - "material/map-marker-off", - "material/map-marker-outline", - "material/map-marker-path", - "material/map-marker-plus-outline", - "material/map-marker-plus", - "material/map-marker-question-outline", - "material/map-marker-question", - "material/map-marker-radius-outline", - "material/map-marker-radius", - "material/map-marker-remove-outline", - "material/map-marker-remove-variant", - "material/map-marker-remove", - "material/map-marker-right-outline", - "material/map-marker-right", - "material/map-marker-star-outline", - "material/map-marker-star", - "material/map-marker-up", - "material/map-marker", - "material/map-minus", - "material/map-outline", - "material/map-plus", - "material/map-search-outline", - "material/map-search", - "material/map", - "material/mapbox", - "material/margin", - "material/marker-cancel", - "material/marker-check", - "material/marker", - "material/mastodon", - "material/material-design", - "material/material-ui", - "material/math-compass", - "material/math-cos", - "material/math-integral-box", - "material/math-integral", - "material/math-log", - "material/math-norm-box", - "material/math-norm", - "material/math-sin", - "material/math-tan", - "material/matrix", - "material/medal-outline", - "material/medal", - "material/medical-bag", - "material/medical-cotton-swab", - "material/medication-outline", - "material/medication", - "material/meditation", - "material/memory", - "material/menorah-fire", - "material/menorah", - "material/menu-down-outline", - "material/menu-down", - "material/menu-left-outline", - "material/menu-left", - "material/menu-open", - "material/menu-right-outline", - "material/menu-right", - "material/menu-swap-outline", - "material/menu-swap", - "material/menu-up-outline", - "material/menu-up", - "material/menu", - "material/merge", - "material/message-alert-outline", - "material/message-alert", - "material/message-arrow-left-outline", - "material/message-arrow-left", - "material/message-arrow-right-outline", - "material/message-arrow-right", - "material/message-badge-outline", - "material/message-badge", - "material/message-bookmark-outline", - "material/message-bookmark", - "material/message-bulleted-off", - "material/message-bulleted", - "material/message-check-outline", - "material/message-check", - "material/message-cog-outline", - "material/message-cog", - "material/message-draw", - "material/message-fast-outline", - "material/message-fast", - "material/message-flash-outline", - "material/message-flash", - "material/message-image-outline", - "material/message-image", - "material/message-lock-outline", - "material/message-lock", - "material/message-minus-outline", - "material/message-minus", - "material/message-off-outline", - "material/message-off", - "material/message-outline", - "material/message-plus-outline", - "material/message-plus", - "material/message-processing-outline", - "material/message-processing", - "material/message-question-outline", - "material/message-question", - "material/message-reply-outline", - "material/message-reply-text-outline", - "material/message-reply-text", - "material/message-reply", - "material/message-settings-outline", - "material/message-settings", - "material/message-star-outline", - "material/message-star", - "material/message-text-clock-outline", - "material/message-text-clock", - "material/message-text-fast-outline", - "material/message-text-fast", - "material/message-text-lock-outline", - "material/message-text-lock", - "material/message-text-outline", - "material/message-text", - "material/message-video", - "material/message", - "material/meteor", - "material/meter-electric-outline", - "material/meter-electric", - "material/meter-gas-outline", - "material/meter-gas", - "material/metronome-tick", - "material/metronome", - "material/micro-sd", - "material/microphone-message-off", - "material/microphone-message", - "material/microphone-minus", - "material/microphone-off", - "material/microphone-outline", - "material/microphone-plus", - "material/microphone-question-outline", - "material/microphone-question", - "material/microphone-settings", - "material/microphone-variant-off", - "material/microphone-variant", - "material/microphone", - "material/microscope", - "material/microsoft-access", - "material/microsoft-azure-devops", - "material/microsoft-azure", - "material/microsoft-bing", - "material/microsoft-dynamics-365", - "material/microsoft-edge", - "material/microsoft-excel", - "material/microsoft-internet-explorer", - "material/microsoft-office", - "material/microsoft-onedrive", - "material/microsoft-onenote", - "material/microsoft-outlook", - "material/microsoft-powerpoint", - "material/microsoft-sharepoint", - "material/microsoft-teams", - "material/microsoft-visual-studio-code", - "material/microsoft-visual-studio", - "material/microsoft-windows-classic", - "material/microsoft-windows", - "material/microsoft-word", - "material/microsoft-xbox-controller-battery-alert", - "material/microsoft-xbox-controller-battery-charging", - "material/microsoft-xbox-controller-battery-empty", - "material/microsoft-xbox-controller-battery-full", - "material/microsoft-xbox-controller-battery-low", - "material/microsoft-xbox-controller-battery-medium", - "material/microsoft-xbox-controller-battery-unknown", - "material/microsoft-xbox-controller-menu", - "material/microsoft-xbox-controller-off", - "material/microsoft-xbox-controller-view", - "material/microsoft-xbox-controller", - "material/microsoft-xbox", - "material/microsoft", - "material/microwave-off", - "material/microwave", - "material/middleware-outline", - "material/middleware", - "material/midi-port", - "material/midi", - "material/mine", - "material/minecraft", - "material/mini-sd", - "material/minidisc", - "material/minus-box-multiple-outline", - "material/minus-box-multiple", - "material/minus-box-outline", - "material/minus-box", - "material/minus-circle-multiple-outline", - "material/minus-circle-multiple", - "material/minus-circle-off-outline", - "material/minus-circle-off", - "material/minus-circle-outline", - "material/minus-circle", - "material/minus-network-outline", - "material/minus-network", - "material/minus-thick", - "material/minus", - "material/mirror-rectangle", - "material/mirror-variant", - "material/mirror", - "material/mixed-martial-arts", - "material/mixed-reality", - "material/molecule-co", - "material/molecule-co2", - "material/molecule", - "material/monitor-account", - "material/monitor-arrow-down-variant", - "material/monitor-arrow-down", - "material/monitor-cellphone-star", - "material/monitor-cellphone", - "material/monitor-dashboard", - "material/monitor-edit", - "material/monitor-eye", - "material/monitor-lock", - "material/monitor-multiple", - "material/monitor-off", - "material/monitor-screenshot", - "material/monitor-share", - "material/monitor-shimmer", - "material/monitor-small", - "material/monitor-speaker-off", - "material/monitor-speaker", - "material/monitor-star", - "material/monitor", - "material/moon-first-quarter", - "material/moon-full", - "material/moon-last-quarter", - "material/moon-new", - "material/moon-waning-crescent", - "material/moon-waning-gibbous", - "material/moon-waxing-crescent", - "material/moon-waxing-gibbous", - "material/moped-electric-outline", - "material/moped-electric", - "material/moped-outline", - "material/moped", - "material/more", - "material/mortar-pestle-plus", - "material/mortar-pestle", - "material/mosque-outline", - "material/mosque", - "material/mother-heart", - "material/mother-nurse", - "material/motion-outline", - "material/motion-pause-outline", - "material/motion-pause", - "material/motion-play-outline", - "material/motion-play", - "material/motion-sensor-off", - "material/motion-sensor", - "material/motion", - "material/motorbike-electric", - "material/motorbike-off", - "material/motorbike", - "material/mouse-bluetooth", - "material/mouse-move-down", - "material/mouse-move-up", - "material/mouse-move-vertical", - "material/mouse-off", - "material/mouse-variant-off", - "material/mouse-variant", - "material/mouse", - "material/move-resize-variant", - "material/move-resize", - "material/movie-check-outline", - "material/movie-check", - "material/movie-cog-outline", - "material/movie-cog", - "material/movie-edit-outline", - "material/movie-edit", - "material/movie-filter-outline", - "material/movie-filter", - "material/movie-minus-outline", - "material/movie-minus", - "material/movie-off-outline", - "material/movie-off", - "material/movie-open-check-outline", - "material/movie-open-check", - "material/movie-open-cog-outline", - "material/movie-open-cog", - "material/movie-open-edit-outline", - "material/movie-open-edit", - "material/movie-open-minus-outline", - "material/movie-open-minus", - "material/movie-open-off-outline", - "material/movie-open-off", - "material/movie-open-outline", - "material/movie-open-play-outline", - "material/movie-open-play", - "material/movie-open-plus-outline", - "material/movie-open-plus", - "material/movie-open-remove-outline", - "material/movie-open-remove", - "material/movie-open-settings-outline", - "material/movie-open-settings", - "material/movie-open-star-outline", - "material/movie-open-star", - "material/movie-open", - "material/movie-outline", - "material/movie-play-outline", - "material/movie-play", - "material/movie-plus-outline", - "material/movie-plus", - "material/movie-remove-outline", - "material/movie-remove", - "material/movie-roll", - "material/movie-search-outline", - "material/movie-search", - "material/movie-settings-outline", - "material/movie-settings", - "material/movie-star-outline", - "material/movie-star", - "material/movie", - "material/mower-bag-on", - "material/mower-bag", - "material/mower-on", - "material/mower", - "material/muffin", - "material/multicast", - "material/multimedia", - "material/multiplication-box", - "material/multiplication", - "material/mushroom-off-outline", - "material/mushroom-off", - "material/mushroom-outline", - "material/mushroom", - "material/music-accidental-double-flat", - "material/music-accidental-double-sharp", - "material/music-accidental-flat", - "material/music-accidental-natural", - "material/music-accidental-sharp", - "material/music-box-multiple-outline", - "material/music-box-multiple", - "material/music-box-outline", - "material/music-box", - "material/music-circle-outline", - "material/music-circle", - "material/music-clef-alto", - "material/music-clef-bass", - "material/music-clef-treble", - "material/music-note-bluetooth-off", - "material/music-note-bluetooth", - "material/music-note-eighth-dotted", - "material/music-note-eighth", - "material/music-note-half-dotted", - "material/music-note-half", - "material/music-note-minus", - "material/music-note-off-outline", - "material/music-note-off", - "material/music-note-outline", - "material/music-note-plus", - "material/music-note-quarter-dotted", - "material/music-note-quarter", - "material/music-note-sixteenth-dotted", - "material/music-note-sixteenth", - "material/music-note-whole-dotted", - "material/music-note-whole", - "material/music-note", - "material/music-off", - "material/music-rest-eighth", - "material/music-rest-half", - "material/music-rest-quarter", - "material/music-rest-sixteenth", - "material/music-rest-whole", - "material/music", - "material/mustache", - "material/nail", - "material/nas", - "material/nativescript", - "material/nature-people", - "material/nature", - "material/navigation-outline", - "material/navigation-variant-outline", - "material/navigation-variant", - "material/navigation", - "material/near-me", - "material/necklace", - "material/needle-off", - "material/needle", - "material/netflix", - "material/network-off-outline", - "material/network-off", - "material/network-outline", - "material/network-pos", - "material/network-strength-1-alert", - "material/network-strength-1", - "material/network-strength-2-alert", - "material/network-strength-2", - "material/network-strength-3-alert", - "material/network-strength-3", - "material/network-strength-4-alert", - "material/network-strength-4-cog", - "material/network-strength-4", - "material/network-strength-off-outline", - "material/network-strength-off", - "material/network-strength-outline", - "material/network", - "material/new-box", - "material/newspaper-check", - "material/newspaper-minus", - "material/newspaper-plus", - "material/newspaper-remove", - "material/newspaper-variant-multiple-outline", - "material/newspaper-variant-multiple", - "material/newspaper-variant-outline", - "material/newspaper-variant", - "material/newspaper", - "material/nfc-search-variant", - "material/nfc-tap", - "material/nfc-variant-off", - "material/nfc-variant", - "material/nfc", - "material/ninja", - "material/nintendo-game-boy", - "material/nintendo-switch", - "material/nintendo-wii", - "material/nintendo-wiiu", - "material/nix", - "material/nodejs", - "material/noodles", - "material/not-equal-variant", - "material/not-equal", - "material/note-alert-outline", - "material/note-alert", - "material/note-check-outline", - "material/note-check", - "material/note-edit-outline", - "material/note-edit", - "material/note-minus-outline", - "material/note-minus", - "material/note-multiple-outline", - "material/note-multiple", - "material/note-off-outline", - "material/note-off", - "material/note-outline", - "material/note-plus-outline", - "material/note-plus", - "material/note-remove-outline", - "material/note-remove", - "material/note-search-outline", - "material/note-search", - "material/note-text-outline", - "material/note-text", - "material/note", - "material/notebook-check-outline", - "material/notebook-check", - "material/notebook-edit-outline", - "material/notebook-edit", - "material/notebook-heart-outline", - "material/notebook-heart", - "material/notebook-minus-outline", - "material/notebook-minus", - "material/notebook-multiple", - "material/notebook-outline", - "material/notebook-plus-outline", - "material/notebook-plus", - "material/notebook-remove-outline", - "material/notebook-remove", - "material/notebook", - "material/notification-clear-all", - "material/npm", - "material/nuke", - "material/null", - "material/numeric-0-box-multiple-outline", - "material/numeric-0-box-multiple", - "material/numeric-0-box-outline", - "material/numeric-0-box", - "material/numeric-0-circle-outline", - "material/numeric-0-circle", - "material/numeric-0", - "material/numeric-1-box-multiple-outline", - "material/numeric-1-box-multiple", - "material/numeric-1-box-outline", - "material/numeric-1-box", - "material/numeric-1-circle-outline", - "material/numeric-1-circle", - "material/numeric-1", - "material/numeric-10-box-multiple-outline", - "material/numeric-10-box-multiple", - "material/numeric-10-box-outline", - "material/numeric-10-box", - "material/numeric-10-circle-outline", - "material/numeric-10-circle", - "material/numeric-10", - "material/numeric-2-box-multiple-outline", - "material/numeric-2-box-multiple", - "material/numeric-2-box-outline", - "material/numeric-2-box", - "material/numeric-2-circle-outline", - "material/numeric-2-circle", - "material/numeric-2", - "material/numeric-3-box-multiple-outline", - "material/numeric-3-box-multiple", - "material/numeric-3-box-outline", - "material/numeric-3-box", - "material/numeric-3-circle-outline", - "material/numeric-3-circle", - "material/numeric-3", - "material/numeric-4-box-multiple-outline", - "material/numeric-4-box-multiple", - "material/numeric-4-box-outline", - "material/numeric-4-box", - "material/numeric-4-circle-outline", - "material/numeric-4-circle", - "material/numeric-4", - "material/numeric-5-box-multiple-outline", - "material/numeric-5-box-multiple", - "material/numeric-5-box-outline", - "material/numeric-5-box", - "material/numeric-5-circle-outline", - "material/numeric-5-circle", - "material/numeric-5", - "material/numeric-6-box-multiple-outline", - "material/numeric-6-box-multiple", - "material/numeric-6-box-outline", - "material/numeric-6-box", - "material/numeric-6-circle-outline", - "material/numeric-6-circle", - "material/numeric-6", - "material/numeric-7-box-multiple-outline", - "material/numeric-7-box-multiple", - "material/numeric-7-box-outline", - "material/numeric-7-box", - "material/numeric-7-circle-outline", - "material/numeric-7-circle", - "material/numeric-7", - "material/numeric-8-box-multiple-outline", - "material/numeric-8-box-multiple", - "material/numeric-8-box-outline", - "material/numeric-8-box", - "material/numeric-8-circle-outline", - "material/numeric-8-circle", - "material/numeric-8", - "material/numeric-9-box-multiple-outline", - "material/numeric-9-box-multiple", - "material/numeric-9-box-outline", - "material/numeric-9-box", - "material/numeric-9-circle-outline", - "material/numeric-9-circle", - "material/numeric-9-plus-box-multiple-outline", - "material/numeric-9-plus-box-multiple", - "material/numeric-9-plus-box-outline", - "material/numeric-9-plus-box", - "material/numeric-9-plus-circle-outline", - "material/numeric-9-plus-circle", - "material/numeric-9-plus", - "material/numeric-9", - "material/numeric-negative-1", - "material/numeric-off", - "material/numeric-positive-1", - "material/numeric", - "material/nut", - "material/nutrition", - "material/nuxt", - "material/oar", - "material/ocarina", - "material/oci", - "material/ocr", - "material/octagon-outline", - "material/octagon", - "material/octagram-outline", - "material/octagram", - "material/octahedron-off", - "material/octahedron", - "material/odnoklassniki", - "material/offer", - "material/office-building-cog-outline", - "material/office-building-cog", - "material/office-building-marker-outline", - "material/office-building-marker", - "material/office-building-minus-outline", - "material/office-building-minus", - "material/office-building-outline", - "material/office-building-plus-outline", - "material/office-building-plus", - "material/office-building-remove-outline", - "material/office-building-remove", - "material/office-building", - "material/oil-lamp", - "material/oil-level", - "material/oil-temperature", - "material/oil", - "material/om", - "material/omega", - "material/one-up", - "material/onepassword", - "material/opacity", - "material/open-in-app", - "material/open-in-new", - "material/open-source-initiative", - "material/openid", - "material/opera", - "material/orbit-variant", - "material/orbit", - "material/order-alphabetical-ascending", - "material/order-alphabetical-descending", - "material/order-bool-ascending-variant", - "material/order-bool-ascending", - "material/order-bool-descending-variant", - "material/order-bool-descending", - "material/order-numeric-ascending", - "material/order-numeric-descending", - "material/origin", - "material/ornament-variant", - "material/ornament", - "material/outdoor-lamp", - "material/overscan", - "material/owl", - "material/pac-man", - "material/package-check", - "material/package-down", - "material/package-up", - "material/package-variant-closed-check", - "material/package-variant-closed-minus", - "material/package-variant-closed-plus", - "material/package-variant-closed-remove", - "material/package-variant-closed", - "material/package-variant-minus", - "material/package-variant-plus", - "material/package-variant-remove", - "material/package-variant", - "material/package", - "material/page-first", - "material/page-last", - "material/page-layout-body", - "material/page-layout-footer", - "material/page-layout-header-footer", - "material/page-layout-header", - "material/page-layout-sidebar-left", - "material/page-layout-sidebar-right", - "material/page-next-outline", - "material/page-next", - "material/page-previous-outline", - "material/page-previous", - "material/pail-minus-outline", - "material/pail-minus", - "material/pail-off-outline", - "material/pail-off", - "material/pail-outline", - "material/pail-plus-outline", - "material/pail-plus", - "material/pail-remove-outline", - "material/pail-remove", - "material/pail", - "material/palette-advanced", - "material/palette-outline", - "material/palette-swatch-outline", - "material/palette-swatch-variant", - "material/palette-swatch", - "material/palette", - "material/palm-tree", - "material/pan-bottom-left", - "material/pan-bottom-right", - "material/pan-down", - "material/pan-horizontal", - "material/pan-left", - "material/pan-right", - "material/pan-top-left", - "material/pan-top-right", - "material/pan-up", - "material/pan-vertical", - "material/pan", - "material/panda", - "material/pandora", - "material/panorama-fisheye", - "material/panorama-horizontal-outline", - "material/panorama-horizontal", - "material/panorama-outline", - "material/panorama-sphere-outline", - "material/panorama-sphere", - "material/panorama-variant-outline", - "material/panorama-variant", - "material/panorama-vertical-outline", - "material/panorama-vertical", - "material/panorama-wide-angle-outline", - "material/panorama-wide-angle", - "material/panorama", - "material/paper-cut-vertical", - "material/paper-roll-outline", - "material/paper-roll", - "material/paperclip-check", - "material/paperclip-lock", - "material/paperclip-minus", - "material/paperclip-off", - "material/paperclip-plus", - "material/paperclip-remove", - "material/paperclip", - "material/parachute-outline", - "material/parachute", - "material/paragliding", - "material/parking", - "material/party-popper", - "material/passport-biometric", - "material/passport", - "material/pasta", - "material/patio-heater", - "material/patreon", - "material/pause-box-outline", - "material/pause-box", - "material/pause-circle-outline", - "material/pause-circle", - "material/pause-octagon-outline", - "material/pause-octagon", - "material/pause", - "material/paw-off-outline", - "material/paw-off", - "material/paw-outline", - "material/paw", - "material/peace", - "material/peanut-off-outline", - "material/peanut-off", - "material/peanut-outline", - "material/peanut", - "material/pen-lock", - "material/pen-minus", - "material/pen-off", - "material/pen-plus", - "material/pen-remove", - "material/pen", - "material/pencil-box-multiple-outline", - "material/pencil-box-multiple", - "material/pencil-box-outline", - "material/pencil-box", - "material/pencil-circle-outline", - "material/pencil-circle", - "material/pencil-lock-outline", - "material/pencil-lock", - "material/pencil-minus-outline", - "material/pencil-minus", - "material/pencil-off-outline", - "material/pencil-off", - "material/pencil-outline", - "material/pencil-plus-outline", - "material/pencil-plus", - "material/pencil-remove-outline", - "material/pencil-remove", - "material/pencil-ruler", - "material/pencil", - "material/penguin", - "material/pentagon-outline", - "material/pentagon", - "material/pentagram", - "material/percent-box-outline", - "material/percent-box", - "material/percent-circle-outline", - "material/percent-circle", - "material/percent-outline", - "material/percent", - "material/periodic-table", - "material/perspective-less", - "material/perspective-more", - "material/ph", - "material/phone-alert-outline", - "material/phone-alert", - "material/phone-bluetooth-outline", - "material/phone-bluetooth", - "material/phone-cancel-outline", - "material/phone-cancel", - "material/phone-check-outline", - "material/phone-check", - "material/phone-classic-off", - "material/phone-classic", - "material/phone-clock", - "material/phone-dial-outline", - "material/phone-dial", - "material/phone-forward-outline", - "material/phone-forward", - "material/phone-hangup-outline", - "material/phone-hangup", - "material/phone-in-talk-outline", - "material/phone-in-talk", - "material/phone-incoming-outgoing-outline", - "material/phone-incoming-outgoing", - "material/phone-incoming-outline", - "material/phone-incoming", - "material/phone-lock-outline", - "material/phone-lock", - "material/phone-log-outline", - "material/phone-log", - "material/phone-message-outline", - "material/phone-message", - "material/phone-minus-outline", - "material/phone-minus", - "material/phone-missed-outline", - "material/phone-missed", - "material/phone-off-outline", - "material/phone-off", - "material/phone-outgoing-outline", - "material/phone-outgoing", - "material/phone-outline", - "material/phone-paused-outline", - "material/phone-paused", - "material/phone-plus-outline", - "material/phone-plus", - "material/phone-refresh-outline", - "material/phone-refresh", - "material/phone-remove-outline", - "material/phone-remove", - "material/phone-return-outline", - "material/phone-return", - "material/phone-ring-outline", - "material/phone-ring", - "material/phone-rotate-landscape", - "material/phone-rotate-portrait", - "material/phone-settings-outline", - "material/phone-settings", - "material/phone-sync-outline", - "material/phone-sync", - "material/phone-voip", - "material/phone", - "material/pi-box", - "material/pi-hole", - "material/pi", - "material/piano-off", - "material/piano", - "material/pickaxe", - "material/picture-in-picture-bottom-right-outline", - "material/picture-in-picture-bottom-right", - "material/picture-in-picture-top-right-outline", - "material/picture-in-picture-top-right", - "material/pier-crane", - "material/pier", - "material/pig-variant-outline", - "material/pig-variant", - "material/pig", - "material/piggy-bank-outline", - "material/piggy-bank", - "material/pill-multiple", - "material/pill-off", - "material/pill", - "material/pillar", - "material/pin-off-outline", - "material/pin-off", - "material/pin-outline", - "material/pin", - "material/pine-tree-box", - "material/pine-tree-fire", - "material/pine-tree", - "material/pinterest", - "material/pinwheel-outline", - "material/pinwheel", - "material/pipe-disconnected", - "material/pipe-leak", - "material/pipe-valve", - "material/pipe-wrench", - "material/pipe", - "material/pirate", - "material/pistol", - "material/piston", - "material/pitchfork", - "material/pizza", - "material/plane-car", - "material/plane-train", - "material/play-box-lock-open-outline", - "material/play-box-lock-open", - "material/play-box-lock-outline", - "material/play-box-lock", - "material/play-box-multiple-outline", - "material/play-box-multiple", - "material/play-box-outline", - "material/play-box", - "material/play-circle-outline", - "material/play-circle", - "material/play-network-outline", - "material/play-network", - "material/play-outline", - "material/play-pause", - "material/play-protected-content", - "material/play-speed", - "material/play", - "material/playlist-check", - "material/playlist-edit", - "material/playlist-minus", - "material/playlist-music-outline", - "material/playlist-music", - "material/playlist-play", - "material/playlist-plus", - "material/playlist-remove", - "material/playlist-star", - "material/plex", - "material/pliers", - "material/plus-box-multiple-outline", - "material/plus-box-multiple", - "material/plus-box-outline", - "material/plus-box", - "material/plus-circle-multiple-outline", - "material/plus-circle-multiple", - "material/plus-circle-outline", - "material/plus-circle", - "material/plus-lock-open", - "material/plus-lock", - "material/plus-minus-box", - "material/plus-minus-variant", - "material/plus-minus", - "material/plus-network-outline", - "material/plus-network", - "material/plus-outline", - "material/plus-thick", - "material/plus", - "material/podcast", - "material/podium-bronze", - "material/podium-gold", - "material/podium-silver", - "material/podium", - "material/point-of-sale", - "material/pokeball", - "material/pokemon-go", - "material/poker-chip", - "material/polaroid", - "material/police-badge-outline", - "material/police-badge", - "material/police-station", - "material/poll", - "material/polo", - "material/polymer", - "material/pool-thermometer", - "material/pool", - "material/popcorn", - "material/post-lamp", - "material/post-outline", - "material/post", - "material/postage-stamp", - "material/pot-mix-outline", - "material/pot-mix", - "material/pot-outline", - "material/pot-steam-outline", - "material/pot-steam", - "material/pot", - "material/pound-box-outline", - "material/pound-box", - "material/pound", - "material/power-cycle", - "material/power-off", - "material/power-on", - "material/power-plug-off-outline", - "material/power-plug-off", - "material/power-plug-outline", - "material/power-plug", - "material/power-settings", - "material/power-sleep", - "material/power-socket-au", - "material/power-socket-ch", - "material/power-socket-de", - "material/power-socket-eu", - "material/power-socket-fr", - "material/power-socket-it", - "material/power-socket-jp", - "material/power-socket-uk", - "material/power-socket-us", - "material/power-socket", - "material/power-standby", - "material/power", - "material/powershell", - "material/prescription", - "material/presentation-play", - "material/presentation", - "material/pretzel", - "material/printer-3d-nozzle-alert-outline", - "material/printer-3d-nozzle-alert", - "material/printer-3d-nozzle-heat-outline", - "material/printer-3d-nozzle-heat", - "material/printer-3d-nozzle-off-outline", - "material/printer-3d-nozzle-off", - "material/printer-3d-nozzle-outline", - "material/printer-3d-nozzle", - "material/printer-3d-off", - "material/printer-3d", - "material/printer-alert", - "material/printer-check", - "material/printer-eye", - "material/printer-off-outline", - "material/printer-off", - "material/printer-outline", - "material/printer-pos", - "material/printer-search", - "material/printer-settings", - "material/printer-wireless", - "material/printer", - "material/priority-high", - "material/priority-low", - "material/professional-hexagon", - "material/progress-alert", - "material/progress-check", - "material/progress-clock", - "material/progress-close", - "material/progress-download", - "material/progress-helper", - "material/progress-pencil", - "material/progress-question", - "material/progress-star", - "material/progress-upload", - "material/progress-wrench", - "material/projector-off", - "material/projector-screen-off-outline", - "material/projector-screen-off", - "material/projector-screen-outline", - "material/projector-screen-variant-off-outline", - "material/projector-screen-variant-off", - "material/projector-screen-variant-outline", - "material/projector-screen-variant", - "material/projector-screen", - "material/projector", - "material/propane-tank-outline", - "material/propane-tank", - "material/protocol", - "material/publish-off", - "material/publish", - "material/pulse", - "material/pump-off", - "material/pump", - "material/pumpkin", - "material/purse-outline", - "material/purse", - "material/puzzle-check-outline", - "material/puzzle-check", - "material/puzzle-edit-outline", - "material/puzzle-edit", - "material/puzzle-heart-outline", - "material/puzzle-heart", - "material/puzzle-minus-outline", - "material/puzzle-minus", - "material/puzzle-outline", - "material/puzzle-plus-outline", - "material/puzzle-plus", - "material/puzzle-remove-outline", - "material/puzzle-remove", - "material/puzzle-star-outline", - "material/puzzle-star", - "material/puzzle", - "material/pyramid-off", - "material/pyramid", - "material/qi", - "material/qqchat", - "material/qrcode-edit", - "material/qrcode-minus", - "material/qrcode-plus", - "material/qrcode-remove", - "material/qrcode-scan", - "material/qrcode", - "material/quadcopter", - "material/quality-high", - "material/quality-low", - "material/quality-medium", - "material/quora", - "material/rabbit-variant-outline", - "material/rabbit-variant", - "material/rabbit", - "material/racing-helmet", - "material/racquetball", - "material/radar", - "material/radiator-disabled", - "material/radiator-off", - "material/radiator", - "material/radio-am", - "material/radio-fm", - "material/radio-handheld", - "material/radio-off", - "material/radio-tower", - "material/radio", - "material/radioactive-circle-outline", - "material/radioactive-circle", - "material/radioactive-off", - "material/radioactive", - "material/radiobox-blank", - "material/radiobox-marked", - "material/radiology-box-outline", - "material/radiology-box", - "material/radius-outline", - "material/radius", - "material/railroad-light", - "material/rake", - "material/raspberry-pi", - "material/raw-off", - "material/raw", - "material/ray-end-arrow", - "material/ray-end", - "material/ray-start-arrow", - "material/ray-start-end", - "material/ray-start-vertex-end", - "material/ray-start", - "material/ray-vertex", - "material/razor-double-edge", - "material/razor-single-edge", - "material/react", - "material/read", - "material/receipt-outline", - "material/receipt-text-check-outline", - "material/receipt-text-check", - "material/receipt-text-minus-outline", - "material/receipt-text-minus", - "material/receipt-text-outline", - "material/receipt-text-plus-outline", - "material/receipt-text-plus", - "material/receipt-text-remove-outline", - "material/receipt-text-remove", - "material/receipt-text", - "material/receipt", - "material/record-circle-outline", - "material/record-circle", - "material/record-player", - "material/record-rec", - "material/record", - "material/rectangle-outline", - "material/rectangle", - "material/recycle-variant", - "material/recycle", - "material/reddit", - "material/redhat", - "material/redo-variant", - "material/redo", - "material/reflect-horizontal", - "material/reflect-vertical", - "material/refresh-auto", - "material/refresh-circle", - "material/refresh", - "material/regex", - "material/registered-trademark", - "material/reiterate", - "material/relation-many-to-many", - "material/relation-many-to-one-or-many", - "material/relation-many-to-one", - "material/relation-many-to-only-one", - "material/relation-many-to-zero-or-many", - "material/relation-many-to-zero-or-one", - "material/relation-one-or-many-to-many", - "material/relation-one-or-many-to-one-or-many", - "material/relation-one-or-many-to-one", - "material/relation-one-or-many-to-only-one", - "material/relation-one-or-many-to-zero-or-many", - "material/relation-one-or-many-to-zero-or-one", - "material/relation-one-to-many", - "material/relation-one-to-one-or-many", - "material/relation-one-to-one", - "material/relation-one-to-only-one", - "material/relation-one-to-zero-or-many", - "material/relation-one-to-zero-or-one", - "material/relation-only-one-to-many", - "material/relation-only-one-to-one-or-many", - "material/relation-only-one-to-one", - "material/relation-only-one-to-only-one", - "material/relation-only-one-to-zero-or-many", - "material/relation-only-one-to-zero-or-one", - "material/relation-zero-or-many-to-many", - "material/relation-zero-or-many-to-one-or-many", - "material/relation-zero-or-many-to-one", - "material/relation-zero-or-many-to-only-one", - "material/relation-zero-or-many-to-zero-or-many", - "material/relation-zero-or-many-to-zero-or-one", - "material/relation-zero-or-one-to-many", - "material/relation-zero-or-one-to-one-or-many", - "material/relation-zero-or-one-to-one", - "material/relation-zero-or-one-to-only-one", - "material/relation-zero-or-one-to-zero-or-many", - "material/relation-zero-or-one-to-zero-or-one", - "material/relative-scale", - "material/reload-alert", - "material/reload", - "material/reminder", - "material/remote-desktop", - "material/remote-off", - "material/remote-tv-off", - "material/remote-tv", - "material/remote", - "material/rename-box", - "material/reorder-horizontal", - "material/reorder-vertical", - "material/repeat-off", - "material/repeat-once", - "material/repeat-variant", - "material/repeat", - "material/replay", - "material/reply-all-outline", - "material/reply-all", - "material/reply-circle", - "material/reply-outline", - "material/reply", - "material/reproduction", - "material/resistor-nodes", - "material/resistor", - "material/resize-bottom-right", - "material/resize", - "material/responsive", - "material/restart-alert", - "material/restart-off", - "material/restart", - "material/restore-alert", - "material/restore", - "material/rewind-10", - "material/rewind-15", - "material/rewind-30", - "material/rewind-45", - "material/rewind-5", - "material/rewind-60", - "material/rewind-outline", - "material/rewind", - "material/rhombus-medium-outline", - "material/rhombus-medium", - "material/rhombus-outline", - "material/rhombus-split-outline", - "material/rhombus-split", - "material/rhombus", - "material/ribbon", - "material/rice", - "material/rickshaw-electric", - "material/rickshaw", - "material/ring", - "material/rivet", - "material/road-variant", - "material/road", - "material/robber", - "material/robot-angry-outline", - "material/robot-angry", - "material/robot-confused-outline", - "material/robot-confused", - "material/robot-dead-outline", - "material/robot-dead", - "material/robot-excited-outline", - "material/robot-excited", - "material/robot-happy-outline", - "material/robot-happy", - "material/robot-industrial-outline", - "material/robot-industrial", - "material/robot-love-outline", - "material/robot-love", - "material/robot-mower-outline", - "material/robot-mower", - "material/robot-off-outline", - "material/robot-off", - "material/robot-outline", - "material/robot-vacuum-alert", - "material/robot-vacuum-variant-alert", - "material/robot-vacuum-variant", - "material/robot-vacuum", - "material/robot", - "material/rocket-launch-outline", - "material/rocket-launch", - "material/rocket-outline", - "material/rocket", - "material/rodent", - "material/roller-shade-closed", - "material/roller-shade", - "material/roller-skate-off", - "material/roller-skate", - "material/rollerblade-off", - "material/rollerblade", - "material/rollupjs", - "material/rolodex-outline", - "material/rolodex", - "material/roman-numeral-1", - "material/roman-numeral-10", - "material/roman-numeral-2", - "material/roman-numeral-3", - "material/roman-numeral-4", - "material/roman-numeral-5", - "material/roman-numeral-6", - "material/roman-numeral-7", - "material/roman-numeral-8", - "material/roman-numeral-9", - "material/room-service-outline", - "material/room-service", - "material/rotate-360", - "material/rotate-3d-variant", - "material/rotate-3d", - "material/rotate-left-variant", - "material/rotate-left", - "material/rotate-orbit", - "material/rotate-right-variant", - "material/rotate-right", - "material/rounded-corner", - "material/router-network", - "material/router-wireless-off", - "material/router-wireless-settings", - "material/router-wireless", - "material/router", - "material/routes-clock", - "material/routes", - "material/rowing", - "material/rss-box", - "material/rss-off", - "material/rss", - "material/rug", - "material/rugby", - "material/ruler-square-compass", - "material/ruler-square", - "material/ruler", - "material/run-fast", - "material/run", - "material/rv-truck", - "material/sack-percent", - "material/sack", - "material/safe-square-outline", - "material/safe-square", - "material/safe", - "material/safety-goggles", - "material/sail-boat-sink", - "material/sail-boat", - "material/sale-outline", - "material/sale", - "material/salesforce", - "material/sass", - "material/satellite-uplink", - "material/satellite-variant", - "material/satellite", - "material/sausage-off", - "material/sausage", - "material/saw-blade", - "material/sawtooth-wave", - "material/saxophone", - "material/scale-balance", - "material/scale-bathroom", - "material/scale-off", - "material/scale-unbalanced", - "material/scale", - "material/scan-helper", - "material/scanner-off", - "material/scanner", - "material/scatter-plot-outline", - "material/scatter-plot", - "material/scent-off", - "material/scent", - "material/school-outline", - "material/school", - "material/scissors-cutting", - "material/scooter-electric", - "material/scooter", - "material/scoreboard-outline", - "material/scoreboard", - "material/screen-rotation-lock", - "material/screen-rotation", - "material/screw-flat-top", - "material/screw-lag", - "material/screw-machine-flat-top", - "material/screw-machine-round-top", - "material/screw-round-top", - "material/screwdriver", - "material/script-outline", - "material/script-text-key-outline", - "material/script-text-key", - "material/script-text-outline", - "material/script-text-play-outline", - "material/script-text-play", - "material/script-text", - "material/script", - "material/sd", - "material/seal-variant", - "material/seal", - "material/search-web", - "material/seat-flat-angled", - "material/seat-flat", - "material/seat-individual-suite", - "material/seat-legroom-extra", - "material/seat-legroom-normal", - "material/seat-legroom-reduced", - "material/seat-outline", - "material/seat-passenger", - "material/seat-recline-extra", - "material/seat-recline-normal", - "material/seat", - "material/seatbelt", - "material/security-network", - "material/security", - "material/seed-off-outline", - "material/seed-off", - "material/seed-outline", - "material/seed-plus-outline", - "material/seed-plus", - "material/seed", - "material/seesaw", - "material/segment", - "material/select-all", - "material/select-arrow-down", - "material/select-arrow-up", - "material/select-color", - "material/select-compare", - "material/select-drag", - "material/select-group", - "material/select-inverse", - "material/select-marker", - "material/select-multiple-marker", - "material/select-multiple", - "material/select-off", - "material/select-place", - "material/select-remove", - "material/select-search", - "material/select", - "material/selection-drag", - "material/selection-ellipse-arrow-inside", - "material/selection-ellipse-remove", - "material/selection-ellipse", - "material/selection-marker", - "material/selection-multiple-marker", - "material/selection-multiple", - "material/selection-off", - "material/selection-remove", - "material/selection-search", - "material/selection", - "material/semantic-web", - "material/send-check-outline", - "material/send-check", - "material/send-circle-outline", - "material/send-circle", - "material/send-clock-outline", - "material/send-clock", - "material/send-lock-outline", - "material/send-lock", - "material/send-outline", - "material/send", - "material/serial-port", - "material/server-minus", - "material/server-network-off", - "material/server-network", - "material/server-off", - "material/server-plus", - "material/server-remove", - "material/server-security", - "material/server", - "material/set-all", - "material/set-center-right", - "material/set-center", - "material/set-left-center", - "material/set-left-right", - "material/set-left", - "material/set-merge", - "material/set-none", - "material/set-right", - "material/set-split", - "material/set-square", - "material/set-top-box", - "material/settings-helper", - "material/shaker-outline", - "material/shaker", - "material/shape-circle-plus", - "material/shape-outline", - "material/shape-oval-plus", - "material/shape-plus", - "material/shape-polygon-plus", - "material/shape-rectangle-plus", - "material/shape-square-plus", - "material/shape-square-rounded-plus", - "material/shape", - "material/share-all-outline", - "material/share-all", - "material/share-circle", - "material/share-off-outline", - "material/share-off", - "material/share-outline", - "material/share-variant-outline", - "material/share-variant", - "material/share", - "material/shark-fin-outline", - "material/shark-fin", - "material/shark-off", - "material/shark", - "material/sheep", - "material/shield-account-outline", - "material/shield-account-variant-outline", - "material/shield-account-variant", - "material/shield-account", - "material/shield-airplane-outline", - "material/shield-airplane", - "material/shield-alert-outline", - "material/shield-alert", - "material/shield-bug-outline", - "material/shield-bug", - "material/shield-car", - "material/shield-check-outline", - "material/shield-check", - "material/shield-cross-outline", - "material/shield-cross", - "material/shield-crown-outline", - "material/shield-crown", - "material/shield-edit-outline", - "material/shield-edit", - "material/shield-half-full", - "material/shield-half", - "material/shield-home-outline", - "material/shield-home", - "material/shield-key-outline", - "material/shield-key", - "material/shield-link-variant-outline", - "material/shield-link-variant", - "material/shield-lock-open-outline", - "material/shield-lock-open", - "material/shield-lock-outline", - "material/shield-lock", - "material/shield-moon-outline", - "material/shield-moon", - "material/shield-off-outline", - "material/shield-off", - "material/shield-outline", - "material/shield-plus-outline", - "material/shield-plus", - "material/shield-refresh-outline", - "material/shield-refresh", - "material/shield-remove-outline", - "material/shield-remove", - "material/shield-search", - "material/shield-star-outline", - "material/shield-star", - "material/shield-sun-outline", - "material/shield-sun", - "material/shield-sword-outline", - "material/shield-sword", - "material/shield-sync-outline", - "material/shield-sync", - "material/shield", - "material/shimmer", - "material/ship-wheel", - "material/shipping-pallet", - "material/shoe-ballet", - "material/shoe-cleat", - "material/shoe-formal", - "material/shoe-heel", - "material/shoe-print", - "material/shoe-sneaker", - "material/shopping-music", - "material/shopping-outline", - "material/shopping-search-outline", - "material/shopping-search", - "material/shopping", - "material/shore", - "material/shovel-off", - "material/shovel", - "material/shower-head", - "material/shower", - "material/shredder", - "material/shuffle-disabled", - "material/shuffle-variant", - "material/shuffle", - "material/shuriken", - "material/sickle", - "material/sigma-lower", - "material/sigma", - "material/sign-caution", - "material/sign-direction-minus", - "material/sign-direction-plus", - "material/sign-direction-remove", - "material/sign-direction", - "material/sign-language-outline", - "material/sign-language", - "material/sign-pole", - "material/sign-real-estate", - "material/sign-text", - "material/sign-yield", - "material/signal-2g", - "material/signal-3g", - "material/signal-4g", - "material/signal-5g", - "material/signal-cellular-1", - "material/signal-cellular-2", - "material/signal-cellular-3", - "material/signal-cellular-outline", - "material/signal-distance-variant", - "material/signal-hspa-plus", - "material/signal-hspa", - "material/signal-off", - "material/signal-variant", - "material/signal", - "material/signature-freehand", - "material/signature-image", - "material/signature-text", - "material/signature", - "material/silo-outline", - "material/silo", - "material/silverware-clean", - "material/silverware-fork-knife", - "material/silverware-fork", - "material/silverware-spoon", - "material/silverware-variant", - "material/silverware", - "material/sim-alert-outline", - "material/sim-alert", - "material/sim-off-outline", - "material/sim-off", - "material/sim-outline", - "material/sim", - "material/simple-icons", - "material/sina-weibo", - "material/sine-wave", - "material/sitemap-outline", - "material/sitemap", - "material/size-l", - "material/size-m", - "material/size-s", - "material/size-xl", - "material/size-xs", - "material/size-xxl", - "material/size-xxs", - "material/size-xxxl", - "material/skate-off", - "material/skate", - "material/skateboard", - "material/skateboarding", - "material/skew-less", - "material/skew-more", - "material/ski-cross-country", - "material/ski-water", - "material/ski", - "material/skip-backward-outline", - "material/skip-backward", - "material/skip-forward-outline", - "material/skip-forward", - "material/skip-next-circle-outline", - "material/skip-next-circle", - "material/skip-next-outline", - "material/skip-next", - "material/skip-previous-circle-outline", - "material/skip-previous-circle", - "material/skip-previous-outline", - "material/skip-previous", - "material/skull-crossbones-outline", - "material/skull-crossbones", - "material/skull-outline", - "material/skull-scan-outline", - "material/skull-scan", - "material/skull", - "material/skype-business", - "material/skype", - "material/slack", - "material/slash-forward-box", - "material/slash-forward", - "material/sledding", - "material/sleep-off", - "material/sleep", - "material/slide", - "material/slope-downhill", - "material/slope-uphill", - "material/slot-machine-outline", - "material/slot-machine", - "material/smart-card-off-outline", - "material/smart-card-off", - "material/smart-card-outline", - "material/smart-card-reader-outline", - "material/smart-card-reader", - "material/smart-card", - "material/smog", - "material/smoke-detector-alert-outline", - "material/smoke-detector-alert", - "material/smoke-detector-off-outline", - "material/smoke-detector-off", - "material/smoke-detector-outline", - "material/smoke-detector-variant-alert", - "material/smoke-detector-variant-off", - "material/smoke-detector-variant", - "material/smoke-detector", - "material/smoke", - "material/smoking-off", - "material/smoking-pipe-off", - "material/smoking-pipe", - "material/smoking", - "material/snail", - "material/snake", - "material/snapchat", - "material/snowboard", - "material/snowflake-alert", - "material/snowflake-check", - "material/snowflake-melt", - "material/snowflake-off", - "material/snowflake-thermometer", - "material/snowflake-variant", - "material/snowflake", - "material/snowman", - "material/snowmobile", - "material/snowshoeing", - "material/soccer-field", - "material/soccer", - "material/social-distance-2-meters", - "material/social-distance-6-feet", - "material/sofa-outline", - "material/sofa-single-outline", - "material/sofa-single", - "material/sofa", - "material/solar-panel-large", - "material/solar-panel", - "material/solar-power-variant-outline", - "material/solar-power-variant", - "material/solar-power", - "material/soldering-iron", - "material/solid", - "material/sony-playstation", - "material/sort-alphabetical-ascending-variant", - "material/sort-alphabetical-ascending", - "material/sort-alphabetical-descending-variant", - "material/sort-alphabetical-descending", - "material/sort-alphabetical-variant", - "material/sort-ascending", - "material/sort-bool-ascending-variant", - "material/sort-bool-ascending", - "material/sort-bool-descending-variant", - "material/sort-bool-descending", - "material/sort-calendar-ascending", - "material/sort-calendar-descending", - "material/sort-clock-ascending-outline", - "material/sort-clock-ascending", - "material/sort-clock-descending-outline", - "material/sort-clock-descending", - "material/sort-descending", - "material/sort-numeric-ascending-variant", - "material/sort-numeric-ascending", - "material/sort-numeric-descending-variant", - "material/sort-numeric-descending", - "material/sort-numeric-variant", - "material/sort-reverse-variant", - "material/sort-variant-lock-open", - "material/sort-variant-lock", - "material/sort-variant-off", - "material/sort-variant-remove", - "material/sort-variant", - "material/sort", - "material/soundbar", - "material/soundcloud", - "material/source-branch-check", - "material/source-branch-minus", - "material/source-branch-plus", - "material/source-branch-refresh", - "material/source-branch-remove", - "material/source-branch-sync", - "material/source-branch", - "material/source-commit-end-local", - "material/source-commit-end", - "material/source-commit-local", - "material/source-commit-next-local", - "material/source-commit-start-next-local", - "material/source-commit-start", - "material/source-commit", - "material/source-fork", - "material/source-merge", - "material/source-pull", - "material/source-repository-multiple", - "material/source-repository", - "material/soy-sauce-off", - "material/soy-sauce", - "material/spa-outline", - "material/spa", - "material/space-invaders", - "material/space-station", - "material/spade", - "material/speaker-bluetooth", - "material/speaker-message", - "material/speaker-multiple", - "material/speaker-off", - "material/speaker-pause", - "material/speaker-play", - "material/speaker-stop", - "material/speaker-wireless", - "material/speaker", - "material/spear", - "material/speedometer-medium", - "material/speedometer-slow", - "material/speedometer", - "material/spellcheck", - "material/sphere-off", - "material/sphere", - "material/spider-thread", - "material/spider-web", - "material/spider", - "material/spirit-level", - "material/spoon-sugar", - "material/spotify", - "material/spotlight-beam", - "material/spotlight", - "material/spray-bottle", - "material/spray", - "material/sprinkler-fire", - "material/sprinkler-variant", - "material/sprinkler", - "material/sprout-outline", - "material/sprout", - "material/square-circle", - "material/square-edit-outline", - "material/square-medium-outline", - "material/square-medium", - "material/square-off-outline", - "material/square-off", - "material/square-opacity", - "material/square-outline", - "material/square-root-box", - "material/square-root", - "material/square-rounded-badge-outline", - "material/square-rounded-badge", - "material/square-rounded-outline", - "material/square-rounded", - "material/square-small", - "material/square-wave", - "material/square", - "material/squeegee", - "material/ssh", - "material/stack-exchange", - "material/stack-overflow", - "material/stackpath", - "material/stadium-outline", - "material/stadium-variant", - "material/stadium", - "material/stairs-box", - "material/stairs-down", - "material/stairs-up", - "material/stairs", - "material/stamper", - "material/standard-definition", - "material/star-box-multiple-outline", - "material/star-box-multiple", - "material/star-box-outline", - "material/star-box", - "material/star-check-outline", - "material/star-check", - "material/star-circle-outline", - "material/star-circle", - "material/star-cog-outline", - "material/star-cog", - "material/star-crescent", - "material/star-david", - "material/star-face", - "material/star-four-points-outline", - "material/star-four-points", - "material/star-half-full", - "material/star-half", - "material/star-minus-outline", - "material/star-minus", - "material/star-off-outline", - "material/star-off", - "material/star-outline", - "material/star-plus-outline", - "material/star-plus", - "material/star-remove-outline", - "material/star-remove", - "material/star-settings-outline", - "material/star-settings", - "material/star-shooting-outline", - "material/star-shooting", - "material/star-three-points-outline", - "material/star-three-points", - "material/star", - "material/state-machine", - "material/steam", - "material/steering-off", - "material/steering", - "material/step-backward-2", - "material/step-backward", - "material/step-forward-2", - "material/step-forward", - "material/stethoscope", - "material/sticker-alert-outline", - "material/sticker-alert", - "material/sticker-check-outline", - "material/sticker-check", - "material/sticker-circle-outline", - "material/sticker-emoji", - "material/sticker-minus-outline", - "material/sticker-minus", - "material/sticker-outline", - "material/sticker-plus-outline", - "material/sticker-plus", - "material/sticker-remove-outline", - "material/sticker-remove", - "material/sticker-text-outline", - "material/sticker-text", - "material/sticker", - "material/stocking", - "material/stomach", - "material/stool-outline", - "material/stool", - "material/stop-circle-outline", - "material/stop-circle", - "material/stop", - "material/storage-tank-outline", - "material/storage-tank", - "material/store-24-hour", - "material/store-alert-outline", - "material/store-alert", - "material/store-check-outline", - "material/store-check", - "material/store-clock-outline", - "material/store-clock", - "material/store-cog-outline", - "material/store-cog", - "material/store-edit-outline", - "material/store-edit", - "material/store-marker-outline", - "material/store-marker", - "material/store-minus-outline", - "material/store-minus", - "material/store-off-outline", - "material/store-off", - "material/store-outline", - "material/store-plus-outline", - "material/store-plus", - "material/store-remove-outline", - "material/store-remove", - "material/store-search-outline", - "material/store-search", - "material/store-settings-outline", - "material/store-settings", - "material/store", - "material/storefront-check-outline", - "material/storefront-check", - "material/storefront-edit-outline", - "material/storefront-edit", - "material/storefront-minus-outline", - "material/storefront-minus", - "material/storefront-outline", - "material/storefront-plus-outline", - "material/storefront-plus", - "material/storefront-remove-outline", - "material/storefront-remove", - "material/storefront", - "material/stove", - "material/strategy", - "material/stretch-to-page-outline", - "material/stretch-to-page", - "material/string-lights-off", - "material/string-lights", - "material/subdirectory-arrow-left", - "material/subdirectory-arrow-right", - "material/submarine", - "material/subtitles-outline", - "material/subtitles", - "material/subway-alert-variant", - "material/subway-variant", - "material/subway", - "material/summit", - "material/sun-angle-outline", - "material/sun-angle", - "material/sun-clock-outline", - "material/sun-clock", - "material/sun-compass", - "material/sun-snowflake-variant", - "material/sun-snowflake", - "material/sun-thermometer-outline", - "material/sun-thermometer", - "material/sun-wireless-outline", - "material/sun-wireless", - "material/sunglasses", - "material/surfing", - "material/surround-sound-2-0", - "material/surround-sound-2-1", - "material/surround-sound-3-1", - "material/surround-sound-5-1-2", - "material/surround-sound-5-1", - "material/surround-sound-7-1", - "material/surround-sound", - "material/svg", - "material/swap-horizontal-bold", - "material/swap-horizontal-circle-outline", - "material/swap-horizontal-circle", - "material/swap-horizontal-variant", - "material/swap-horizontal", - "material/swap-vertical-bold", - "material/swap-vertical-circle-outline", - "material/swap-vertical-circle", - "material/swap-vertical-variant", - "material/swap-vertical", - "material/swim", - "material/switch", - "material/sword-cross", - "material/sword", - "material/syllabary-hangul", - "material/syllabary-hiragana", - "material/syllabary-katakana-halfwidth", - "material/syllabary-katakana", - "material/symbol", - "material/symfony", - "material/synagogue-outline", - "material/synagogue", - "material/sync-alert", - "material/sync-circle", - "material/sync-off", - "material/sync", - "material/tab-minus", - "material/tab-plus", - "material/tab-remove", - "material/tab-search", - "material/tab-unselected", - "material/tab", - "material/table-account", - "material/table-alert", - "material/table-arrow-down", - "material/table-arrow-left", - "material/table-arrow-right", - "material/table-arrow-up", - "material/table-border", - "material/table-cancel", - "material/table-chair", - "material/table-check", - "material/table-clock", - "material/table-cog", - "material/table-column-plus-after", - "material/table-column-plus-before", - "material/table-column-remove", - "material/table-column-width", - "material/table-column", - "material/table-edit", - "material/table-eye-off", - "material/table-eye", - "material/table-filter", - "material/table-furniture", - "material/table-headers-eye-off", - "material/table-headers-eye", - "material/table-heart", - "material/table-key", - "material/table-large-plus", - "material/table-large-remove", - "material/table-large", - "material/table-lock", - "material/table-merge-cells", - "material/table-minus", - "material/table-multiple", - "material/table-network", - "material/table-of-contents", - "material/table-off", - "material/table-picnic", - "material/table-pivot", - "material/table-plus", - "material/table-question", - "material/table-refresh", - "material/table-remove", - "material/table-row-height", - "material/table-row-plus-after", - "material/table-row-plus-before", - "material/table-row-remove", - "material/table-row", - "material/table-search", - "material/table-settings", - "material/table-split-cell", - "material/table-star", - "material/table-sync", - "material/table-tennis", - "material/table", - "material/tablet-cellphone", - "material/tablet-dashboard", - "material/tablet", - "material/taco", - "material/tag-arrow-down-outline", - "material/tag-arrow-down", - "material/tag-arrow-left-outline", - "material/tag-arrow-left", - "material/tag-arrow-right-outline", - "material/tag-arrow-right", - "material/tag-arrow-up-outline", - "material/tag-arrow-up", - "material/tag-check-outline", - "material/tag-check", - "material/tag-faces", - "material/tag-heart-outline", - "material/tag-heart", - "material/tag-minus-outline", - "material/tag-minus", - "material/tag-multiple-outline", - "material/tag-multiple", - "material/tag-off-outline", - "material/tag-off", - "material/tag-outline", - "material/tag-plus-outline", - "material/tag-plus", - "material/tag-remove-outline", - "material/tag-remove", - "material/tag-search-outline", - "material/tag-search", - "material/tag-text-outline", - "material/tag-text", - "material/tag", - "material/tailwind", - "material/tally-mark-1", - "material/tally-mark-2", - "material/tally-mark-3", - "material/tally-mark-4", - "material/tally-mark-5", - "material/tangram", - "material/tank", - "material/tanker-truck", - "material/tape-drive", - "material/tape-measure", - "material/target-account", - "material/target-variant", - "material/target", - "material/taxi", - "material/tea-outline", - "material/tea", - "material/teamviewer", - "material/teddy-bear", - "material/telescope", - "material/television-ambient-light", - "material/television-box", - "material/television-classic-off", - "material/television-classic", - "material/television-guide", - "material/television-off", - "material/television-pause", - "material/television-play", - "material/television-shimmer", - "material/television-speaker-off", - "material/television-speaker", - "material/television-stop", - "material/television", - "material/temperature-celsius", - "material/temperature-fahrenheit", - "material/temperature-kelvin", - "material/temple-buddhist-outline", - "material/temple-buddhist", - "material/temple-hindu-outline", - "material/temple-hindu", - "material/tennis-ball", - "material/tennis", - "material/tent", - "material/terraform", - "material/terrain", - "material/test-tube-empty", - "material/test-tube-off", - "material/test-tube", - "material/text-account", - "material/text-box-check-outline", - "material/text-box-check", - "material/text-box-edit-outline", - "material/text-box-edit", - "material/text-box-minus-outline", - "material/text-box-minus", - "material/text-box-multiple-outline", - "material/text-box-multiple", - "material/text-box-outline", - "material/text-box-plus-outline", - "material/text-box-plus", - "material/text-box-remove-outline", - "material/text-box-remove", - "material/text-box-search-outline", - "material/text-box-search", - "material/text-box", - "material/text-long", - "material/text-recognition", - "material/text-search-variant", - "material/text-search", - "material/text-shadow", - "material/text-short", - "material/text", - "material/texture-box", - "material/texture", - "material/theater", - "material/theme-light-dark", - "material/thermometer-alert", - "material/thermometer-auto", - "material/thermometer-bluetooth", - "material/thermometer-check", - "material/thermometer-chevron-down", - "material/thermometer-chevron-up", - "material/thermometer-high", - "material/thermometer-lines", - "material/thermometer-low", - "material/thermometer-minus", - "material/thermometer-off", - "material/thermometer-plus", - "material/thermometer-probe-off", - "material/thermometer-probe", - "material/thermometer-water", - "material/thermometer", - "material/thermostat-auto", - "material/thermostat-box-auto", - "material/thermostat-box", - "material/thermostat", - "material/thought-bubble-outline", - "material/thought-bubble", - "material/thumb-down-outline", - "material/thumb-down", - "material/thumb-up-outline", - "material/thumb-up", - "material/thumbs-up-down-outline", - "material/thumbs-up-down", - "material/ticket-account", - "material/ticket-confirmation-outline", - "material/ticket-confirmation", - "material/ticket-outline", - "material/ticket-percent-outline", - "material/ticket-percent", - "material/ticket", - "material/tie", - "material/tilde-off", - "material/tilde", - "material/timelapse", - "material/timeline-alert-outline", - "material/timeline-alert", - "material/timeline-check-outline", - "material/timeline-check", - "material/timeline-clock-outline", - "material/timeline-clock", - "material/timeline-minus-outline", - "material/timeline-minus", - "material/timeline-outline", - "material/timeline-plus-outline", - "material/timeline-plus", - "material/timeline-question-outline", - "material/timeline-question", - "material/timeline-remove-outline", - "material/timeline-remove", - "material/timeline-text-outline", - "material/timeline-text", - "material/timeline", - "material/timer-10", - "material/timer-3", - "material/timer-alert-outline", - "material/timer-alert", - "material/timer-cancel-outline", - "material/timer-cancel", - "material/timer-check-outline", - "material/timer-check", - "material/timer-cog-outline", - "material/timer-cog", - "material/timer-edit-outline", - "material/timer-edit", - "material/timer-lock-open-outline", - "material/timer-lock-open", - "material/timer-lock-outline", - "material/timer-lock", - "material/timer-marker-outline", - "material/timer-marker", - "material/timer-minus-outline", - "material/timer-minus", - "material/timer-music-outline", - "material/timer-music", - "material/timer-off-outline", - "material/timer-off", - "material/timer-outline", - "material/timer-pause-outline", - "material/timer-pause", - "material/timer-play-outline", - "material/timer-play", - "material/timer-plus-outline", - "material/timer-plus", - "material/timer-refresh-outline", - "material/timer-refresh", - "material/timer-remove-outline", - "material/timer-remove", - "material/timer-sand-complete", - "material/timer-sand-empty", - "material/timer-sand-full", - "material/timer-sand-paused", - "material/timer-sand", - "material/timer-settings-outline", - "material/timer-settings", - "material/timer-star-outline", - "material/timer-star", - "material/timer-stop-outline", - "material/timer-stop", - "material/timer-sync-outline", - "material/timer-sync", - "material/timer", - "material/timetable", - "material/tire", - "material/toaster-off", - "material/toaster-oven", - "material/toaster", - "material/toggle-switch-off-outline", - "material/toggle-switch-off", - "material/toggle-switch-outline", - "material/toggle-switch-variant-off", - "material/toggle-switch-variant", - "material/toggle-switch", - "material/toilet", - "material/toolbox-outline", - "material/toolbox", - "material/tools", - "material/tooltip-account", - "material/tooltip-cellphone", - "material/tooltip-check-outline", - "material/tooltip-check", - "material/tooltip-edit-outline", - "material/tooltip-edit", - "material/tooltip-image-outline", - "material/tooltip-image", - "material/tooltip-minus-outline", - "material/tooltip-minus", - "material/tooltip-outline", - "material/tooltip-plus-outline", - "material/tooltip-plus", - "material/tooltip-remove-outline", - "material/tooltip-remove", - "material/tooltip-text-outline", - "material/tooltip-text", - "material/tooltip", - "material/tooth-outline", - "material/tooth", - "material/toothbrush-electric", - "material/toothbrush-paste", - "material/toothbrush", - "material/torch", - "material/tortoise", - "material/toslink", - "material/tournament", - "material/tow-truck", - "material/tower-beach", - "material/tower-fire", - "material/town-hall", - "material/toy-brick-marker-outline", - "material/toy-brick-marker", - "material/toy-brick-minus-outline", - "material/toy-brick-minus", - "material/toy-brick-outline", - "material/toy-brick-plus-outline", - "material/toy-brick-plus", - "material/toy-brick-remove-outline", - "material/toy-brick-remove", - "material/toy-brick-search-outline", - "material/toy-brick-search", - "material/toy-brick", - "material/track-light-off", - "material/track-light", - "material/trackpad-lock", - "material/trackpad", - "material/tractor-variant", - "material/tractor", - "material/trademark", - "material/traffic-cone", - "material/traffic-light-outline", - "material/traffic-light", - "material/train-car-autorack", - "material/train-car-box-full", - "material/train-car-box-open", - "material/train-car-box", - "material/train-car-caboose", - "material/train-car-centerbeam-full", - "material/train-car-centerbeam", - "material/train-car-container", - "material/train-car-flatbed-car", - "material/train-car-flatbed-tank", - "material/train-car-flatbed", - "material/train-car-gondola-full", - "material/train-car-gondola", - "material/train-car-hopper-covered", - "material/train-car-hopper-full", - "material/train-car-hopper", - "material/train-car-intermodal", - "material/train-car-passenger-door-open", - "material/train-car-passenger-door", - "material/train-car-passenger-variant", - "material/train-car-passenger", - "material/train-car-tank", - "material/train-car", - "material/train-variant", - "material/train", - "material/tram-side", - "material/tram", - "material/transcribe-close", - "material/transcribe", - "material/transfer-down", - "material/transfer-left", - "material/transfer-right", - "material/transfer-up", - "material/transfer", - "material/transit-connection-horizontal", - "material/transit-connection-variant", - "material/transit-connection", - "material/transit-detour", - "material/transit-skip", - "material/transit-transfer", - "material/transition-masked", - "material/transition", - "material/translate-off", - "material/translate-variant", - "material/translate", - "material/transmission-tower-export", - "material/transmission-tower-import", - "material/transmission-tower-off", - "material/transmission-tower", - "material/trash-can-outline", - "material/trash-can", - "material/tray-alert", - "material/tray-arrow-down", - "material/tray-arrow-up", - "material/tray-full", - "material/tray-minus", - "material/tray-plus", - "material/tray-remove", - "material/tray", - "material/treasure-chest", - "material/tree-outline", - "material/tree", - "material/trello", - "material/trending-down", - "material/trending-neutral", - "material/trending-up", - "material/triangle-outline", - "material/triangle-small-down", - "material/triangle-small-up", - "material/triangle-wave", - "material/triangle", - "material/triforce", - "material/trophy-award", - "material/trophy-broken", - "material/trophy-outline", - "material/trophy-variant-outline", - "material/trophy-variant", - "material/trophy", - "material/truck-alert-outline", - "material/truck-alert", - "material/truck-cargo-container", - "material/truck-check-outline", - "material/truck-check", - "material/truck-delivery-outline", - "material/truck-delivery", - "material/truck-fast-outline", - "material/truck-fast", - "material/truck-flatbed", - "material/truck-minus-outline", - "material/truck-minus", - "material/truck-outline", - "material/truck-plus-outline", - "material/truck-plus", - "material/truck-remove-outline", - "material/truck-remove", - "material/truck-snowflake", - "material/truck-trailer", - "material/truck", - "material/trumpet", - "material/tshirt-crew-outline", - "material/tshirt-crew", - "material/tshirt-v-outline", - "material/tshirt-v", - "material/tsunami", - "material/tumble-dryer-alert", - "material/tumble-dryer-off", - "material/tumble-dryer", - "material/tune-variant", - "material/tune-vertical-variant", - "material/tune-vertical", - "material/tune", - "material/tunnel-outline", - "material/tunnel", - "material/turbine", - "material/turkey", - "material/turnstile-outline", - "material/turnstile", - "material/turtle", - "material/twitch", - "material/twitter", - "material/two-factor-authentication", - "material/typewriter", - "material/ubisoft", - "material/ubuntu", - "material/ufo-outline", - "material/ufo", - "material/ultra-high-definition", - "material/umbraco", - "material/umbrella-beach-outline", - "material/umbrella-beach", - "material/umbrella-closed-outline", - "material/umbrella-closed-variant", - "material/umbrella-closed", - "material/umbrella-outline", - "material/umbrella", - "material/undo-variant", - "material/undo", - "material/unfold-less-horizontal", - "material/unfold-less-vertical", - "material/unfold-more-horizontal", - "material/unfold-more-vertical", - "material/ungroup", - "material/unicode", - "material/unicorn-variant", - "material/unicorn", - "material/unicycle", - "material/unity", - "material/unreal", - "material/update", - "material/upload-lock-outline", - "material/upload-lock", - "material/upload-multiple", - "material/upload-network-outline", - "material/upload-network", - "material/upload-off-outline", - "material/upload-off", - "material/upload-outline", - "material/upload", - "material/usb-flash-drive-outline", - "material/usb-flash-drive", - "material/usb-port", - "material/usb", - "material/vacuum-outline", - "material/vacuum", - "material/valve-closed", - "material/valve-open", - "material/valve", - "material/van-passenger", - "material/van-utility", - "material/vanish-quarter", - "material/vanish", - "material/vanity-light", - "material/variable-box", - "material/variable", - "material/vector-arrange-above", - "material/vector-arrange-below", - "material/vector-bezier", - "material/vector-circle-variant", - "material/vector-circle", - "material/vector-combine", - "material/vector-curve", - "material/vector-difference-ab", - "material/vector-difference-ba", - "material/vector-difference", - "material/vector-ellipse", - "material/vector-intersection", - "material/vector-line", - "material/vector-link", - "material/vector-point-edit", - "material/vector-point-minus", - "material/vector-point-plus", - "material/vector-point-select", - "material/vector-point", - "material/vector-polygon-variant", - "material/vector-polygon", - "material/vector-polyline-edit", - "material/vector-polyline-minus", - "material/vector-polyline-plus", - "material/vector-polyline-remove", - "material/vector-polyline", - "material/vector-radius", - "material/vector-rectangle", - "material/vector-selection", - "material/vector-square-close", - "material/vector-square-edit", - "material/vector-square-minus", - "material/vector-square-open", - "material/vector-square-plus", - "material/vector-square-remove", - "material/vector-square", - "material/vector-triangle", - "material/vector-union", - "material/vhs", - "material/vibrate-off", - "material/vibrate", - "material/video-2d", - "material/video-3d-off", - "material/video-3d-variant", - "material/video-3d", - "material/video-4k-box", - "material/video-account", - "material/video-box-off", - "material/video-box", - "material/video-check-outline", - "material/video-check", - "material/video-high-definition", - "material/video-image", - "material/video-input-antenna", - "material/video-input-component", - "material/video-input-hdmi", - "material/video-input-scart", - "material/video-input-svideo", - "material/video-marker-outline", - "material/video-marker", - "material/video-minus-outline", - "material/video-minus", - "material/video-off-outline", - "material/video-off", - "material/video-outline", - "material/video-plus-outline", - "material/video-plus", - "material/video-stabilization", - "material/video-switch-outline", - "material/video-switch", - "material/video-vintage", - "material/video-wireless-outline", - "material/video-wireless", - "material/video", - "material/view-agenda-outline", - "material/view-agenda", - "material/view-array-outline", - "material/view-array", - "material/view-carousel-outline", - "material/view-carousel", - "material/view-column-outline", - "material/view-column", - "material/view-comfy-outline", - "material/view-comfy", - "material/view-compact-outline", - "material/view-compact", - "material/view-dashboard-edit-outline", - "material/view-dashboard-edit", - "material/view-dashboard-outline", - "material/view-dashboard-variant-outline", - "material/view-dashboard-variant", - "material/view-dashboard", - "material/view-day-outline", - "material/view-day", - "material/view-gallery-outline", - "material/view-gallery", - "material/view-grid-outline", - "material/view-grid-plus-outline", - "material/view-grid-plus", - "material/view-grid", - "material/view-headline", - "material/view-list-outline", - "material/view-list", - "material/view-module-outline", - "material/view-module", - "material/view-parallel-outline", - "material/view-parallel", - "material/view-quilt-outline", - "material/view-quilt", - "material/view-sequential-outline", - "material/view-sequential", - "material/view-split-horizontal", - "material/view-split-vertical", - "material/view-stream-outline", - "material/view-stream", - "material/view-week-outline", - "material/view-week", - "material/vimeo", - "material/violin", - "material/virtual-reality", - "material/virus-off-outline", - "material/virus-off", - "material/virus-outline", - "material/virus", - "material/vlc", - "material/voicemail", - "material/volcano-outline", - "material/volcano", - "material/volleyball", - "material/volume-equal", - "material/volume-high", - "material/volume-low", - "material/volume-medium", - "material/volume-minus", - "material/volume-mute", - "material/volume-off", - "material/volume-plus", - "material/volume-source", - "material/volume-variant-off", - "material/volume-vibrate", - "material/vote-outline", - "material/vote", - "material/vpn", - "material/vuejs", - "material/vuetify", - "material/walk", - "material/wall-fire", - "material/wall-sconce-flat-outline", - "material/wall-sconce-flat-variant-outline", - "material/wall-sconce-flat-variant", - "material/wall-sconce-flat", - "material/wall-sconce-outline", - "material/wall-sconce-round-outline", - "material/wall-sconce-round-variant-outline", - "material/wall-sconce-round-variant", - "material/wall-sconce-round", - "material/wall-sconce", - "material/wall", - "material/wallet-giftcard", - "material/wallet-membership", - "material/wallet-outline", - "material/wallet-plus-outline", - "material/wallet-plus", - "material/wallet-travel", - "material/wallet", - "material/wallpaper", - "material/wan", - "material/wardrobe-outline", - "material/wardrobe", - "material/warehouse", - "material/washing-machine-alert", - "material/washing-machine-off", - "material/washing-machine", - "material/watch-export-variant", - "material/watch-export", - "material/watch-import-variant", - "material/watch-import", - "material/watch-variant", - "material/watch-vibrate-off", - "material/watch-vibrate", - "material/watch", - "material/water-alert-outline", - "material/water-alert", - "material/water-boiler-alert", - "material/water-boiler-auto", - "material/water-boiler-off", - "material/water-boiler", - "material/water-check-outline", - "material/water-check", - "material/water-circle", - "material/water-minus-outline", - "material/water-minus", - "material/water-off-outline", - "material/water-off", - "material/water-opacity", - "material/water-outline", - "material/water-percent-alert", - "material/water-percent", - "material/water-plus-outline", - "material/water-plus", - "material/water-polo", - "material/water-pump-off", - "material/water-pump", - "material/water-remove-outline", - "material/water-remove", - "material/water-sync", - "material/water-thermometer-outline", - "material/water-thermometer", - "material/water-well-outline", - "material/water-well", - "material/water", - "material/waterfall", - "material/watering-can-outline", - "material/watering-can", - "material/watermark", - "material/wave", - "material/waveform", - "material/waves-arrow-left", - "material/waves-arrow-right", - "material/waves-arrow-up", - "material/waves", - "material/waze", - "material/weather-cloudy-alert", - "material/weather-cloudy-arrow-right", - "material/weather-cloudy-clock", - "material/weather-cloudy", - "material/weather-dust", - "material/weather-fog", - "material/weather-hail", - "material/weather-hazy", - "material/weather-hurricane", - "material/weather-lightning-rainy", - "material/weather-lightning", - "material/weather-night-partly-cloudy", - "material/weather-night", - "material/weather-partly-cloudy", - "material/weather-partly-lightning", - "material/weather-partly-rainy", - "material/weather-partly-snowy-rainy", - "material/weather-partly-snowy", - "material/weather-pouring", - "material/weather-rainy", - "material/weather-snowy-heavy", - "material/weather-snowy-rainy", - "material/weather-snowy", - "material/weather-sunny-alert", - "material/weather-sunny-off", - "material/weather-sunny", - "material/weather-sunset-down", - "material/weather-sunset-up", - "material/weather-sunset", - "material/weather-tornado", - "material/weather-windy-variant", - "material/weather-windy", - "material/web-box", - "material/web-cancel", - "material/web-check", - "material/web-clock", - "material/web-minus", - "material/web-off", - "material/web-plus", - "material/web-refresh", - "material/web-remove", - "material/web-sync", - "material/web", - "material/webcam-off", - "material/webcam", - "material/webhook", - "material/webpack", - "material/webrtc", - "material/wechat", - "material/weight-gram", - "material/weight-kilogram", - "material/weight-lifter", - "material/weight-pound", - "material/weight", - "material/whatsapp", - "material/wheel-barrow", - "material/wheelchair-accessibility", - "material/wheelchair", - "material/whistle-outline", - "material/whistle", - "material/white-balance-auto", - "material/white-balance-incandescent", - "material/white-balance-iridescent", - "material/white-balance-sunny", - "material/widgets-outline", - "material/widgets", - "material/wifi-alert", - "material/wifi-arrow-down", - "material/wifi-arrow-left-right", - "material/wifi-arrow-left", - "material/wifi-arrow-right", - "material/wifi-arrow-up-down", - "material/wifi-arrow-up", - "material/wifi-cancel", - "material/wifi-check", - "material/wifi-cog", - "material/wifi-lock-open", - "material/wifi-lock", - "material/wifi-marker", - "material/wifi-minus", - "material/wifi-off", - "material/wifi-plus", - "material/wifi-refresh", - "material/wifi-remove", - "material/wifi-settings", - "material/wifi-star", - "material/wifi-strength-1-alert", - "material/wifi-strength-1-lock-open", - "material/wifi-strength-1-lock", - "material/wifi-strength-1", - "material/wifi-strength-2-alert", - "material/wifi-strength-2-lock-open", - "material/wifi-strength-2-lock", - "material/wifi-strength-2", - "material/wifi-strength-3-alert", - "material/wifi-strength-3-lock-open", - "material/wifi-strength-3-lock", - "material/wifi-strength-3", - "material/wifi-strength-4-alert", - "material/wifi-strength-4-lock-open", - "material/wifi-strength-4-lock", - "material/wifi-strength-4", - "material/wifi-strength-alert-outline", - "material/wifi-strength-lock-open-outline", - "material/wifi-strength-lock-outline", - "material/wifi-strength-off-outline", - "material/wifi-strength-off", - "material/wifi-strength-outline", - "material/wifi-sync", - "material/wifi", - "material/wikipedia", - "material/wind-power-outline", - "material/wind-power", - "material/wind-turbine-alert", - "material/wind-turbine-check", - "material/wind-turbine", - "material/window-close", - "material/window-closed-variant", - "material/window-closed", - "material/window-maximize", - "material/window-minimize", - "material/window-open-variant", - "material/window-open", - "material/window-restore", - "material/window-shutter-alert", - "material/window-shutter-auto", - "material/window-shutter-cog", - "material/window-shutter-open", - "material/window-shutter-settings", - "material/window-shutter", - "material/windsock", - "material/wiper-wash-alert", - "material/wiper-wash", - "material/wiper", - "material/wizard-hat", - "material/wordpress", - "material/wrap-disabled", - "material/wrap", - "material/wrench-check-outline", - "material/wrench-check", - "material/wrench-clock-outline", - "material/wrench-clock", - "material/wrench-cog-outline", - "material/wrench-cog", - "material/wrench-outline", - "material/wrench", - "material/xamarin", - "material/xml", - "material/xmpp", - "material/yahoo", - "material/yeast", - "material/yin-yang", - "material/yoga", - "material/youtube-gaming", - "material/youtube-studio", - "material/youtube-subscription", - "material/youtube-tv", - "material/youtube", - "material/yurt", - "material/z-wave", - "material/zend", - "material/zigbee", - "material/zip-box-outline", - "material/zip-box", - "material/zip-disk", - "material/zodiac-aquarius", - "material/zodiac-aries", - "material/zodiac-cancer", - "material/zodiac-capricorn", - "material/zodiac-gemini", - "material/zodiac-leo", - "material/zodiac-libra", - "material/zodiac-pisces", - "material/zodiac-sagittarius", - "material/zodiac-scorpio", - "material/zodiac-taurus", - "material/zodiac-virgo", - "octicons/accessibility-16", - "octicons/alert-16", - "octicons/alert-24", - "octicons/alert-fill-12", - 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}, - { - "$ref": "extensions/pymdownx.json" - } - ] - }, - "uniqueItems": true, - "minItems": 1 -} diff --git a/schema/extensions/markdown.json b/schema/extensions/markdown.json deleted file mode 100644 index 99563b0..0000000 --- a/schema/extensions/markdown.json +++ /dev/null @@ -1,140 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Markdown extensions", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/", - "oneOf": [ - { - "title": "Abbreviations – Python Markdown", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#abbreviations", - "enum": [ - "markdown.extensions.abbr", - "abbr" - ] - }, - { - "title": "Admonition – Python Markdown", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#admonition", - "enum": [ - "markdown.extensions.admonition", - "admonition" - ] - }, - { - "title": "Attribute Lists – Python Markdown", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#attribute-lists", - "enum": [ - "markdown.extensions.attr_list", - "attr_list" - ] - }, - { - "title": "Definition Lists – Python Markdown", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#definition-lists", - "enum": [ - "markdown.extensions.def_list", - "def_list" - ] - }, - { - "title": "Footnotes – Python Markdown", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#footnotes", - "enum": [ - "markdown.extensions.footnotes", - "footnotes" - ] - }, - { - "title": "Markdown in HTML – Python Markdown", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#markdown-in-html", - "enum": [ - "markdown.extensions.md_in_html", - "md_in_html" - ] - }, - { - "title": "Tables – Python Markdown", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#tables", - "enum": [ - "markdown.extensions.tables", - "tables" - ] - }, - { - "oneOf": [ - { - "type": "object", - "properties": { - "toc": { - "$ref": "#/definitions/toc" - }, - "markdown.extensions.toc": { - "$ref": "#/definitions/toc" - } - }, - "additionalProperties": false - }, - { - "title": "Table Of Contents – Python Markdown", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#table-of-contents", - "enum": [ - "markdown.extensions.toc", - "toc" - ] - } - ] - } - ], - "definitions": { - "toc": { - "title": "Table Of Contents – Python Markdown", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#table-of-contents", - "type": "object", - "properties": { - "title": { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#toc-title", - "type": "string" - }, - "permalink": { - "oneOf": [ - { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/extensions/python-markdown/#toc-permalink", - 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"required": [ - "icon", - "name", - "data", - "note" - ] - } - } - }, - "additionalProperties": false, - "required": [ - "title" - ] - } - }, - "additionalProperties": false, - "required": [ - "provider", - "property" - ], - "defaultSnippets": [ - { - "label": "feedback (default)", - "body": { - "feedback": { - "title": "${1:Was this page helpful}", - "ratings": [ - { - "icon": "${2:material/emoticon-happy-outline}", - "name": "${3:This page was helpful}", - "data": 1, - "note": "${4:Thanks for your feedback!}" - }, - { - "icon": "${5:material/emoticon-sad-outline}", - "name": "${6:This page could be improved}", - "data": 0, - "note": "${7:Thanks for your feedback!}" - } - ] - } - } - } - ] - }, - "consent": { - "title": "Cookie consent", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "type": "object", - "properties": { - "title": { - "title": "Cookie consent title", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "type": "string", - "default": "Cookie consent" - }, - "description": { - "title": "Cookie consent description", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "type": "string" - }, - "cookies": { - "title": "Cookies", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "type": "object", - "properties": { - "analytics": { - "$ref": "#/definitions/cookie" - } - }, - "patternProperties": { - "\\w+": { - "$ref": "#/definitions/cookie" - } - }, - "additionalProperties": false, - "defaultSnippets": [ - { - "label": "analytics (default)", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "body": { - "analytics": { - "name": "Google Analytics", - "checked": true - } - } - } - ] - }, - "actions": { - "title": "Cookie consent actions", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "type": "array", - "items": { - "oneOf": [ - { - "title": "Button to accept cookies", - "enum": [ - "accept" - ] - }, - { - "title": "Button to reject cookies", - "enum": [ - "reject" - ] - }, - { - "title": "Button to manage settings", - "enum": [ - "manage" - ] - } - ] - } - } - }, - "additionalProperties": false, - "defaultSnippets": [ - { - "label": "actions (default)", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "body": { - "actions": [ - "accept", - "manage" - ] - } - } - ], - "required": [ - "title", - "description" - ] - }, - "social": { - "title": "Social links", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-the-footer/#social-links", - "type": "array", - "items": { - "title": "Social link", - "type": "object", - "properties": { - "icon": { - "$ref": "#/definitions/icon" - }, - "link": { - "title": "Social link", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-the-footer/#social-link", - "type": "string" - }, - "name": { - "title": "Social link name", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-the-footer/#social-name", - "type": "string" - } - }, - "additionalProperties": false, - "required": [ - "icon", - "link" - ] - } - }, - "alternate": { - "title": "Site language selector", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-language/#site-language-selector", - "type": "array", - "items": { - "title": "Alternate language", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-language/#site-language-selector", - "type": "object", - "properties": { - "name": { - "title": "Alternate language name", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-language/#language-name", - "type": "string" - }, - "link": { - "title": "Alternate language link", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-language/#language-link", - "type": "string" - }, - "lang": { - "title": "Alternate language code (ISO 639-1)", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-language/#language-lang", - "type": "string" - } - }, - "additionalProperties": false, - "required": [ - "name", - "link", - "lang" - ] - } - }, - "tags": { - "title": "Tag identifiers", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-tags/#tag-icons", - "type": "object", - "patternProperties": { - ".*": { - "title": "Tag identifier mapping", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-tags/#tag-icons", - "pattern": "^[\\w-]+$" - } - } - }, - "version": { - "title": "Versioning", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-versioning/#versioning", - "type": "object", - "properties": { - "provider": { - "title": "Versioning provider", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-versioning/#versioning", - "enum": [ - "mike" - ] - }, - "default": { - "title": "Default version", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-versioning/#version-warning", - "default": "stable" - } - } - }, - "generator": { - "title": "Generator notice", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-the-footer/#generator-notice", - "type": "boolean", - "default": true - } - }, - "additionalProperties": true, - "definitions": { - "cookie": { - "title": "Cookie", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "oneOf": [ - { - "type": "object", - "properties": { - "name": { - "title": "Cookie name", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "type": "string" - }, - "checked": { - "title": "Initial state", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "type": "boolean", - "default": true - } - }, - "additionalProperties": false, - "required": [ - "name" - ] - }, - { - "title": "Cookie name", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#cookie-consent", - "type": "string" - } - ] - }, - "icon": { - "oneOf": [ - { - "$ref": "assets/icons.json" - }, - { - "title": "Unknown icon", - "type": "string" - } - ] - } - }, - "defaultSnippets": [ - { - "label": "analytics (default)", - "body": { - "analytics": { - "provider": "${1:google}", - "property": "${2:UA-XXXXXXXX-X}" - } - } - } - ] -} diff --git a/schema/nav.json b/schema/nav.json deleted file mode 100644 index 89cf4fb..0000000 --- a/schema/nav.json +++ /dev/null @@ -1,34 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Navigation tree", - "markdownDescription": "https://www.mkdocs.org/user-guide/configuration/#nav", - "type": "array", - "items": { - "oneOf": [ - { - "title": "Navigation item", - "markdownDescription": "https://www.mkdocs.org/user-guide/configuration/#nav", - "pattern": "\\.md$" - }, - { - "type": "object", - "markdownDescription": "https://www.mkdocs.org/user-guide/configuration/#nav", - "patternProperties": { - ".*": { - "oneOf": [ - { - "title": "Navigation item", - "markdownDescription": "https://www.mkdocs.org/user-guide/configuration/#nav", - "pattern": "\\.md$" - }, - { - "$ref": "#" - } - ] - } - } - } - ] - }, - "additionalItems": false -} diff --git a/schema/plugins.json b/schema/plugins.json deleted file mode 100644 index adcb7dc..0000000 --- a/schema/plugins.json +++ /dev/null @@ -1,86 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Plugins", - "markdownDescription": "https://www.mkdocs.org/dev-guide/plugins/", - "type": "array", - "items": { - "oneOf": [ - { - "$ref": "#/definitions/built-in" - }, - { - "$ref": "#/definitions/external" - }, - { - "$ref": "#/definitions/external-community" - } - ] - }, - "uniqueItems": true, - "minItems": 1, - "definitions": { - "built-in": { - "description": "Built-in plugins", - "oneOf": [ - { - "$ref": "plugins/meta.json" - }, - { - "$ref": "plugins/offline.json" - }, - { - "$ref": "plugins/privacy.json" - }, - { - "$ref": "plugins/search.json" - }, - { - "$ref": "plugins/social.json" - }, - { - "$ref": "plugins/tags.json" - } - ] - }, - "external": { - "description": "External plugins, schema provided by us", - "oneOf": [ - { - "$ref": "plugins/external/git-authors.json" - }, - { - "$ref": "plugins/external/git-committers.json" - }, - { - "$ref": "plugins/external/git-revision-date.json" - }, - { - "$ref": "plugins/external/minify.json" - }, - { - "$ref": "plugins/external/redirects.json" - } - ] - }, - "external-community": { - "description": "External plugins, schema provided by the community", - "oneOf": [ - { - "$ref": "https://raw.githubusercontent.com/mondeja/mkdocs-include-markdown-plugin/master/schema.json" - }, - { - "$ref": "https://raw.githubusercontent.com/mondeja/mkdocs-material-relative-language-selector/master/schema.json" - }, - { - "$ref": "https://raw.githubusercontent.com/Guts/mkdocs-rss-plugin/main/docs/schema.json" - }, - { - "$ref": "https://raw.githubusercontent.com/timvink/mkdocs-git-revision-date-localized-plugin/master/docs/schema.json" - }, - { - "$ref": "https://raw.githubusercontent.com/blueswen/mkdocs-glightbox/main/schema.json" - } - ] - } - } -} diff --git a/schema/plugins/external/git-authors.json b/schema/plugins/external/git-authors.json deleted file mode 100644 index 4bf452a..0000000 --- a/schema/plugins/external/git-authors.json +++ /dev/null @@ -1,39 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Git authors plugin", - "oneOf": [ - { - "markdownDescription": "https://timvink.github.io/mkdocs-git-authors-plugin/", - "enum": [ - "git-authors" - ] - }, - { - "type": "object", - "properties": { - "git-authors": { - "markdownDescription": "https://timvink.github.io/mkdocs-git-authors-plugin/options.html", - "type": "object", - "properties": { - "enabled": { - "title": "Enable plugin", - "markdownDescription": "https://timvink.github.io/mkdocs-git-authors-plugin/options.html#enabled", - "type": "boolean", - "default": true - }, - "exclude": { - "title": "List of Markdown file patterns", - "markdownDescription": "https://timvink.github.io/mkdocs-git-authors-plugin/options.html#exclude", - "type": "array", - "items": { - "pattern": "(\\*|\\.md)$" - } - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false - } - ] -} diff --git a/schema/plugins/external/git-committers.json b/schema/plugins/external/git-committers.json deleted file mode 100644 index c6c43f0..0000000 --- a/schema/plugins/external/git-committers.json +++ /dev/null @@ -1,44 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Git committers plugin", - "oneOf": [ - { - "markdownDescription": "https://github.com/ojacques/mkdocs-git-committers-plugin-2", - "enum": [ - "git-committers" - ] - }, - { - "type": "object", - "properties": { - "git-committers": { - "markdownDescription": "https://github.com/ojacques/mkdocs-git-committers-plugin-2", - "type": "object", - "properties": { - "enabled": { - "title": "Enable plugin", - "markdownDescription": "https://github.com/ojacques/mkdocs-git-committers-plugin-2#config", - "type": "boolean", - "default": true - }, - "repository": { - "title": "Repository slug", - "markdownDescription": "https://github.com/ojacques/mkdocs-git-committers-plugin-2#config", - "type": "string" - }, - "token": { - "title": "Personal access token", - "markdownDescription": "https://github.com/ojacques/mkdocs-git-committers-plugin-2#config", - "type": "string" - } - }, - "additionalProperties": false, - "required": [ - "repository" - ] - } - }, - "additionalProperties": false - } - ] -} diff --git a/schema/plugins/external/git-revision-date.json b/schema/plugins/external/git-revision-date.json deleted file mode 100644 index 97d9dba..0000000 --- a/schema/plugins/external/git-revision-date.json +++ /dev/null @@ -1,42 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Git revision date plugin", - "oneOf": [ - { - "markdownDescription": "https://github.com/zhaoterryy/mkdocs-git-revision-date-plugin", - "enum": [ - "git-revision-date" - ] - }, - { - "type": "object", - "properties": { - "git-revision-date": { - "markdownDescription": "https://github.com/zhaoterryy/mkdocs-git-revision-date-plugin", - "type": "object", - "properties": { - "enable_if_env": { - "title": "Enable plugin when environment variable is set", - "markdownDescription": "https://github.com/zhaoterryy/mkdocs-git-revision-date-plugin#options", - "type": "string" - }, - "modify_md": { - "title": "Enable plugin to be used in Markdown files", - "markdownDescription": "https://github.com/zhaoterryy/mkdocs-git-revision-date-plugin#options", - "type": "boolean", - "default": true - }, - "as_datetime": { - "title": "Output as Python datetime", - "markdownDescription": "https://github.com/zhaoterryy/mkdocs-git-revision-date-plugin#options", - "type": "boolean", - "default": false - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false - } - ] -} diff --git a/schema/plugins/external/minify.json b/schema/plugins/external/minify.json deleted file mode 100644 index d4bff5d..0000000 --- a/schema/plugins/external/minify.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Minify plugin", - "type": "object", - "properties": { - "minify": { - "markdownDescription": "https://github.com/byrnereese/mkdocs-minify-plugin", - "type": "object", - "dependencies": { - "minify_js": [ - "js_files" - ], - "minify_css": [ - "css_files" - ] - }, - "properties": { - "minify_html": { - "title": "Minify HTML files", - "markdownDescription": "https://github.com/byrnereese/mkdocs-minify-plugin#options", - "type": "boolean", - "default": true - }, - "minify_js": { - "title": "Minify JavaScript files", - "markdownDescription": "https://github.com/byrnereese/mkdocs-minify-plugin#options", - "type": "boolean" - }, - "minify_css": { - "title": "Minify CSS files", - "markdownDescription": "https://github.com/byrnereese/mkdocs-minify-plugin#options", - "type": "boolean" - }, - "htmlmin_opts": { - "title": "Options for HTML minifier", - "markdownDescription": "https://github.com/byrnereese/mkdocs-minify-plugin#options", - "type": "object" - }, - "js_files": { - "title": "JavaScript files to minify", - "markdownDescription": "https://github.com/byrnereese/mkdocs-minify-plugin#options", - "type": "array", - "items": { - "title": "Path to JavaScript file", - "markdownDescription": "https://github.com/byrnereese/mkdocs-minify-plugin#options", - "pattern": "\\.js$" - }, - "uniqueItems": true, - "minItems": 1 - }, - "css_files": { - "title": "CSS files to minify", - "markdownDescription": "https://github.com/byrnereese/mkdocs-minify-plugin#options", - "type": "array", - "items": { - "title": "Path to CSS file", - "markdownDescription": "https://github.com/byrnereese/mkdocs-minify-plugin#options", - "pattern": "\\.css$" - }, - "uniqueItems": true, - "minItems": 1 - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false -} diff --git a/schema/plugins/external/redirects.json b/schema/plugins/external/redirects.json deleted file mode 100644 index a473be4..0000000 --- a/schema/plugins/external/redirects.json +++ /dev/null @@ -1,51 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Redirects plugin", - "type": "object", - "properties": { - "redirects": { - "markdownDescription": "https://github.com/datarobot/mkdocs-redirects", - "type": "object", - "properties": { - "redirect_maps": { - "title": "Mapping of Markdown files", - "markdownDescription": "https://github.com/datarobot/mkdocs-redirects#using", - "type": "object", - "patternProperties": { - "\\.md$": { - "oneOf": [ - { - "title": "Internal redirect", - "markdownDescription": "https://github.com/datarobot/mkdocs-redirects#using", - "pattern": "\\.md$" - }, - { - "title": "External redirect", - "markdownDescription": "https://github.com/datarobot/mkdocs-redirects#using", - "pattern": "^https?:" - } - ] - } - }, - "defaultSnippets": [ - { - "label": "Internal redirect", - "body": { - "${1:from}.md": "${2:to}.md" - } - }, - { - "label": "External redirect", - "body": { - "${1:from}.md": "https://${2:to.url}" - } - } - ], - "additionalProperties": false - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false -} diff --git a/schema/plugins/meta.json b/schema/plugins/meta.json deleted file mode 100644 index d1d9cb1..0000000 --- a/schema/plugins/meta.json +++ /dev/null @@ -1,31 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Built-in meta plugin", - "oneOf": [ - { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/reference/#built-in-meta-plugin", - "enum": [ - "meta" - ] - }, - { - "type": "object", - "properties": { - "meta": { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/reference/#built-in-meta-plugin", - "type": "object", - "properties": { - "meta_file": { - "title": "Meta file name", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/reference/#meta-file", - "pattern": "\\.yml$", - "default": "\"**/.meta.yml\"" - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false - } - ] -} diff --git a/schema/plugins/offline.json b/schema/plugins/offline.json deleted file mode 100644 index 36281ca..0000000 --- a/schema/plugins/offline.json +++ /dev/null @@ -1,31 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Built-in offline plugin", - "oneOf": [ - { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/building-for-offline-usage/#built-in-offline-plugin", - "enum": [ - "offline" - ] - }, - { - "type": "object", - "properties": { - "offline": { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/building-for-offline-usage/#built-in-offline-plugin", - "type": "object", - "properties": { - "enabled": { - "title": "Enable plugin", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/building-for-offline-usage/#enabled", - "type": "boolean", - "default": true - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false - } - ] -} diff --git a/schema/plugins/privacy.json b/schema/plugins/privacy.json deleted file mode 100644 index d229704..0000000 --- a/schema/plugins/privacy.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Built-in privacy plugin", - "oneOf": [ - { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#built-in-privacy-plugin", - "enum": [ - "privacy" - ] - }, - { - "type": "object", - "properties": { - "privacy": { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#built-in-privacy-plugin", - "type": "object", - "properties": { - "enabled": { - "title": "Enable plugin", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#enabled", - "type": "boolean", - "default": true - }, - "externals": { - "title": "External assets", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#externals", - "oneOf": [ - { - "title": "Bundle external assets", - "enum": [ - "bundle" - ] - }, - { - "title": "Report external assets as warnings", - "enum": [ - "report" - ] - } - ], - "default": "bundle" - }, - "externals_dir": { - "title": "External assets download directory", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#externals-dir", - "type": "string", - "default": "assets/externals" - }, - "externals_exclude": { - "title": "External assets to be excluded", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#externals-exclude", - "type": "array", - "items": { - "title": "External assets matching this pattern will not be bundled", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/ensuring-data-privacy/#externals-exclude", - "pattern": ".*" - }, - "uniqueItems": true, - "minItems": 1 - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false - } - ] -} diff --git a/schema/plugins/search.json b/schema/plugins/search.json deleted file mode 100644 index ce48920..0000000 --- a/schema/plugins/search.json +++ /dev/null @@ -1,179 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Built-in search plugin", - "oneOf": [ - { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#built-in-search-plugin", - "enum": [ - "search" - ] - }, - { - "type": "object", - "properties": { - "search": { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#built-in-search-plugin", - "type": "object", - "properties": { - "lang": { - "oneOf": [ - { - "$ref": "#/definitions/lang" - }, - { - "type": "array", - "items": { - "$ref": "#/definitions/lang" - }, - "uniqueItems": true, - "minItems": 1 - } - ], - "default": "en" - }, - "separator": { - "title": "Separator for indexing and query tokenization", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#search-separator", - "type": "string" - }, - "jieba_dict": { - "title": "Jieba dictionary replacement", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#jieba-dict", - "type": "string" - }, - "jieba_dict_user": { - "title": "Jieba dictionary augmentation", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#jieba-dict", - "type": "string" - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false - } - ], - "definitions": { - "lang": { - "title": "Site search language", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#search-lang", - "oneOf": [ - { - "title": "Site search language: Arabic", - "enum": [ - "ar" - ] - }, - { - "title": "Site search language: Danish", - "enum": [ - "da" - ] - }, - { - "title": "Site search language: German", - "enum": [ - "de" - ] - }, - { - "title": "Site search language: Dutch", - "enum": [ - "du" - ] - }, - { - "title": "Site search language: English", - "enum": [ - "en" - ] - }, - { - "title": "Site search language: Spanish", - "enum": [ - "es" - ] - }, - { - "title": "Site search language: Finnish", - "enum": [ - "fi" - ] - }, - { - "title": "Site search language: French", - "enum": [ - "fr" - ] - }, - { - "title": "Site search language: Hungarian", - "enum": [ - "hu" - ] - }, - { - "title": "Site search language: Italian", - "enum": [ - "it" - ] - }, - { - "title": "Site search language: Japanese", - "enum": [ - "ja" - ] - }, - { - "title": "Site search language: Norwegian", - "enum": [ - "no" - ] - }, - { - "title": "Site search language: Portuguese", - "enum": [ - "pt" - ] - }, - { - "title": "Site search language: Romanian", - "enum": [ - "ro" - ] - }, - { - "title": "Site search language: Russian", - "enum": [ - "ru" - ] - }, - { - "title": "Site search language: Swedish", - "enum": [ - "sv" - ] - }, - { - "title": "Site search language: Thai", - "enum": [ - "th" - ] - }, - { - "title": "Site search language: Turkish", - "enum": [ - "tr" - ] - }, - { - "title": "Site search language: Vietnamese", - "enum": [ - "vi" - ] - } - ] - } - } -} - diff --git a/schema/plugins/social.json b/schema/plugins/social.json deleted file mode 100644 index e70c9cc..0000000 --- a/schema/plugins/social.json +++ /dev/null @@ -1,68 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Built-in social plugin", - "oneOf": [ - { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-social-cards/#built-in-social-plugin", - "enum": [ - "social" - ] - }, - { - "type": "object", - "properties": { - "social": { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-social-cards/#built-in-social-plugin", - "type": "object", - "properties": { - "cards": { - "title": "Social card generation", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-social-cards/#cards", - "type": "boolean", - "default": true - }, - "cards_color": { - "title": "Social card color palette", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-social-cards/#cards-color", - "type": "object", - "properties": { - "fill": { - "title": "Background fill color", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-social-cards/#cards-color", - "type": "string" - }, - "text": { - "title": "Foreground text color", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-social-cards/#cards-color", - "type": "string" - } - }, - "additionalProperties": false, - "required": [ - "fill", - "text" - ] - }, - "cards_font": { - "$ref": "../assets/fonts.json" - }, - "cards_dir": { - "title": "Social card directory", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-social-cards/#cards-dir", - "type": "string", - "default": "assets/images/social" - } - }, - "additionalProperties": false, - "defaultSnippets": [ - { - "label": "cards_font", - "body": "cards_font: ${1:Roboto}" - } - ] - } - }, - "additionalProperties": false - } - ] -} diff --git a/schema/plugins/tags.json b/schema/plugins/tags.json deleted file mode 100644 index 5a7ab1a..0000000 --- a/schema/plugins/tags.json +++ /dev/null @@ -1,45 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Built-in tags plugin", - "oneOf": [ - { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-tags/#built-in-tags-plugin", - "enum": [ - "tags" - ] - }, - { - "type": "object", - "properties": { - "tags": { - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-tags/#built-in-tags-plugin", - "type": "object", - "properties": { - "tags_file": { - "title": "Markdown file to render tags index", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-tags/#tags-file", - "pattern": "\\.md$", - "default": "tags.md" - }, - "tags_extra_files": { - "title": "Markdown files to render additional tags indexes", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-tags/#tags-extra-files", - "type": "object", - "patternProperties": { - "\\.md$": { - "type": "array", - "items": { - "type": "string" - } - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false - } - ] -} diff --git a/schema/theme.json b/schema/theme.json deleted file mode 100644 index 6ca89d1..0000000 --- a/schema/theme.json +++ /dev/null @@ -1,945 +0,0 @@ -{ - "$schema": "https://json-schema.org/draft-07/schema", - "title": "Theme configuration", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/", - "type": "object", - "properties": { - "name": { - "title": "Theme name", - "markdownDescription": "https://www.mkdocs.org/user-guide/configuration/#name", - "oneOf": [ - { - "enum": [ - "material" - ] - }, - { - "type": "null" - } - ], - "default": "material" - }, - "custom_dir": { - "title": "Directory with theme overrides", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/customization/#setup-and-theme-structure", - "type": "string", - "defaultSnippets": [ - { - "body": "${1:overrides}" - } - ] - }, - "static_templates": { - "title": "Static templates to render", - "markdownDescription": "https://www.mkdocs.org/user-guide/configuration/#static_templates", - "type": "array", - "items": { - "title": "Path to HTML file", - "markdownDescription": "https://www.mkdocs.org/user-guide/configuration/#static_templates", - "pattern": "\\.html$" - }, - "uniqueItems": true, - "minItems": 1 - }, - "language": { - "title": "Site language", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-language/", - "oneOf": [ - { - "title": "Site language: Custom", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-language/#custom-translations", - "enum": [ - "custom" - ] - }, - { - "title": "Site language: Afrikaans", - "enum": [ - "af" - ] - }, - { - "title": "Site language: Arabic", - "enum": [ - "ar" - ] - }, - { - "title": "Site language: Bulgarian", - "enum": [ - "bg" - ] - }, - { - "title": "Site language: Bengali (Bangla)", - "enum": [ - "bn" - ] - }, - { - "title": "Site language: Catalan", - "enum": [ - "ca" - ] - }, - { - "title": "Site language: Czech", - "enum": [ - "cs" - ] - }, - { - "title": "Site language: Danish", - "enum": [ - "da" - ] - }, - { - "title": "Site language: German", - "enum": [ - "de" - ] - }, - { - "title": "Site language: Greek", - "enum": [ - "el" - ] - }, - { - "title": "Site language: English", - "enum": [ - "en" - ] - }, - { - "title": "Site language: Esperanto", - "enum": [ - "eo" - ] - }, - { - "title": "Site language: Spanish", - "enum": [ - "es" - ] - }, - { - "title": "Site language: Estonian", - "enum": [ - "et" - ] - }, - { - "title": "Site language: Persian (Farsi)", - "enum": [ - "fa" - ] - }, - { - "title": "Site language: Finnish", - "enum": [ - "fi" - ] - }, - { - "title": "Site language: French", - "enum": [ - "fr" - ] - }, - { - "title": "Site language: Galician", - "enum": [ - "gl" - ] - }, - { - "title": "Site language: Hebrew", - "enum": [ - "he" - ] - }, - { - "title": "Site language: Hindi", - "enum": [ - "hi" - ] - }, - { - "title": "Site language: Croatian", - "enum": [ - "hr" - ] - }, - { - "title": "Site language: Hungarian", - "enum": [ - "hu" - ] - }, - { - "title": "Site language: Armenian", - "enum": [ - "hy" - ] - }, - { - "title": "Site language: Indonesian", - "enum": [ - "id" - ] - }, - { - "title": "Site language: Icelandic", - "enum": [ - "is" - ] - }, - { - "title": "Site language: Italian", - "enum": [ - "it" - ] - }, - { - "title": "Site language: Japanese", - "enum": [ - "ja" - ] - }, - { - "title": "Site language: Georgian", - "enum": [ - "ka" - ] - }, - { - "title": "Site language: Korean", - "enum": [ - "kr" - ] - }, - { - "title": "Site language: Lithuanian", - "enum": [ - "lt" - ] - }, - { - "title": "Site language: Latvian", - "enum": [ - "lv" - ] - }, - { - "title": "Site language: Macedonian", - "enum": [ - "mk" - ] - }, - { - "title": "Site language: Mongolian", - "enum": [ - "mn" - ] - }, - { - "title": "Site language: Bahasa Malaysia", - "enum": [ - "ms" - ] - }, - { - "title": "Site language: Burmese", - "enum": [ - "my" - ] - }, - { - "title": "Site language: Dutch", - "enum": [ - "nl" - ] - }, - { - "title": "Site language: Norwegian (Nynorsk)", - "enum": [ - "nn" - ] - }, - { - "title": "Site language: Norwegian", - "enum": [ - "no" - ] - }, - { - "title": "Site language: Polish", - "enum": [ - "pl" - ] - }, - { - "title": "Site language: Portuguese", - "enum": [ - "pt" - ] - }, - { - "title": "Site language: Portuguese (Brasilian)", - "enum": [ - "pt-BR" - ] - }, - { - "title": "Site language: Romanian", - "enum": [ - "ro" - ] - }, - { - "title": "Site language: Russian", - "enum": [ - "ru" - ] - }, - { - "title": "Site language: Serbo-Croatian", - "enum": [ - "sh" - ] - }, - { - "title": "Site language: Sinhalese", - "enum": [ - "si" - ] - }, - { - "title": "Site language: Slovak", - "enum": [ - "sk" - ] - }, - { - "title": "Site language: Slovenian", - "enum": [ - "sl" - ] - }, - { - "title": "Site language: Serbian", - "enum": [ - "sr" - ] - }, - { - "title": "Site language: Swedish", - "enum": [ - "sv" - ] - }, - { - "title": "Site language: Thai", - "enum": [ - "th" - ] - }, - { - "title": "Site language: Tagalog", - "enum": [ - "tl" - ] - }, - { - "title": "Site language: Turkish", - "enum": [ - "tr" - ] - }, - { - "title": "Site language: Ukrainian", - "enum": [ - "uk" - ] - }, - { - "title": "Site language: Urdu", - "enum": [ - "ur" - ] - }, - { - "title": "Site language: Uzbek", - "enum": [ - "uz" - ] - }, - { - "title": "Site language: Vietnamese", - "enum": [ - "vi" - ] - }, - { - "title": "Site language: Chinese (Simplified)", - "enum": [ - "zh" - ] - }, - { - "title": "Site language: Chinese (Traditional)", - "enum": [ - "zh-Hant" - ] - }, - { - "title": "Site language: Chinese (Taiwanese)", - "enum": [ - "zh-TW" - ] - } - ], - "default": "en" - }, - "direction": { - "title": "Directionality", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-language/#directionality", - "enum": [ - "ltr", - "rtl" - ] - }, - "favicon": { - "title": "Favicon", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-logo-and-icons/#favicon", - "pattern": "\\.(ico|png|svg|jpe?g)$", - "defaultSnippets": [ - { - "body": "${1:path/to/file}.png" - } - ] - }, - "logo": { - "title": "Logo", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-logo-and-icons/#logo", - "pattern": "\\.(png|svg|jpe?g)$", - "defaultSnippets": [ - { - "body": "${1:path/to/file}.png" - } - ] - }, - "icon": { - "title": "Icons", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-logo-and-icons/", - "type": "object", - "properties": { - "edit": { - "$ref": "#/definitions/icon" - }, - "logo": { - "$ref": "#/definitions/icon" - }, - "repo": { - "$ref": "#/definitions/icon" - }, - "admonition": { - "title": "Admonition icon", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/reference/admonitions/#admonition-icons", - "type": "object", - "properties": { - "note": { - "$ref": "#/definitions/icon" - }, - "abstract": { - "$ref": "#/definitions/icon" - }, - "info": { - "$ref": "#/definitions/icon" - }, - "tip": { - "$ref": "#/definitions/icon" - }, - "success": { - "$ref": "#/definitions/icon" - }, - "question": { - "$ref": "#/definitions/icon" - }, - "warning": { - "$ref": "#/definitions/icon" - }, - "failure": { - "$ref": "#/definitions/icon" - }, - "danger": { - "$ref": "#/definitions/icon" - }, - "bug": { - "$ref": "#/definitions/icon" - }, - "example": { - "$ref": "#/definitions/icon" - }, - "quote": { - "$ref": "#/definitions/icon" - } - }, - "additionalProperties": false, - "defaultSnippets": [ - { - "label": "note", - "body": "note: ${1:material/pencil}" - }, - { - "label": "abstract", - "body": "abstract: ${1:material/clipboard-text}" - }, - { - "label": "info", - "body": "info: ${1:material/information}" - }, - { - "label": "tip", - "body": "tip: ${1:material/fire}" - }, - { - "label": "success", - "body": "success: ${1:material/check-bold}" - }, - { - "label": "question", - "body": "question: ${1:material/help-circle}" - }, - { - "label": "warning", - "body": "warning: ${1:material/alert}" - }, - { - "label": "failure", - "body": "failure: ${1:material/close-thick}" - }, - { - "label": "danger", - "body": "danger: ${1:material/lightning-bolt}" - }, - { - "label": "bug", - "body": "bug: ${1:material/bug}" - }, - { - "label": "example", - "body": "example: ${1:material/format-list-numbered}" - }, - { - "label": "quote", - "body": "quote: ${1:material/format-quote-close}" - } - ] - }, - "tag": { - "title": "Tag icon", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-tags/#tag-icons", - "type": "object", - "patternProperties": { - "^\\w+$": { - "$ref": "#/definitions/icon" - } - }, - "additionalProperties": false - } - }, - "additionalProperties": false, - "defaultSnippets": [ - { - "label": "edit", - "body": "edit: ${1:material/pencil}" - }, - { - "label": "logo", - "body": "logo: ${1:material/library}" - }, - { - "label": "repo", - "body": "repo: ${1:fontawesome/brands/git-alt}" - } - ] - }, - "features": { - "title": "Feature flags", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/", - "type": "array", - "items": { - "oneOf": [ - { - "title": "Mark as read", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-the-header/#mark-as-read", - "enum": [ - "announce.dismiss" - ] - }, - { - "title": "Code annotations", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/reference/code-blocks/#code-annotations", - "enum": [ - "content.code.annotate" - ] - }, - { - "title": "Linked content tabs", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/reference/content-tabs/#linked-content-tabs", - "enum": [ - "content.tabs.link" - ] - }, - { - "title": "Improved tooltips", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/reference/tooltips/#improved-tooltips", - "enum": [ - "content.tooltips" - ] - }, - { - "title": "Header hides automatically when scrolling", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-the-header/#automatic-hiding", - "enum": [ - "header.autohide" - ] - }, - { - "title": "Navigation expansion", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#navigation-expansion", - "enum": [ - "navigation.expand" - ] - }, - { - "title": "Section index pages", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#section-index-pages", - "enum": [ - "navigation.indexes" - ] - }, - { - "title": "Instant loading", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#instant-loading", - "enum": [ - "navigation.instant" - ] - }, - { - "title": "Navigation pruning", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#navigation-pruning", - "enum": [ - "navigation.prune" - ] - }, - { - "title": "Navigation sections", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#navigation-sections", - "enum": [ - "navigation.sections" - ] - }, - { - "title": "Navigation tabs", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#navigation-tabs", - "enum": [ - "navigation.tabs" - ] - }, - { - "title": "Sticky navigation tabs", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#sticky-navigation-tabs", - "enum": [ - "navigation.tabs.sticky" - ] - }, - { - "title": "Back-to-top button", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#back-to-top-button", - "enum": [ - "navigation.top" - ] - }, - { - "title": "Anchor tracking", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#anchor-tracking", - "enum": [ - "navigation.tracking" - ] - }, - { - "title": "Search higlighting", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#search-highlighting", - "enum": [ - "search.highlight" - ] - }, - { - "title": "Search sharing", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#search-sharing", - "enum": [ - "search.share" - ] - }, - { - "title": "Search suggestions", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-site-search/#search-suggestions", - "enum": [ - "search.suggest" - ] - }, - { - "title": "Integrated table of contents", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#anchor-following", - "enum": [ - "toc.follow" - ] - }, - { - "title": "Integrated table of contents", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/setting-up-navigation/#navigation-integration", - "enum": [ - "toc.integrate" - ] - } - ] - }, - "uniqueItems": true, - "minItems": 1 - }, - "palette": { - "oneOf": [ - { - "title": "Color palette", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/", - "type": "object", - "properties": { - "scheme": { - "$ref": "#/definitions/scheme" - }, - "primary": { - "$ref": "#/definitions/primary" - }, - "accent": { - "$ref": "#/definitions/accent" - } - }, - "additionalProperties": false - }, - { - "title": "Color palette", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/", - "type": "array", - "items": { - "type": "object", - "properties": { - "scheme": { - "$ref": "#/definitions/scheme" - }, - "primary": { - "$ref": "#/definitions/primary" - }, - "accent": { - "$ref": "#/definitions/accent" - }, - "media": { - "oneOf": [ - { - "title": "System preference", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/#system-preference", - "type": "string", - "enum": [ - "\"(prefers-color-scheme: light)\"", - "\"(prefers-color-scheme: dark)\"" - ] - }, - { - "type": "string" - } - ], - "defaultSnippets": [ - { - "label": "\"(prefers-color-scheme: light)\"", - "body": "\"(prefers-color-scheme: ${1:light})\"" - } - ] - }, - "toggle": { - "title": "Color palette toggle", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/#color-palette-toggle", - "properties": { - "icon": { - "$ref": "#/definitions/icon" - }, - "name": { - "title": "Color palette toggle name", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/#toggle-name", - "type": "string" - } - }, - "additionalProperties": false, - "required": [ - "icon", - "name" - ] - } - }, - "additionalProperties": false, - "required": [ - "toggle" - ] - }, - "uniqueItems": true, - "minItems": 1 - } - ], - "default": { - "scheme": "default", - "primary": "indigo", - "accent": "indigo" - } - }, - "font": { - "oneOf": [ - { - "title": "Google Fonts", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-fonts/", - "properties": { - "text": { - "$ref": "assets/fonts.json" - }, - "code": { - "$ref": "assets/fonts.json" - } - }, - "additionalProperties": false - }, - { - "title": "Disable Google Fonts", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-fonts/#autoloading", - "enum": [ - false - ] - } - ], - "defaultSnippets": [ - { - "body": { - "text": "${1:Roboto}", - "code": "${2:Roboto Mono}" - } - } - ] - }, - "include_search_page": { - "title": "Only necessary when installing from git", - "markdownDescription": "Must be set to `false`", - "enum": [ - false - ] - }, - "search_index_only": { - "title": "Only necessary when installing from git", - "markdownDescription": "Must be set to `false`", - "enum": [ - true - ] - } - }, - "additionalProperties": false, - "required": [ - "name" - ], - "definitions": { - "scheme": { - "title": "Color scheme", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/#color-scheme", - "oneOf": [ - { - "enum": [ - "default", - "slate" - ] - }, - { - "type": "string" - } - ], - "defaultSnippets": [ - { - "label": "default", - "body": "${1:default}" - } - ] - }, - "primary": { - "title": "Primary color", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/#primary-color", - "enum": [ - "red", - "pink", - "purple", - "deep purple", - "indigo", - "blue", - "light blue", - "cyan", - "teal", - "green", - "light green", - "lime", - "yellow", - "amber", - "orange", - "deep orange", - "brown", - "grey", - "blue grey", - "black", - "white" - ] - }, - "accent": { - "title": "Accent color", - "markdownDescription": "https://squidfunk.github.io/mkdocs-material/setup/changing-the-colors/#accent-color", - "enum": [ - "red", - "pink", - "purple", - "deep purple", - "indigo", - "blue", - "light blue", - "cyan", - "teal", - "green", - "light green", - "lime", - "yellow", - "amber", - "orange", - "deep orange", - "brown", - "grey", - "blue grey", - "black", - "white" - ] - }, - "icon": { - "oneOf": [ - { - "$ref": "assets/icons.json" - }, - { - "title": "Unknown icon", - "type": "string" - } - ] - } - } -} diff --git a/search.json b/search.json new file mode 100644 index 0000000..5ed4df0 --- /dev/null +++ b/search.json @@ -0,0 +1,681 @@ +[ + { + "objectID": "workshop/workshop_Conference2023.html", + "href": "workshop/workshop_Conference2023.html", + "title": "\nSandbox Workshop\n", + "section": "", + "text": "Sandbox Workshop" + }, + { + "objectID": "workshop/workshop_Conference2023.html#the-sandbox-concept", + "href": "workshop/workshop_Conference2023.html#the-sandbox-concept", + "title": "\nSandbox Workshop\n", + "section": "The Sandbox concept", + "text": "The Sandbox concept\nThe Health Data Science Sandbox aims to be a training resource for bioinformaticians, data scientists, and those generally curious about how to investigate large biomedical datasets. We are an active and developing project seeking interested users (both trainees and educators). All of our open-source materials are available on our Github page and much more information is available on the rest of the website you are currently visiting! We work with both UCloud and Computerome (major Danish academic supercomputers) - see our HPC Access page for more info on each set up." + }, + { + "objectID": "workshop/workshop_Conference2023.html#access-sandbox-resources", + "href": "workshop/workshop_Conference2023.html#access-sandbox-resources", + "title": "\nSandbox Workshop\n", + "section": "Access Sandbox resources", + "text": "Access Sandbox resources\nWe currently provide training materials and resources as topical apps on UCloud, the supercomputer located at the University of Southern Denmark. To use these resources, you’ll need the following:\n\na Danish university ID so you can sign on to UCloud via WAYF. See this guide and/or follow along with our live demo.\nthe ability to navigate in linux / RStudio / Jupyter. You don’t need to be an expert, but it is beyond our ambitions (and course material) to teach you how to code and how to run analyses simultaneously. We recommend a basic R or Python course before diving in.\nour invite link to the correct UCloud project that will be shared on the day of the workshop. This way, we can provide you compute resources for the active sessions of the workshop. To use Sandbox materials outside of the workshop, you’ll need to check with the local DeiC office at your university about how to request compute hours on UCloud." + }, + { + "objectID": "workshop/workshop_Conference2023.html#try-out-a-module", + "href": "workshop/workshop_Conference2023.html#try-out-a-module", + "title": "\nSandbox Workshop\n", + "section": "Try out a module", + "text": "Try out a module\nSo our Sandbox data scientists have finished their intro at the workshop? Great, now it’s time to choose your poison (cough) topic of interest for today. Your options are below:\n ### Genomics If you’re interested in NGS technologies and applications ranging from genome assembly to variant calling to metagenomics, join Sandbox Data Scientist Samuele Soraggi in testing out our Genomics Sandbox app. This app supports a semester-length course on NGS as well as a Population Genomics course run regularly at Aarhus University. Sign into UCloud and then click this invite link.\n ### Transcriptomics If you’re interested in bulk or single cell RNA sequencing analysis and visualization, join Sandbox Data Scientist Jose Alejandro Romero Herrera (Alex) in testing out our Transcriptomics Sandbox app. This app supports regular 3-4 day workshops at University of Copenhagen and provides stand-alone visualisation tools. Sign into UCloud and then click this invite link.\n ### Proteomics Interested in modern methods for protein structure prediction? Join Sandbox Data Scientist Jacob Fredegaard Hansen as he walks you through how to use ColabFold on UCloud. Jacob can also demo our Proteomics Sandbox, which contains a suite of proteomics analysis tools that will support a future course in clinical proteomics but is already available on UCloud for interested users. Sign into UCloud and then click this invite link." + }, + { + "objectID": "workshop/workshop_Conference2023.html#discussion-and-feedback", + "href": "workshop/workshop_Conference2023.html#discussion-and-feedback", + "title": "\nSandbox Workshop\n", + "section": "Discussion and feedback", + "text": "Discussion and feedback\nWe hope you enjoyed the live demo. If you have broader questions, suggestions, or concerns, now is the time to raise them! If you are totally toast for the day, remember that you can check out longer versions of our tutorials as well as other topics and tools in each of the Sandbox modules or join us for a multi-day in person course.\nAs data scientists, we also would be really happy for some quantifiable info and feedback - we want to build things that the Danish health data science community is excited to use. Please answer these 5 questions for us before you head out for the day (link activated on day of the workshop).\n\nNice meeting you and we hope to see you again!" + }, + { + "objectID": "workshop/workshop_april2024.html#access-sandbox-resources", + "href": "workshop/workshop_april2024.html#access-sandbox-resources", + "title": "Sandbox Workshop", + "section": "Access Sandbox resources", + "text": "Access Sandbox resources\nOur first choice is to provide all the training materials, tutorials, and tools as interactive apps on UCloud, the supercomputer located at the University of Southern Denmark. Anyone using these resources needs the following:\n\na Danish university ID so you can sign on to UCloud via WAYF1.\n\n \n\n for UCloud Access click here \n\n \n\nbasic ability to navigate in Linux/RStudio/Jupyter. You don’t need to be an expert, but it is beyond our ambitions (and course material) to teach you how to code from zero and how to run analyses simultaneously. We recommend a basic R or Python course before diving in.\nFor workshop participants: Use our invite link to the correct UCloud workspace that will be shared on the day of the workshop. This way, we can provide you with compute resources for the active sessions of the workshop2 Click the link below after your first uCloud access and accept the invite that shows.\n\n \n\n Invite link to uCloud workspace \n\n   \n\n\n\n\n\n\nNote\n\n\n\nOur apps can run on other clusters, simply by pulling a so-called docker container. You only need to have either docker or singularity installed on the cluster. GenomeDK supports singularity and thus can run our learning material as well. Ask us if you want to help the apps out of uCloud. Instructions will soon be available within our HPC access instructions." + }, + { + "objectID": "workshop/workshop_april2024.html#our-omics-apps", + "href": "workshop/workshop_april2024.html#our-omics-apps", + "title": "Sandbox Workshop", + "section": "Our OMICS apps", + "text": "Our OMICS apps\nThe agenda starts with an introduction to High Performance Computing (HPC) and uCloud. You will try two apps during the workshop, but we are developing others, and have deployed three apps already.\n \n\n\n\nProteomics Sandbox: Our sandbox modern with a suite of proteomics analysis tools, used for example in clinical proteomics. This app is not alone, since our data scientist Jacob has also made the app ColabFold on UCloud, with methods for protein structure prediction.\n\n\n \n\n\n\nTranscriptomics Sandbox : Our sandbox for bulk or single-cell RNA sequencing analysis and visualization - amongst others two regular workshops and provides stand-alone visualization tools. In the next update, we will introduce advanced tutorials for more complex single-cell RNA sequencing analysis from some of our supported courses.\n\n\n \n\n\n\nGenomics Sandbox: Our sandbox NGS data analysis and applications range from genome assembly to variant calling to metagenomics. We have currently a semester-long population genomics course and an NGS course with many applications (alignment, VCF analysis, bulk-RNA data, single-cell RNA sequencing)" + }, + { + "objectID": "workshop/workshop_april2024.html#discussion-and-feedback", + "href": "workshop/workshop_april2024.html#discussion-and-feedback", + "title": "Sandbox Workshop", + "section": "Discussion and feedback", + "text": "Discussion and feedback\nWe hope you enjoyed the live demo. If you have broader questions, suggestions, or concerns, now is the time to raise them! If you are totally toast for the day, remember that you can check out longer versions of our tutorials as well as other topics and tools in each of the Sandbox modules or join us for a multi-day in-person course (follow our news here).\nAs data scientists, we also would be really happy for some quantifiable info and feedback - we want to build things that the Danish health data science community is excited to use. Please answer these 5 questions for us before you head out for the day 3.\n \n\n\n\n\n\n\n\nNice meeting you and we hope to see you again!" + }, + { + "objectID": "workshop/workshop_april2024.html#footnotes", + "href": "workshop/workshop_april2024.html#footnotes", + "title": "Sandbox Workshop", + "section": "Footnotes", + "text": "Footnotes\n\n\nOther institutions (e.g. hospitals, libraries, …) can log on through WAYF. See all institutions here↩︎\nTo use Sandbox materials outside of the workshop: remember that each new user has hundreds of hours of free computing credit and around 50GB of free storage, which can be used to run any uCloud software. If you run out of credit (which takes a long time) you’ll need to check with the local DeiC office at your university about how to request compute hours on UCloud. Contact us at the Sandbox if you need help or want more information.↩︎\nlink activated on day one of the workshop.↩︎" + }, + { + "objectID": "news/upcoming/2024-07-01-NGS-analysis.html", + "href": "news/upcoming/2024-07-01-NGS-analysis.html", + "title": "Intro to NGS data analysis - Summer School", + "section": "", + "text": "This workshop is a regularly hosted summer school to teach NGS data analysis, and is taught by Stig Andersen, Mikkel Schierup, and Samuele Soraggi (supporting via the HDS Sandbox). You can find additional information here." + }, + { + "objectID": "news/past/2022-09-06-genomics-launch.html", + "href": "news/past/2022-09-06-genomics-launch.html", + "title": "Genomics Sandbox app launched on UCloud!", + "section": "", + "text": "We have deployed our first standalone Sandbox app on UCloud! Please see the Access page for instructions on how to find our Sandbox apps on UCloud - this first one is titled ‘Genomics Sandbox’ and module documentation is linked from the UCloud app page as well as here in Modules." + }, + { + "objectID": "news/past/2023-05-31-rollout-ucloud.html", + "href": "news/past/2023-05-31-rollout-ucloud.html", + "title": "Sandbox App updates on UCloud rolled out", + "section": "", + "text": "New versions of the Genomics Sandbox App, the Transcriptomics Sandbox App, and the Proteomics Sandbox App have all been launched on UCloud this month! Check out the new components in the training modules such as a GWAS module in Genomics and new tools in Transcriptomics and Proteomics. Updates were also informed by the different courses supported during Spring 2023. With these courses wrapping up this month, the associated new training materials have also been included in the new versions of the apps." + }, + { + "objectID": "news/past/2022-11-30-advancedstatlearning.html", + "href": "news/past/2022-11-30-advancedstatlearning.html", + "title": "Sandbox support for ‘Advanced Statistical Learning’", + "section": "", + "text": "Sandbox data scientist Samuele Soraggi spent two weeks teaching for the Fall 2023 course ‘Advanced Statistical Learning’ taught by Prof. Asger Hobolth at Aarhus University." + }, + { + "objectID": "news/past/2022-06-01-genomics-au.html", + "href": "news/past/2022-06-01-genomics-au.html", + "title": "Genomics course at Aarhus University", + "section": "", + "text": "A month-long course in Genomics taught by Professors Mikkel Schierup and Stig Andersen has started with lead supercomputing support on UCloud by Sandbox data scientist and course instructor Samuele Soraggi. Computational exercises in NGS analysis were deployed in a UCloud project for use by 47 graduate students with primarily molecular biology and clinical backgrounds and no prior supercomputing experience! Post-course update: We received many positive reviews on use of the Genomics Sandbox training materials on UCloud!" + }, + { + "objectID": "news/past/2023-12-12-SE3D.html", + "href": "news/past/2023-12-12-SE3D.html", + "title": "NNF Collaborative Data Science award news: the SE3D project!", + "section": "", + "text": "Today we got the news that we will be able to hire 5 new research staff focused on synthetic health data over the next 4 years. The SE3D project - Synthetic health data: ethical development and deployment via deep learning approaches - will be led by Sandbox PIs Martin Boegsted (AAU) and Anders Krogh (KU) alongside Sandbox project lead Jennifer Bartell (KU) and a new collaborator, Prof. Jan Trzaskowski from AAU Law. We’re really excited to set up this research arm that shares so many Sandbox interests and potential for interaction. The project starts from 1 May 2024, with much thanks to the NNF for their continued support of our ideas. Look out for job ads in the spring from KU and AAU!" + }, + { + "objectID": "news/past/2024-02-09-proteomics-sandbox.html", + "href": "news/past/2024-02-09-proteomics-sandbox.html", + "title": "Course support at SDU", + "section": "", + "text": "During the Spring Semester 2024, Sandbox data scientist Jacob Fredegaard Hansen will be assisting with teaching and tools in the course BMB834: Protein Structure, Dynamics, and Modelling at the University of Southern Denmark. Here, Jacob will provide Sandbox support, and materials will be used for applying computational methods for protein structure retrieval and visualization, as well as for applying high-performance computing (HPC) methods for protein structure modeling.ß" + }, + { + "objectID": "news/past/2023-08-29-aarhus-workshop.html", + "href": "news/past/2023-08-29-aarhus-workshop.html", + "title": "Sandbox workshop in Aarhus", + "section": "", + "text": "Sandbox data scientist Samuele Soraggi hosted a three day speed run through Sandbox apps at the Bioinformatics Research Center. The 26 participants joined for genomics, transcriptomics, and/or proteomics app demos depending on their interests. This thorough omics demo had maxed out participant sign-ups and an enthusiastic crew enjoyed the sessions alongside a bit of networking across disciplines. We plan to host more of these type of workshops given the event’s success!" + }, + { + "objectID": "news/past/2023-01-18-bulk-KU.html", + "href": "news/past/2023-01-18-bulk-KU.html", + "title": "Second bulk RNA-seq course at the University of Copenhagen", + "section": "", + "text": "On 18th of January we taught the second iteration of our bulk RNA-seq course to researchers (from PhD students to professors) at SUND at the University of Copenhagen. We had ~50 workshop participants joining us for three days of lectures and exercises on UCloud. This time, we introduced preprocessing theory (read QC, alignment and quantification) and the use of automated workflows using the nf-core rnaseq pipeline.\nFor those that could not enroll for this session, you can find the updated material here. We have moved the datasets and slides to a zenodo repository\nWe’d like to extend our thanks to our workshop collaborators, data scientists from the SUND DataLab at KU’s Center for Health Data Science as well as the genomics platform at the NNF Center for Stem Cell Medicine (reNEW)." + }, + { + "objectID": "news/past/2022-08-18-bulk-ku.html", + "href": "news/past/2022-08-18-bulk-ku.html", + "title": "Bulk RNA-seq course at University of Copenhagen", + "section": "", + "text": "Today we began teaching our brand new bulk RNA-seq course to researchers (from PhD students to professors) at SUND at the University of Copenhagen. We had 32 workshop participants join us for two days of lectures and exercises on UCloud. We’d like to extend our thanks to our workshop collaborators, data scientists from the SUND DataLab at KU’s Center for Health Data Science as well as the genomics platform at the NNF Center for Stem Cell Medicine (reNEW).\nFor those that could not enroll for this session, you can find the relevant material here." + }, + { + "objectID": "news/past/2024-04-18-sandbox-workshop.html", + "href": "news/past/2024-04-18-sandbox-workshop.html", + "title": "Workshop: Digging into the Health Data Science Sandbox", + "section": "", + "text": "This workshop offers an introduction to the training materials and tools of the Health Data Science Sandbox, a national infrastructure project. The Sandbox team is building training resources and guides for learning bioinformatics, predictive modeling in precision medicine, high performance computing and data carpentry that is accessible to all Danish university employees (PhD students and up) via academic supercomputing infrastructure.\nYou will be introduced to our current training set-up, meet our helpful data scientists, be guided through how to use our apps, and can make requests for the next topic we tackle!" + }, + { + "objectID": "news/past/2024-01-31-manuscript.html", + "href": "news/past/2024-01-31-manuscript.html", + "title": "A primer for Synthetic health data", + "section": "", + "text": "In collaboration with Prof. Henning Langberg at KU Public Health and funding from Erhvervsfyrtaarn Sund Vaegt, Jennifer Bartell has developed a manuscript that discusses technical, regulatory, and deployment solutions and challenges for synthetic health data from a broad perspective. This manuscript was developed in collaboration with Sandbox partners Sander Boisen Valentin and Martin Boegsted of AAU, and we plan to submit it to a journal soon. For now, check out our manuscript on arXiv!" + }, + { + "objectID": "news/past/2023-06-19-KU-bulk.html", + "href": "news/past/2023-06-19-KU-bulk.html", + "title": "Workshop on bulkRNA-seq data", + "section": "", + "text": "Our teaching team (from the Sandbox, the HeaDS DataLab, and reNEW’s genomics platform) hosted another 3 day workshop on bulk RNA-seq. The 34 participants used the updated version of the UCloud Transcriptomics App which provided the smoothest experience yet for both trainers and trainees. A new goal for the next course run is to add a student project to support independent implementation and exploration of the course content." + }, + { + "objectID": "access/index.html", + "href": "access/index.html", + "title": "HPC access", + "section": "", + "text": "The Sandbox is collaborating with the two major academic high performance computing platforms in Denmark. Computerome is located at the Technical University of Denmark (and co-owned by the University of Copenhagen) while UCloud is owned by the University of Southern Denmark. These HPC platforms each have their own strengths which we leverage in the Sandbox in different ways." + }, + { + "objectID": "access/index.html#ucloud", + "href": "access/index.html#ucloud", + "title": "HPC access", + "section": "UCloud", + "text": "UCloud\nUCloud is a relatively new HPC platform that can be accessed by students at Danish universities (via a WAYF university login). It has a user friendly graphical user interface that supports straightforward project, user, and resource management. UCloud provides access to many tools via selectable Apps matched with a range of flexible compute resources, and the Sandbox is deploying training modules in this form such that any UCloud user can easily access Sandbox materials independently. The Sandbox is also hosting workshops and training events on UCloud in conjunction with in-person training.\n\n\n\n\n\n\nAccess Sandbox Apps on UCloud\n\n\n\nFind detailed instructions on accessing Sandbox apps here via UCloud. Check out UCloud’s extensive user docs here." + }, + { + "objectID": "access/index.html#computerome", + "href": "access/index.html#computerome", + "title": "HPC access", + "section": "Computerome", + "text": "Computerome\nComputerome is the home of many sensitive health datasets via collaborations between DTU, KU, Rigshospitalet, and other major health sector players in the Capital Region of Denmark. Computerome has recently launched their secure cloud platform, DELPHI, and in collaboration with the Sandbox has built a Course Platform on the same backbone such that courses and training can be conducted in the same environment as real research would be performed in the secure cloud. The Sandbox is supporting courses in the Course Platform, but it is also available for independent use by educators at Danish universities. Please see their website for more information on independent use and pricing, and contact us if you’d like to collaborate on hosting a course on Computerome. We can help with tool installation, environment testing, and user support (ranging from using the environment to course content if we have Sandbox staff with matching expertise).\nParticipants in courses co-hosted by the Sandbox can check here for access instructions." + }, + { + "objectID": "access/index.html#genomedk", + "href": "access/index.html#genomedk", + "title": "HPC access", + "section": "GenomeDK", + "text": "GenomeDK\nIn development." + }, + { + "objectID": "access/index.html#any-other-computing-cluster", + "href": "access/index.html#any-other-computing-cluster", + "title": "HPC access", + "section": "Any other computing cluster", + "text": "Any other computing cluster\nIn development." + }, + { + "objectID": "access/index.html#your-local-pc", + "href": "access/index.html#your-local-pc", + "title": "HPC access", + "section": "Your local PC", + "text": "Your local PC\nIn development." + }, + { + "objectID": "access/genomedk.html", + "href": "access/genomedk.html", + "title": "Introduction to NGS data analysis", + "section": "", + "text": "sss" + }, + { + "objectID": "access/UCloud.html", + "href": "access/UCloud.html", + "title": "UCloud", + "section": "", + "text": "User accounts on UCloud are enabled by university login credentials using WAYF (Where Are You From). Access the WAYF login portal here, and then find your affiliated Danish university using the search bar. After login, we suggest setting up Two Factor Authentication by clicking on the icon in the top-right corner of the screen. Once you are an approved user of UCloud, you can access the Sandbox environment via different ‘Sandbox’ apps linked to topical modules that you deploy using your own storage and computing resources - just go to Apps once you have signed into UCloud and search ‘Sandbox’ to find what we have deployed. Each app page has its own Documentation link that will direct you to Sandbox-based usage guidelines which may be customized to the app’s particular tools and scope. Apps will have different ‘courses’ that you can initially choose which make a personal copy of training materials in your workspace for you to edit.\nEach Danish university has its usage relationship with UCloud as governed by their local front office of DeiC - check with your university IT support / DeiC representatives about requesting computational resources. For example, the University of Copenhagen has previously allotted an initial chunk of free UCloud compute hours to staff (from PhD students to professors as well as non-academic staff). If you have further questions about getting compute resources, please contact Sandbox staff.\nExtensive documentation on the general use of UCloud (how to use apps and run jobs, etc.) is available in the UCloud user guide.\n\n\n\n\n\n\nTip\n\n\n\nClick on the images to view them in full size.\n\n\n\n\n\n\nLog onto UCloud at the address http://cloud.sdu.dk using university credentials.\n\n\n\nWhen you are logged in, choose the project from the dashboard (highlighted in red) from which you would like to utilize compute resources. Every user has their personal workspace (My workspace). You can also provision your own project (check with your local DeiC office if you’re new to UCloud) or you can be invited to someone else’s project. If you’ve previously selected a project, it will be launched by default. If it’s your first time, you’ll be in your workspace. If you’ve joined one of our courses or workshops, your instructor will let you know which to choose.\nFor this example, we select Sandbox_workshop.\n\n\n\nDashboard: your workspace\n\n\nOn the left side, you can see the structure of the project (content changes when you select a different project):\n\nFiles: all folders/files you have access to. You can navigate through folders, download, upload, or share files with collaborators. You might have varying rights across folders, mostly depending on whether they are yours or have been shared with you\nShares/Projects: you have been invited to\nResources: allocated to your workspace or a project (shared)\nApps: gain access to the apps catalog on ucloud. We refer to apps as the software applications that can be deployed on the cloud. It’s recommended to explore the featured ones. Use the search bar to find the sandbox apps\nRuns: from where you submit your jobs and past runs information\n\n\n\n\n\n\n\nImportant\n\n\n\nDon’t forget to accept the invitation to access new projects. Remember to switch projects to access other files and resources. Test switching among projects and observe how the dashboard changes.\n\n\nAt the bottom left corner, you will find your user ID, which you may need to provide once the course starts or for future collaborations, such as being added to other people’s projects. You can also find it on UCloud docs.\nIn the dashboard, you will also find news, your favorite apps, recent runs, resources, and other notifications between other applications: - Resource allocations: indicate your currently allocated resources (e.g., KU employees have access to 1000kr in computing). - Grant applications: apply for more resources (computing or storage if you run out of them)\n\n\n\nThen click on Apps in the left panel to investigate what tools and environments you can use (green circle). The easiest way to find Sandbox resources is to search via the toolbar (red circle). In this example, we’ll select the Genomics Sandbox (which will bring you to the submission screen).\n\n\n\nDashboard: all apps\n\n\n\n\n\n\n\n\nTip\n\n\n\nMark them as favorites so they appear on your dashboard.\n\n\n\n\n\nClick on the app button to get into the settings window. First, we recommend reading the documentation of the app (highlighted in green). Then, you can configure the app as shown below, or be provided with a configuration file made available in a workshop’s project folders (import parameters) which will take care of everything for you.\n\n\n\nDashboard jobs: configuration step\n\n\nIn this example, we configure our session by:\n\nentering a job name (descriptive of the task)\nselecting the time (in hours) we want to use a node for (it can be modified afterward)\nselecting a 4 CPU standard node with 24 GB memory\nchoosing the course “Introduction to NGS Data Analysis”\noptional: add folders to access while in this job\nhitting submit (there may be a wait)\n\n\n\n\n\n\n\nImportant\n\n\n\nThe first 3 steps set up our computing resources for the period we want to work and can be customized as needed. However, only step 2 can be modified after submitting the job. For some of the Sandbox apps, you might want to select folders (Home and the Notebooks/Data from the module to avoid downloading it every time you start a new job). If you are in doubt, read the documentation specific to the app you are interested in.\nSelect the version of the app (if in doubt, use the latest one). This allows you to run specific versions of software.\n\n\nThere are different types of apps, and therefore, interfaces. Some, like RStudio or Jupyter Notebooks, have their own graphical user interface, whereas others are command-line interfaces. Lastly, you can also deploy a virtual desktop and virtual machine, which allow you to spin up a virtual computer.\n\n\n\nWait to go through the queue. When the session starts, the timer begins to count down. In a couple of minutes, you should be able to open the interface through the button (green circle) in a new window (refresh the window if needed).\n\n\n\nDashboard jobs: running the app\n\n\nThis page will remain open while you work (or you can return to it via ‘Runs’ in the left panel). You can end your session early by pressing and holding ‘Stop application’ (pink circle), you can see how much time you have left (red circle) and you can add hours to your session as you go (buttons in blue square).\n\n\n\nIf you are testing the genomic app, your interface should look like in the image below. Different apps might use other development environments. In this case, you will be working from JupyterLab. You can open Jupyter Notebooks (yellow square), R studio (blue square) or a terminal (black square) among others. In this case, #1 and #2 have all the software and packages that you will need pre-installed (this is not the case with Python 3 to the left).\n\n\n\nJupyterLab interface: running the app\n\n\nYou can navigate through the different folders and start running the Python notebooks (pink arrow).\n\n\n\nJupyterLab interface: openning notebook\n\n\nIf you are an advanced user, you can also create your own Python files and select the kernel NGS (python) to use the pre-installed software. Learn how to manage (upload and download new data) and share files that you have created/developed with collaborators here.\n\n\n\n\n\n\nTip\n\n\n\nCreate your own directories to save the output of your jobs. You will be able to access them later in your project folders under the resources you are using\nIf you haven’t created any directories, look for the generated files under a folder with the same name as the job name you used.\n\n\nYou are ready to start using Ucloud and the sandbox tools!\n\n\n\nDashboard: your workspace\nDashboard: all apps\nDashboard jobs: configuration step\nDashboard jobs: running the app\nJupyterLab interface: running the app\nJupyterLab interface: openning notebook" + }, + { + "objectID": "access/UCloud.html#example-how-to-open-a-sandbox-app", + "href": "access/UCloud.html#example-how-to-open-a-sandbox-app", + "title": "UCloud", + "section": "", + "text": "Log onto UCloud at the address http://cloud.sdu.dk using university credentials.\n\n\n\nWhen you are logged in, choose the project from the dashboard (highlighted in red) from which you would like to utilize compute resources. Every user has their personal workspace (My workspace). You can also provision your own project (check with your local DeiC office if you’re new to UCloud) or you can be invited to someone else’s project. If you’ve previously selected a project, it will be launched by default. If it’s your first time, you’ll be in your workspace. If you’ve joined one of our courses or workshops, your instructor will let you know which to choose.\nFor this example, we select Sandbox_workshop.\n\n\n\nDashboard: your workspace\n\n\nOn the left side, you can see the structure of the project (content changes when you select a different project):\n\nFiles: all folders/files you have access to. You can navigate through folders, download, upload, or share files with collaborators. You might have varying rights across folders, mostly depending on whether they are yours or have been shared with you\nShares/Projects: you have been invited to\nResources: allocated to your workspace or a project (shared)\nApps: gain access to the apps catalog on ucloud. We refer to apps as the software applications that can be deployed on the cloud. It’s recommended to explore the featured ones. Use the search bar to find the sandbox apps\nRuns: from where you submit your jobs and past runs information\n\n\n\n\n\n\n\nImportant\n\n\n\nDon’t forget to accept the invitation to access new projects. Remember to switch projects to access other files and resources. Test switching among projects and observe how the dashboard changes.\n\n\nAt the bottom left corner, you will find your user ID, which you may need to provide once the course starts or for future collaborations, such as being added to other people’s projects. You can also find it on UCloud docs.\nIn the dashboard, you will also find news, your favorite apps, recent runs, resources, and other notifications between other applications: - Resource allocations: indicate your currently allocated resources (e.g., KU employees have access to 1000kr in computing). - Grant applications: apply for more resources (computing or storage if you run out of them)\n\n\n\nThen click on Apps in the left panel to investigate what tools and environments you can use (green circle). The easiest way to find Sandbox resources is to search via the toolbar (red circle). In this example, we’ll select the Genomics Sandbox (which will bring you to the submission screen).\n\n\n\nDashboard: all apps\n\n\n\n\n\n\n\n\nTip\n\n\n\nMark them as favorites so they appear on your dashboard.\n\n\n\n\n\nClick on the app button to get into the settings window. First, we recommend reading the documentation of the app (highlighted in green). Then, you can configure the app as shown below, or be provided with a configuration file made available in a workshop’s project folders (import parameters) which will take care of everything for you.\n\n\n\nDashboard jobs: configuration step\n\n\nIn this example, we configure our session by:\n\nentering a job name (descriptive of the task)\nselecting the time (in hours) we want to use a node for (it can be modified afterward)\nselecting a 4 CPU standard node with 24 GB memory\nchoosing the course “Introduction to NGS Data Analysis”\noptional: add folders to access while in this job\nhitting submit (there may be a wait)\n\n\n\n\n\n\n\nImportant\n\n\n\nThe first 3 steps set up our computing resources for the period we want to work and can be customized as needed. However, only step 2 can be modified after submitting the job. For some of the Sandbox apps, you might want to select folders (Home and the Notebooks/Data from the module to avoid downloading it every time you start a new job). If you are in doubt, read the documentation specific to the app you are interested in.\nSelect the version of the app (if in doubt, use the latest one). This allows you to run specific versions of software.\n\n\nThere are different types of apps, and therefore, interfaces. Some, like RStudio or Jupyter Notebooks, have their own graphical user interface, whereas others are command-line interfaces. Lastly, you can also deploy a virtual desktop and virtual machine, which allow you to spin up a virtual computer.\n\n\n\nWait to go through the queue. When the session starts, the timer begins to count down. In a couple of minutes, you should be able to open the interface through the button (green circle) in a new window (refresh the window if needed).\n\n\n\nDashboard jobs: running the app\n\n\nThis page will remain open while you work (or you can return to it via ‘Runs’ in the left panel). You can end your session early by pressing and holding ‘Stop application’ (pink circle), you can see how much time you have left (red circle) and you can add hours to your session as you go (buttons in blue square).\n\n\n\nIf you are testing the genomic app, your interface should look like in the image below. Different apps might use other development environments. In this case, you will be working from JupyterLab. You can open Jupyter Notebooks (yellow square), R studio (blue square) or a terminal (black square) among others. In this case, #1 and #2 have all the software and packages that you will need pre-installed (this is not the case with Python 3 to the left).\n\n\n\nJupyterLab interface: running the app\n\n\nYou can navigate through the different folders and start running the Python notebooks (pink arrow).\n\n\n\nJupyterLab interface: openning notebook\n\n\nIf you are an advanced user, you can also create your own Python files and select the kernel NGS (python) to use the pre-installed software. Learn how to manage (upload and download new data) and share files that you have created/developed with collaborators here.\n\n\n\n\n\n\nTip\n\n\n\nCreate your own directories to save the output of your jobs. You will be able to access them later in your project folders under the resources you are using\nIf you haven’t created any directories, look for the generated files under a folder with the same name as the job name you used.\n\n\nYou are ready to start using Ucloud and the sandbox tools!\n\n\n\nDashboard: your workspace\nDashboard: all apps\nDashboard jobs: configuration step\nDashboard jobs: running the app\nJupyterLab interface: running the app\nJupyterLab interface: openning notebook" + }, + { + "objectID": "datasets/datapolicy.html", + "href": "datasets/datapolicy.html", + "title": "Data policy", + "section": "", + "text": "A priority of the Sandbox is to guide health data science learning using real-world-similar datasets. A major component is addressing how to analyze and leverage person-specific data, such as electronic health records, without invading personal privacy or straying from GDPR guidelines on sensitive data use. We are therefore focused on using either publicly accessible datasets (that are generally well anonymized to enable such release) or we are using/creating synthetic datasets that mimic real-world datasets without replicating real people’s data such that they can be identified. In either case, it is essential for Sandbox users to treat person-specific data respectfully and be aware of the additional responsibility and limitations of working with this type of data as part of their career in health data science.\nWe recommend that users interested in this type of data complete an ethics course on research using health datasets before digging into any analysis. A well regarded course that is also often required for using public databases that contain person-specific data is the Human Subject and Data Research Ethics course designed by the Massachusetts Institute of Technology. The course is hosted at CITI, the Collaborative Institutional Training Initiative. Completing the course is free of charge and provides you with a certificate which you may need to upload to certain databases to gain access. Set up an account at CITI, add an Institutional affiliation with ‘Massachusetts Institute of Technology Affiliates’, and then find and complete the course titled ‘Data or Specimens Only Research’ to obtain a certificate (in pdf form)." + }, + { + "objectID": "datasets/datapolicy.html#with-respect-to-person-specific-datasets", + "href": "datasets/datapolicy.html#with-respect-to-person-specific-datasets", + "title": "Data policy", + "section": "", + "text": "A priority of the Sandbox is to guide health data science learning using real-world-similar datasets. A major component is addressing how to analyze and leverage person-specific data, such as electronic health records, without invading personal privacy or straying from GDPR guidelines on sensitive data use. We are therefore focused on using either publicly accessible datasets (that are generally well anonymized to enable such release) or we are using/creating synthetic datasets that mimic real-world datasets without replicating real people’s data such that they can be identified. In either case, it is essential for Sandbox users to treat person-specific data respectfully and be aware of the additional responsibility and limitations of working with this type of data as part of their career in health data science.\nWe recommend that users interested in this type of data complete an ethics course on research using health datasets before digging into any analysis. A well regarded course that is also often required for using public databases that contain person-specific data is the Human Subject and Data Research Ethics course designed by the Massachusetts Institute of Technology. The course is hosted at CITI, the Collaborative Institutional Training Initiative. Completing the course is free of charge and provides you with a certificate which you may need to upload to certain databases to gain access. Set up an account at CITI, add an Institutional affiliation with ‘Massachusetts Institute of Technology Affiliates’, and then find and complete the course titled ‘Data or Specimens Only Research’ to obtain a certificate (in pdf form)." + }, + { + "objectID": "datasets/datapolicy.html#public-domain-data", + "href": "datasets/datapolicy.html#public-domain-data", + "title": "Data policy", + "section": "Public domain data", + "text": "Public domain data\nThe intended scope of the Sandbox is broad, and we will be pulling from many different public access databases (especially for training modules on omics analysis). Databases can be topically broad, giant repositories or field-specific, and each may have its own usage rules. We plan to provide our own copies of publically available datasets where allowed to ensure compatibility with the linked module is preserved, but some datasets may need to be downloaded by users themselves under specific access / distribution restrictions. Many omics datasets do not present significant data sensitivity concerns in comparison to real-world data such as electronic health records (EHRs) and clinical trial datasets.\nThere are large public de-identified EHR datasets that serve as benchmark resources for teaching and comparing new methods with old, but these are not numerous and often have restricted usage and sharing terms in addition to being quite dated. Historical approaches to dataset anonymization and de-identification have been substantially challenged in the age of digitalized healthcare and increasing data integration, which means meaningfully large ‘anonymized’ datasets are now rarely released." + }, + { + "objectID": "datasets/datapolicy.html#synthetic-data", + "href": "datasets/datapolicy.html#synthetic-data", + "title": "Data policy", + "section": "Synthetic data", + "text": "Synthetic data\n\n\n\n\n\n\nVia our collaborators and broader network, the Sandbox has the opportunity to simulate/synthesize data resembling different databases and registries from the Danish health sector. We are exploring methods of creating useful synthetic datasets with national and EU-level data access policies and GDPR restrictions in mind, while developing initial datasets using publicly available data from Danish research studies and other resources.\nUltimately, a new era of synthetic data is rapidly developing. The funded Sandbox proposal focused on generating synthetic data using mechanistic models, agent-based models, or draws from multivariate distributions (such as copulas), which are methods that do not present any significant GDPR-related concerns with sharing the produced datasets as they are derived from population-level characteristics and prior knowledge. However, new deep learning-based methods of data synthesis can theoretically learn complex, nonlinear patterns within a sensitive dataset and generate a synthetic dataset that replicates these patterns. This is a really promising approach for sharing high utility synthetic datasets, but it also elevates risk of accidentally sharing too much about the real dataset and skirting the boundaries of GDPR and ethical data handling. There is an inherent trade-off between privacy preservation and similarity of the synthetic dataset to the original dataset, with method development focused on moving closer to the ideal zone of high privacy AND high similarity. The figure at right is a rough approximation of this relationship versus current families of synthesis methods.\nPlease see Synthetic Data for more information about our approach to this technology." + }, + { + "objectID": "datasets/index.html", + "href": "datasets/index.html", + "title": "Datasets", + "section": "", + "text": "A priority of the Sandbox is to guide health data science learning using real-world-similar datasets. A major component is addressing how to analyze and leverage person-specific data, such as electronic health records, without invading personal privacy or straying from GDPR guidelines on sensitive data use. We are therefore focused on using either publicly accessible datasets (that are generally well anonymized to enable such release) or we are using/creating synthetic datasets that mimic real-world datasets without replicating real people’s data such that they can be identified. In either case, it is essential for Sandbox users to treat person-specific data respectfully and be aware of the additional responsibility and limitations of working with this type of data as part of their career in health data science.\nWe recommend that users interested in this type of data complete an ethics course on research using health datasets before digging into any analysis. A well regarded course that is also often required for using public databases that contain person-specific data is the Human Subject and Data Research Ethics course designed by the Massachusetts Institute of Technology. The course is hosted at CITI, the Collaborative Institutional Training Initiative. Completing the course is free of charge and provides you with a certificate which you may need to upload to certain databases to gain access. Set up an account at CITI, add an Institutional affiliation with ‘Massachusetts Institute of Technology Affiliates’, and then find and complete the course titled ‘Data or Specimens Only Research’ to obtain a certificate (in pdf form).\n\n\nThe intended scope of the Sandbox is broad, and we will be pulling from many different public access databases in our development of teaching modules. There are classical datasets that serve as benchmark resources for teaching and comparing new methods with old, and also brand new datasets that will support modules on emerging technologies (such as spatial single cell RNA-seq analysis). Databases can be topically broad giant repositories or field-specific, and each may have its own usage rules. We plan to provide our own copies of publically available datasets where allowed to ensure compatibility with the linked module is preserved, but some datasets may need to be downloaded by users themselves under specific access / distribution restrictions.\n\n\n\nThe Sandbox is focused on supporting Danish health data science education and research. Via our collaborators and broader network, we have the opportunity to simulate/synthesize data resembling different databases and registries from the Danish health sector in addition to using traditional data simulation techniques to replicate general datasets. We are exploring methods of creating useful synthetic datasets with local access guidelines/GDPR restrictions in mind, while developing initial datasets using published data from Danish studies and publically available resources." + }, + { + "objectID": "datasets/index.html#public-domain-data", + "href": "datasets/index.html#public-domain-data", + "title": "Datasets", + "section": "", + "text": "The intended scope of the Sandbox is broad, and we will be pulling from many different public access databases in our development of teaching modules. There are classical datasets that serve as benchmark resources for teaching and comparing new methods with old, and also brand new datasets that will support modules on emerging technologies (such as spatial single cell RNA-seq analysis). Databases can be topically broad giant repositories or field-specific, and each may have its own usage rules. We plan to provide our own copies of publically available datasets where allowed to ensure compatibility with the linked module is preserved, but some datasets may need to be downloaded by users themselves under specific access / distribution restrictions." + }, + { + "objectID": "datasets/index.html#syntheticsimulated-data", + "href": "datasets/index.html#syntheticsimulated-data", + "title": "Datasets", + "section": "", + "text": "The Sandbox is focused on supporting Danish health data science education and research. Via our collaborators and broader network, we have the opportunity to simulate/synthesize data resembling different databases and registries from the Danish health sector in addition to using traditional data simulation techniques to replicate general datasets. We are exploring methods of creating useful synthetic datasets with local access guidelines/GDPR restrictions in mind, while developing initial datasets using published data from Danish studies and publically available resources." + }, + { + "objectID": "news.html", + "href": "news.html", + "title": "News", + "section": "", + "text": "Sandbox data scientists routinely lead or contribute to courses and workshops at host universities in Denmark. Check out upcoming events here! All our past events are listed in the table below.\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nIntro to NGS data analysis - Summer School\n\n\n\nGenomics\n\n\nAU\n\n\ncourse\n\n\n\nFully booked\n\n\n\nJul 1, 2024\n\n\n\n\n\n\n\n\n\n\n\n\n\n\nHPC launch\n\n\n\nHPC\n\n\nRDM\n\n\nKU\n\n\ncourse\n\n\n\nClick to sign-up\n\n\n\nOct 30, 2024\n\n\n\n\n\n\n\n\n\n\n\n\nHPC Pipes\n\n\n\nsnakemake\n\n\nconda\n\n\nKU\n\n\ncourse\n\n\n\nClick to sign-up\n\n\n\nNov 15, 2024\n\n\n\n\n\n\n\n\nNo matching items\n\n\n\n \n \n \n Order By\n Default\n \n Event title\n \n \n \n \n \n \n \n\n\n\n\n\nEvent title\n\n\nDates\n\n\nLocation\n\n\nOrganizers\n\n\n\n\n\n\nWorkshop: Digging into the Health Data Science Sandbox\n\n\n18-19 April 2024\n\n\nKU\n\n\nJennifer Bartell\n\n\n\n\nCourse support at SDU\n\n\n9 February 2024\n\n\nSDU\n\n\nJacob Fredegaard Hansen\n\n\n\n\nDDSA PhD meetup and D3A conference\n\n\n1 February 2024\n\n\nDDSA\n\n\nJennifer Bartell\n\n\n\n\nA primer for Synthetic health data\n\n\n31 January 2024\n\n\n \n\n\nJennifer Bartell\n\n\n\n\nNNF Collaborative Data Science award news: the SE3D project!\n\n\n12 December 2023\n\n\nKU\n\n\nJennifer Bartell\n\n\n\n\nUpdates from SDU\n\n\n9 November 2023\n\n\nSDU\n\n\nJacob Fredegaard Hansen\n\n\n\n\nA course on RDS for NGS data\n\n\n7 November 2023\n\n\nDTU\n\n\nJose AR Herrera\n\n\n\n\nFrom Data Chaos to Data Harmony\n\n\n7 November 2023\n\n\nDeiC conference\n\n\nJennifer Bartell\n\n\n\n\n‘Digging into the Health Data Science Sandbox’ workshop\n\n\n7 September 2023\n\n\nAU\n\n\nJennifer Bartell\n\n\n\n\nSandbox workshop in Aarhus\n\n\n29 August 2023\n\n\nAU\n\n\nSamuele Soraggi\n\n\n\n\nWorkshop on bulkRNA-seq data\n\n\n19 June 2023\n\n\nKU\n\n\nJennifer Bartell\n\n\n\n\nSandbox App updates on UCloud rolled out\n\n\n31 May 2023\n\n\nKU\n\n\nJennifer Bartell\n\n\n\n\nSecond bulk RNA-seq course at the University of Copenhagen\n\n\n18 January 2023\n\n\nKU\n\n\nJennifer Bartell\n\n\n\n\nSandbox support for Spring 2023 courses\n\n\n10 January 2023\n\n\nKU\n\n\nJennifer Bartell\n\n\n\n\nSoft launch of the new Course Platform at Computerome\n\n\n8 January 2023\n\n\nKU\n\n\nJesper R Christiansen\n\n\n\n\nSandbox support for ‘Advanced Statistical Learning’\n\n\n30 November 2022\n\n\nAU\n\n\nSamuele Soraggi\n\n\n\n\nSandbox support within ‘Workshops in Applied Bioinformatics’ at SDU\n\n\n15 November 2022\n\n\nSDU\n\n\nJacob Fredegaard Hansen\n\n\n\n\nTranscriptomics Sandbox app launched on UCloud!\n\n\n15 November 2022\n\n\nKU\n\n\nJose AR Herrera\n\n\n\n\nGenomics Sandbox app launched on UCloud!\n\n\n6 September 2022\n\n\nAU\n\n\nSamuele Soraggi\n\n\n\n\nBulk RNA-seq course at University of Copenhagen\n\n\n18 August 2022\n\n\nKU\n\n\nJennifer Bartell\n\n\n\n\nGenomics course at Aarhus University\n\n\n1 June 2022\n\n\nAU\n\n\nSamuele Soraggi\n\n\n\n\nBasics of Personalized Medicine - final wrap-up\n\n\n22 April 2022\n\n\nAAU\n\n\nJennifer Bartell\n\n\n\n\nBasics of Personalized Medicine - MSc course\n\n\n1 April 2022\n\n\nAAU\n\n\nJennifer Bartell\n\n\n\n\n\nNo matching items" + }, + { + "objectID": "modules/bulk_rnaseq.html", + "href": "modules/bulk_rnaseq.html", + "title": "Bulk RNAseq", + "section": "", + "text": ":material-web-plus: Course Page\n\nThis workshop material includes a tutorial on how to approach RNAseq data, starting from your count matrix. Thus, the workshop only briefly touches upon laboratory protocols, library preparation, and experimental design of RNA sequencing experiments, mainly for the purpose of outlining considerations in the downstream bioinformatic analysis. This workshop is based on the materials developed by members of the teaching team at the Harvard Chan Bioinformatics Core (HBC), a collection of modified tutorials from the DESeq2 and R language vignettes.\nIntended use: The aim of this repository is to run a comprehensive but introductory workshop on bulk-RNAseq bioinformatic analyses. Each of the modules of this workshop is accompanied by a powerpoint slideshow explaining the steps and the theory behind a typical bioinformatics analysis (ideally with a teacher). Many of the slides are annotated with extra information and/or point to original sources for extra reading material.\n\n\nBy the end of this workshop, you should be able to analyse your own bulk RNAseq count matrix:\n\nNormalize your data.\nExplore your samples with PCAs and heatmaps.\nPerform Differential Expression Analysis.\nAnnotate your results.\n\n!!! agenda “Syllabus” 1. Course Introduction 2. Setup 3. Experimental planning 4. Data Explanation 5. Preprocessing 6. RNAseq counts 7. Exploratory analysis 8. Differential Expression Analysis 9. Functional Analysis 10. Summarized workflow\n!!! info “Workshop prerequisites” - Knowledge of R, Rstudio and Rmarkdown. It is recommended that you have at least followed our workshop R basics - Basic knowledge of RNAseq technology - Basic knowledge of data science and statistics such as PCA, clustering and statistical testing\n\n\n\nCenter for Health Data Science, University of Copenhagen.\nHugo Tavares, Bioinformatics Training Facility, University of Cambridge.\nSilvia Raineri, Center for Stem Cell Medicine (reNew), University of Copenhagen.\nHarvard Chan Bioinformatics Core (HBC), check out their github repo" + }, + { + "objectID": "modules/bulk_rnaseq.html#goals", + "href": "modules/bulk_rnaseq.html#goals", + "title": "Bulk RNAseq", + "section": "", + "text": "By the end of this workshop, you should be able to analyse your own bulk RNAseq count matrix:\n\nNormalize your data.\nExplore your samples with PCAs and heatmaps.\nPerform Differential Expression Analysis.\nAnnotate your results.\n\n!!! agenda “Syllabus” 1. Course Introduction 2. Setup 3. Experimental planning 4. Data Explanation 5. Preprocessing 6. RNAseq counts 7. Exploratory analysis 8. Differential Expression Analysis 9. Functional Analysis 10. Summarized workflow\n!!! info “Workshop prerequisites” - Knowledge of R, Rstudio and Rmarkdown. It is recommended that you have at least followed our workshop R basics - Basic knowledge of RNAseq technology - Basic knowledge of data science and statistics such as PCA, clustering and statistical testing\n\n\n\nCenter for Health Data Science, University of Copenhagen.\nHugo Tavares, Bioinformatics Training Facility, University of Cambridge.\nSilvia Raineri, Center for Stem Cell Medicine (reNew), University of Copenhagen.\nHarvard Chan Bioinformatics Core (HBC), check out their github repo" + }, + { + "objectID": "modules/index.html", + "href": "modules/index.html", + "title": "Training modules", + "section": "", + "text": "Sandbox resources have been organized as training modules focused on key topics in health data science. We are constantly adding additional resources and have plans to create additional modules on medical imaging and wearable device data. Feel free to adapt these resources for your own purposes (with credit to the National Health Data Science Sandbox project and other projects they acknowledge in the specific materials).\nYou can access our training modules through:" + }, + { + "objectID": "modules/index.html#sandbox-hpc", + "href": "modules/index.html#sandbox-hpc", + "title": "Training modules", + "section": "Data Carpentry and management", + "text": "Data Carpentry and management\n\n\n\n\n\n\n\nComputing skills are an important foundation for health data science (and using the above training modules), but formal training is often lacking as biomedical researchers navigate increasingly difficult computational tasks in their projects. These skills range from programming to the use of high-performance computers (HPC) to proper research data management.\n\nRDM for biodata (workshop on how to handle NGS data following simple guidelines to increase the FAIRability of your data)\nHPC launch (workshop in development)\nHPC pipes (workshop in development)\nHeaDS DataLab workshop materials (workshops for programming and good practices developed by the Center for Health Data Science at the University of Copenhagen, which are sometimes co-taught by Sandbox staff! Includes R, python, bash, and git!)" + }, + { + "objectID": "modules/index.html#genomics", + "href": "modules/index.html#genomics", + "title": "Training modules", + "section": "Genomics", + "text": "Genomics\n\n\n\n\n\n\n\nGenomics is the study of genomes, the complete set of an organism’s DNA. Genomics research now encompasses functional and structural studies, epigenomics, and metagenomics, and genomic medicine is under active implementation and extension in the health sector.\nUse the Genomics Sandbox App on UCloud to explore the resources below:\n\nIntroduction to Next Generation Sequencing data (last update: June 2023)\nIntroduction to Population Genomics (implementation of a course by Prof. Kasper Munch of Aarhus University) (last update: March 2023)\nIntroduction to GWAS (last update: March 2023)" + }, + { + "objectID": "modules/index.html#transcriptomics", + "href": "modules/index.html#transcriptomics", + "title": "Training modules", + "section": "Transcriptomics", + "text": "Transcriptomics\n\n\n\n\n\n\n\nTranscriptomics is the study of transcriptomes, which investigates RNA transcripts within a cell or tissue to determine what genes are being expressed and in what proportion. These RNA transcripts include mRNAs, tRNA, rRNA, and other non-coding RNA present in a cell.\nUse the Transcriptomics Sandbox App on UCloud to explore these resources:\n\nBulk RNAseq (last update: June 2023)\nSingle-Cell RNAseq (last update: May 2023)\nCirrocumulus (a popular tool for visualizing different types of RNA-seq data and downstream analysis)\nRNAseq in RStudio (RStudio session with pre-installed RNAseq analysis packages for exploring with your own uploaded data)" + }, + { + "objectID": "modules/index.html#proteomics", + "href": "modules/index.html#proteomics", + "title": "Training modules", + "section": "Proteomics", + "text": "Proteomics\n\n\n\n\n\n\n\nProteomics is the study of proteins that are produced by an organism. Proteomics allows us to analyze protein composition and structure, which have great importance in determining their function.\nUse the Proteomics Sandbox App on UCloud to explore pre-installed tools for proteomics analysis and other resources:\n\nProteomics Sandbox Documentation (last update: May 2023)\nIntroduction to Clinical Proteomics (course under development)\n\nWe also offer a tutorial on UCloud’s ColabFold app, a tool that allows predictions with AlphaFold2 or RoseTTAFold.\n\nColabFold Intro (last update: October 2022)" + }, + { + "objectID": "modules/index.html#EHC", + "href": "modules/index.html#EHC", + "title": "Training modules", + "section": "Electronic Health Records", + "text": "Electronic Health Records\n\n\n\n\n\n\n\nElectronic health records (EHRs) are digital records kept in the public health sector that record the medical histories of individuals, and access is normally highly restricted to preserve patient privacy. This data is sometimes also shared (partly or in full) in secondary patient registries that support research on a specific disease or condition (such as breast cancer or cystic fibrosis). These datasets are extraordinarily valuable in the development of predictive models used in precision medicine.\nThe chronic lymphocytic leukemia synthetic dataset listed below is generated solely from public data. It is of low utility, so we don’t recommend its use beyond the course it was designed for (with much explanation for the students on its construction and caveats). Please see Synthetic Data for more information.\n\nChronic Lymphocytic Leukemia synthetic dataset created for use in “Fra realworld data til personlig medicin”, a course from the University of Copenhagen’s MS in Personlig Medicin (last update: January 2023)\nIntro to EHR analysis (workshop under development)" + }, + { + "objectID": "modules/transcriptomics.html", + "href": "modules/transcriptomics.html", + "title": "Transcriptomics", + "section": "", + "text": "Transcriptomics\nTranscriptomics is the study of RNA transcripts and provides insight into gene expression patterns. State-of-the-art approaches rely on high-throughput sequencing of transcripts sampled by various methods." + }, + { + "objectID": "modules/AlphaFold_0122.html", + "href": "modules/AlphaFold_0122.html", + "title": "AlphaFold", + "section": "", + "text": "AlphaFold\n:fontawesome-brands-github: GitHub Repository\nUpdated: January 2022\nStatus: Under expansion\nThis module will contain a basic standalone tutorial on how to run the newly implemented AlphaFold app in the Sandbox (UCloud version).\nIntended use: The aim of this repository is to on-board users for AlphaFold on Computerome/UCloud.\n!!! abstract “Syllabus” 1. Introduction to protein structural analysis 2. Evaluating predicted structures (AlphaFold DB) 3. Using the AlphaFold app to predict new structures (AlphaFold) 4. Replicating an AlphaFold study 5. Future developments possible with AlphaFold\n!!! info “Workshop requirements” Knowledge of Python and Jupyter notebooks\n\nAcknowledgements\n\nCenter for Health Data Science, University of Copenhagen." + }, + { + "objectID": "modules/proteomics.html", + "href": "modules/proteomics.html", + "title": "Proteomics", + "section": "", + "text": "Proteomics\nProteomics is the study of proteins summed across a complete sample (ranging from a single cell to a whole organism). High-throughput measurement is conducted using mass spectrometry techniques and protein arrays, and provides insight into protein expression profiles and interactions." + }, + { + "objectID": "contributors.html", + "href": "contributors.html", + "title": "Introduction to NGS data analysis", + "section": "", + "text": "Jose Alejandro Romero Herrera :custom-orcid: :simple-github:" + }, + { + "objectID": "contributors.html#credit-table", + "href": "contributors.html#credit-table", + "title": "Introduction to NGS data analysis", + "section": "CRediT table", + "text": "CRediT table\n\n\n\nCRediT role\nInitials\n\n\n\n\nConceptualization\n\n\n\nData curation\n\n\n\nFormal Analysis\n\n\n\nFunding acquisition\n\n\n\nInvestigation\n\n\n\nMethodology\n\n\n\nProject administration\n\n\n\nResources\n\n\n\nSoftware\n\n\n\nSupervision\n\n\n\nValidation\n\n\n\nVisualization\n\n\n\nWriting - original draft\n\n\n\nWriting - review & editing" + }, + { + "objectID": "modules/course_template.html", + "href": "modules/course_template.html", + "title": "\nCourse Template\n", + "section": "", + "text": "Course Template\nLorem ipsum dolor sit amet, consectetur adipiscing elit. Nulla et euismod nulla. Curabitur feugiat, tortor non consequat finibus, justo purus auctor massa, nec semper lorem quam in massa.\nJennifer Bartell Jose Alejandro Romero Herrera Samuele Soraggi\n!!! abstract “Overview” 💬 Questions:\n- Why are we doing this?\n- What is the meaning of life?" + }, + { + "objectID": "modules/course_template.html#introduction", + "href": "modules/course_template.html#introduction", + "title": "\nCourse Template\n", + "section": "Introduction", + "text": "Introduction\n\nLook at this!\n\nLorem markdownum voluntas et praeteritae aliquando Cauno thyrso inevitabile est, interdum fingit educat, aliquo ungues solito sermo. Miscent pulveris me fletus moenia sed simul aequoris removit, te incursu.\n\nIncursurus liquidis Troiae\nEn ad staminaque ullam\nPellis erat collo Hectoreis cadavera quia draconem" + }, + { + "objectID": "modules/course_template.html#agenda", + "href": "modules/course_template.html#agenda", + "title": "\nCourse Template\n", + "section": "Agenda", + "text": "Agenda\n!!! note “In this tutorial, we will cover:” * First item * Second item" + }, + { + "objectID": "modules/course_template.html#section-1", + "href": "modules/course_template.html#section-1", + "title": "\nCourse Template\n", + "section": "Section 1", + "text": "Section 1\nLorem markdownum voluntas et praeteritae aliquando Cauno thyrso inevitabile est, interdum fingit educat, aliquo ungues solito sermo. Miscent pulveris me fletus moenia sed simul aequoris removit, te incursu.\n??? question “How does this thing work?”\nBy looking at it long enough!" + }, + { + "objectID": "modules/course_template.html#section-2", + "href": "modules/course_template.html#section-2", + "title": "\nCourse Template\n", + "section": "Section 2", + "text": "Section 2\nLorem markdownum voluntas et praeteritae aliquando Cauno thyrso inevitabile est, interdum fingit educat, aliquo ungues solito sermo. Miscent pulveris me fletus moenia sed simul aequoris removit, te incursu.\n??? note\nLorem ipsum dolor sit amet, consectetur adipiscing elit. Nulla et euismod\nnulla. Curabitur feugiat, tortor non consequat finibus, justo purus auctor\nmassa, nec semper lorem quam in massa." + }, + { + "objectID": "modules/course_template.html#section-3", + "href": "modules/course_template.html#section-3", + "title": "\nCourse Template\n", + "section": "Section 3", + "text": "Section 3\nLorem markdownum voluntas et praeteritae aliquando Cauno thyrso inevitabile est, interdum fingit educat, aliquo ungues solito sermo. Miscent pulveris me fletus moenia sed simul aequoris removit, te incursu.\n!!! info “Are you using an Apple chip?”\nContinue to do so." + }, + { + "objectID": "modules/genomics.html", + "href": "modules/genomics.html", + "title": "Genomics", + "section": "", + "text": "Genomics\nGenomics is the study of genomes, the complete set of an organism’s DNA. Genomics research now encompasses functional and structural studies, epigenomics, and metagenomics, and genomic medicine is under active implementation and extension in the health sector.\nModules linked to genomics topics are currently under construction." + }, + { + "objectID": "modules/clinProteomics_0122.html", + "href": "modules/clinProteomics_0122.html", + "title": "Clinical Proteomics", + "section": "", + "text": ":fontawesome-brands-github: GitHub Repository\nUpdated: January 2021\nStatus: Under expansion\nThe general strategy for the clinical proteomics module is to provide software, computing resources, datsets and storage using UCloud. Written material (instructions etc.), example notebooks and other auxiliary files will be provided in a Github repository.\n\nProteomics Sandbox app will be used for GUI programs\n\nPrimarily for identification / quantification\nFragPipe / MSFragger for database search (and perhaps open search)\nPDV for visualizing spectral matches\nSearchGUI and PeptideShaker also available\n\nJupyterLab app for data analysis after quantification\n\nInit script to activate conda environment and install custom kernel\nNotebooks provided through Github (https://github.com/hds-sandbox/proteomics-course)\n\nDatasets, (installed) software and JSON config files stored in UCloud project folders\n\nStudents currently need to be project members\n\n\nIntended use: Self-guided introduction to basic proteomics\n!!! abstract “Syllabus” 1. Identify and quantify peptides/proteins * “Database search” using MSFragger/FragPipe or MaxQuant * Visualize peptide spectrum matches using e.g. PDV, IDPicker, IPSA, … 2. Quality control analysis 3. Bioinformatics * Reintegrate clinical metadata * JupyterLab / RStudio + e.g. PolySTest / VSClust / … 4. PhosphoProteomics\n!!! info “Workshop requirements” Knowledge of Python and Jupyter Notebooks\n\n\n\nBMB online computational proteomics course\nNordBioNet summer school 2021 (workshops)\nIntroduction to bioinformatics for proteomics - Prof. Harald Barsnes, University of Bergen\nQC workshop and Quantitative Analysis workshop, long 2019 version - Prof. Veit Schwammle, University of Southern Denmark\nSimulation of proteomics data - Dr. Marie Locard-Paulet, University of Copenhagen\nProteogenomics - Dr. Marc Vaudel, University of Bergen\n\n\n\n\nCenter for Health Data Science, University of Copenhagen." + }, + { + "objectID": "modules/clinProteomics_0122.html#other-learning-resources", + "href": "modules/clinProteomics_0122.html#other-learning-resources", + "title": "Clinical Proteomics", + "section": "", + "text": "BMB online computational proteomics course\nNordBioNet summer school 2021 (workshops)\nIntroduction to bioinformatics for proteomics - Prof. Harald Barsnes, University of Bergen\nQC workshop and Quantitative Analysis workshop, long 2019 version - Prof. Veit Schwammle, University of Southern Denmark\nSimulation of proteomics data - Dr. Marie Locard-Paulet, University of Copenhagen\nProteogenomics - Dr. Marc Vaudel, University of Bergen\n\n\n\n\nCenter for Health Data Science, University of Copenhagen." + }, + { + "objectID": "modules/EHRs.html", + "href": "modules/EHRs.html", + "title": "EHRs", + "section": "", + "text": "Electronic Health Records\nElectronic health records (EHRs) are digital records kept in the public health sector that record the medical histories of individuals, and access is normally highly restricted to preserve patient privacy. This data is sometimes also shared (partly or in full) in secondary patient registries that support research of a specific disease or condition (such as cystic fibrosis). These datasets are extraordinarily valuable in the development of predictive models used in precision medicine.\nModules linked to EHR analysis are currently under development." + }, + { + "objectID": "recommended/recommended.html", + "href": "recommended/recommended.html", + "title": "Recommended", + "section": "", + "text": "Many outside resources are available to support education in health data science, ranging from beginner-level introductions to R or Python (the primary languages of health data science) to other teaching resources and tutorials created at universities and life science organizations.\nWe encourage you to explore the training platform provided by ELIXIR (Europe’s distributed infrastructure for life-science data). On this platform (TeSS), you can find a registry of training materials as well as webinars, workshops, and in-person courses in bioinformatics, modelling, data management, and life science database usage among other topics." + }, + { + "objectID": "recommended/recommended.html#recommended-resources-in-health-data-science", + "href": "recommended/recommended.html#recommended-resources-in-health-data-science", + "title": "Recommended", + "section": "", + "text": "Many outside resources are available to support education in health data science, ranging from beginner-level introductions to R or Python (the primary languages of health data science) to other teaching resources and tutorials created at universities and life science organizations.\nWe encourage you to explore the training platform provided by ELIXIR (Europe’s distributed infrastructure for life-science data). On this platform (TeSS), you can find a registry of training materials as well as webinars, workshops, and in-person courses in bioinformatics, modelling, data management, and life science database usage among other topics." + }, + { + "objectID": "about/about.html", + "href": "about/about.html", + "title": "About the Sandbox", + "section": "", + "text": "An infrastructure project for health data science training and research in Denmark\nThe National Health Data Science Sandbox project kicked off in 2021 with 5 years of funding via the Data Science Research Infrastructure initiative from the Novo Nordisk Foundation. Health data science experts at five Danish universities are contributing to the Sandbox with coordination from the Center for Health Data Science under lead PI Professor Anders Krogh. Data scientists hosted in the research groups of each PI are building infrastructure and training modules on Computerome and UCloud, the primary academic high performance computing (HPC) platforms in Denmark. If you have any questions or would like to get in touch with one of our data scientists, please contact us here.\n\n\n\n\n\nOur computational ‘sandbox’ allows data scientists to explore datasets, tools and analysis pipelines in the same high performance computing environments where real research projects are conducted. Rather than a single, hefty environment, we’re deploying modularized topical environments tailored for independent use on each HPC platform. We aim to support three key user groups based at Danish universities:\n\ntrainees: use our training modules to learn analysis techniques with some guidance and guardrails - for your data type of interest AND for general good practices for HPC environments\n\nresearchers: prototype your tools and algorithms with an array of good quality datasets that are GDPR compliant and free to access\neducators: develop your next course with computational assignments in the HPC environment your students will use for their research\n\nActivity developing independent training modules and hosting workshops has centered on UCloud, while collaborative construction of a flexible Course Platform has been completed on Computerome for use by the Sandbox and independent educators. Publicly sourced datasets are being used in training modules on UCloud, while generation of synthetic data is an ongoing project at Computerome. Sandbox resources are under active construction, so check out our other pages for the current status on HPC Access, Datasets, and Modules. We run workshops using completed training modules on a regular basis and provide active support for Sandbox-hosted courses through a slack workspace. See our Contact page for more information.\n\n\nPartner with the Sandbox\nThe Sandbox welcomes proposals for new courses, modules, and prototyping projects from researchers and educators. We’d like to partner with lecturers engaged with us in developing needed materials collaboratively - we would love to have input from subject experts or help promote exciting new tools and analysis methods via modules! Please contact us with your ideas at nhds_sandbox@sund.ku.dk.\n\nWe thank the Novo Nordisk Foundation for funding support. If you use the Sandbox for research or reference it in text or presentations, please acknowledge the Health Data Science Sandbox project and its funder the Novo Nordisk Foundation (grant number NNF20OC0063268)." + }, + { + "objectID": "datasets/datasets.html", + "href": "datasets/datasets.html", + "title": "Datasets", + "section": "", + "text": "Datasets\nHere we provide details of datasets used in our various modules as well as a specific guide on using electronic health record datasets." + }, + { + "objectID": "datasets/synthdata.html", + "href": "datasets/synthdata.html", + "title": "Synthetic data", + "section": "", + "text": "It is necessary to clarify what we mean when we refer to synthetic data within the Sandbox project. While the term has been used for decades to describe all kinds of ‘non-real’ data including those derived from models and simulations, developments in deep generative modeling have dramatically expanded our understanding of what synthetic data can be. In the age of deepfakes and news articles written entirely by ChatGPT, synthetic data derived from deep learning is in a wholly different class from data simulated with a mechanistic or agent-based model.\nThe Sandbox is actually interested in any form of synthetic data - our highest priority is providing safe-to-use data to trainees and researchers that does not raise any concerns about sensitive data with respect to the EU’s General Data Protection Regulation (GDPR) and local Danish data regulations. So, we are using both old school and new school forms of data synthesis. However, the discussion on this page is heavily weighted towards our interest in new school synthesis - with our connections to generative modeling researchers and high quality data, we are naturally interested in figuring out a safe way to deploy synthetic datasets derived from deep learning and other high similarity approaches.\n\n\n\n\n\n\nThe TLDR for synthetic data in the Sandbox\n\n\n\n- The development of synthetic datasets should be viewed as a research project. The technology is generally untested with few examples of public roll-out, and its deployment should be future-proofed as much as possible against attacks and potential sensitive data disclosure.\n- Synthetic data generation and evaluation approaches should be tailored to each dataset of interest. With current technology, it is unlikely that high quality, safe-to-share datasets will be produced at any kind of production scale without a massive effort devoted to pre-processing, data harmonization, and customized routines for different families of datasets.\n- The Sandbox is not openly sharing any synthetic datasets generated from person-specific sensitive data. We think these datasets will be useful to approved researchers that ideally gain access via an approved data portal with registration and data use agreements with relevant data authorities. We are not currently that portal.\n\n\n\n\n\nWe have explored the performance of copulas, multiple imputation, sequential synthesis, and several generative adversarial network (GAN) approaches with a cancer dataset which we were developing for a course in the MS in Personal Medicine program at University of Copenhagen. We quickly discovered that factors such as missingness, collinearity, and the ratio of patients to features cause just as many problems for synthetic data generation as they do in predictive modeling. We are currently evaluating the above techniques as well as additional deep learning approaches such as variational autoencoders (VAEs) and Bayesian graphs against a collection of benchmark health datasets to better understand the positives and negatives of each technique when faced with common challenges in real world health data.\nRecently, a few interesting libraries / pipelines have been released that enable testing of different synthetic data generation approaches alongside a range of evaluation metrics. We are actively exploring these tools as we test different generation approaches and examining their implementation of evaluation metrics. We plan to add additional components and features as we resolve challenges with different target datasets.\n\n\n\nThere are 3 key principles to consider when judging the overall quality of a synthetic dataset: fidelity to the original dataset, risk to privacy, and prediction utility. Fidelity and utility are often grouped together as similarity to the original data which exists in a trade-off with privacy - the more similar your synthetic dataset to the original, the higher your risk to patient privacy. However, the distinction between them is important as they can be achieved independently of each other depending on the project frame. Fidelity refers to reproduction of the multivariate shape and structure of the original data (including complex nonlinear relationships) while utility refers to how well the synthetic dataset matches the predictive accuracy of the original dataset. Risk to privacy includes both risk of patient reidentification and risk of sensitive information disclosure about a patient. There are many proposed evaluation metrics for measuring different aspects of these three qualities. We are actively investigating the performance of these metrics against our different datasets.\n\nWe should point out that while using quantitative metrics to assess privacy preservation is a critical step in creating a synthetic dataset, positive results do not absolve us from any concerns regarding risk to privacy in the synthetic data. Regulatory guidelines regarding the safety of synthetic data and the ability to openly share it are extremely unclear. No authorities have specified quantitative cut-offs using these metrics that enable open release, for example. For this reason, we have developed our own internal guidelines for how to handle this aspect of the project, which are based on a comprehensive examination of relevant EU and Danish legislation (i.e. the GDPR, the Artificial Intelligence Act, the Danish Health Law, and the Danish Data Protection Act). We continue work on synthesis with hope that new legislation such as the development of the European Health Data Space will provide further guidance in the future.\n\n\n\nWe are currently focused on exploring methods and metrics by developing reproducible, well documented examples and use cases of synthetic data in partnership with other researchers, legal advisors, and data authorities. We’re relying primarily on publicly available tabular health datasets in this exploration phase, but we will also work with sensitive data in the future. Our rules aim to preserve the trust of the public in how their health data is handled by data authorities and researchers.\n\n\n\n\n\n\nSandbox Rules for Synthetic Data\n\n\n\n1. Creation of synthetic data involves processing sensitive data, and this requires obtaining project approvals from data authorities when performing this work on sensitive data. Any synthetic data work with restricted-access, sensitive data by the Sandbox will only be conducted with these approvals in place in the frame of a research project.\n2. Goals for each synthetic dataset project should be defined at project initiation: how will the synthetic dataset be used, who is the intended audience, and how might it be shared? This frame should govern every consequent decision for that dataset and be shared alongside the final dataset.\n3. Quantitative metrics for fidelity, utility, and privacy preservation should be implemented for each dataset and shared alongside the final dataset.\n4. A cost-benefit analysis should be performed after the project is completed - is any risk to privacy appropriately balanced by value of the dataset in achieving its stated aims and contributing to the public good?\n5. Data authorities with ethical and strategic stakes in who accesses the synthetic dataset should be included in decisions about how it is used and who is allowed to access it. \n6. Synthetic datasets created from person-specific sensitive data rather than population characteristics can still pose privacy risks, and any users of the dataset should be approved and registered. 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The Sandbox will not release any such datasets publicly and will instead work with appropriate data authorities to decide how such datasets should be governed in a responsible way." + }, + { + "objectID": "access/Computerome.html", + "href": "access/Computerome.html", + "title": "Computerome", + "section": "", + "text": "Accessing the Sandbox on Computerome\nWe do not currently support independent use of Sandbox materials on Computerome. Access is supported via courses collaborating with the Sandbox and run on Computerome’s Course Platform. Check here for more info.\nThe below instructions are provided as reference for course participants.\nTo set up a user account on Computerome, you will need to provide administrators with your name, email address, and phone number for two-factor authentication. Once approved as a user, you will receive your username and server address (URL) by email, and you will receive an initial course-platform password by text.\nOn Computerome, the Sandbox environment is deployed as a virtual machine with a Linux desktop as user interface. This environment can be accessed through VMware Horizon using two different methods: (A) a desktop client (which you install on your computer) or (B) a web-based client (for those without install privileges on their computer). Please follow the appropriate instructions (A versus B) depending on your access preference.\n!!! note “Sign-In Instructions” 1. On FIRST login, enter the provided server address (URL) in a browser window to access the environment using your provided credentials. The URL will take you to a VMware Horizon access portal where you can * (A) choose to install the desktop client (left: ‘Install VMware Horizon Client’). You will then open this client for all subsequent logins instead of using the server address, and can login starting from step 2. * (B) access the environment via browser (right: ‘VMware Horizon HTML Access’). You will always use the server address in your browswer to access this entry point if this is your chosen method of access.\n2. Select the cloud icon\n * (A) which is linked to the server URL. This option appears when you have successfully installed and opened the VMware Horizon client.\n * (B) which is linked to the Sandbox course. This option appears after you have selected VMware Horizon HTML Access.\n\n3. Enter your username and your course-platform password. \n * On the first sign-in, this will be the course-platform password texted to you. You will then be prompted to create your own permanent password to replace this password which you will use for all future sign-ins.\n\n4. When prompted, enter the one-time password texted to you from DTU (NOT the same password as the course-platform password).\n * (A) If it is your first login / you logged off at last access, press any key when greeted with the blue time status screen. This will allow you to select your own user account in a dialog box.\n\n5. Sign-in using your course-platform password again after choosing the correct language for the environment in the upper right corner of the screen (this is important for the keyboard and typing your password). Danish (the da option) is default, so those with English keyboards will need to switch to English (the en option) at every login.\n\n6. Congratulations, you have entered the Sandbox environment. Relevant links for courses should be present on your desktop.\n!!! warning “Exit Instructions” To exit the environment, you have two options with different outcomes. You can log off and kill all running processes, or you can disconnect and your processes will continue running. “Power off” is disabled for users as this will shut down your virtual machine, local settings and user files may be lost, and the virtual machine will need to be manually restarted for your account.\n1. To exit and kill all running processes, select the power icon in the upper right corner, then select your name and choose \"log off\" in the pop up window.\n2. To exit and preserve running processes,\n * (A) hover at the top of the screen for a few seconds until your VMware Client menu is accessible, choose \"Connection\", and select \"Disconnect\".\n * (B) close the browser tab where you are accessing the Sandbox environment." + }, + { + "objectID": "access/other.html", + "href": "access/other.html", + "title": "Introduction to NGS data analysis", + "section": "", + "text": "sss" + }, + { + "objectID": "index.html", + "href": "index.html", + "title": "Introduction to Next Generation Sequencing data", + "section": "", + "text": "Computing and didactical support from the Danish Health Data Science Sandbox\n\n\n\nThe material for this course is organized in four separated jupyter notebooks in both bash, python and R where you will benefit of an interactive coding setup on jupyterlab. Each lesson is in the menu above.\n\n\nThe first exercise lesson is executed with the web interface usegalaxy.org. Click on 1.Galaxy Exercise in the menu for instructions)\n\n\n\n\nThe following exercise lessons will work on a computing environment with jupyterlab. Use 2.Instructions to find out how to run it, selecting the computing environment you need (danish clusters uCloud and GenomeDK, your PC, or another cluster).\n\n\n\nif you need to have a look at the exercises as a reference, then the menu 3.Compiled exercises contains all the compiled exercises on jupyterlab in a document format, from which you can also copy-paste the code." + }, + { + "objectID": "index.html#course-material", + "href": "index.html#course-material", + "title": "Introduction to Next Generation Sequencing data", + "section": "", + "text": "The material for this course is organized in four separated jupyter notebooks in both bash, python and R where you will benefit of an interactive coding setup on jupyterlab. Each lesson is in the menu above.\n\n\nThe first exercise lesson is executed with the web interface usegalaxy.org. Click on 1.Galaxy Exercise in the menu for instructions)" + }, + { + "objectID": "index.html#following-exercises", + "href": "index.html#following-exercises", + "title": "Introduction to Next Generation Sequencing data", + "section": "", + "text": "The following exercise lessons will work on a computing environment with jupyterlab. Use 2.Instructions to find out how to run it, selecting the computing environment you need (danish clusters uCloud and GenomeDK, your PC, or another cluster)." + }, + { + "objectID": "index.html#compiled-exercises", + "href": "index.html#compiled-exercises", + "title": "Introduction to Next Generation Sequencing data", + "section": "", + "text": "if you need to have a look at the exercises as a reference, then the menu 3.Compiled exercises contains all the compiled exercises on jupyterlab in a document format, from which you can also copy-paste the code." + }, + { + "objectID": "index.html#course-material-2022", + "href": "index.html#course-material-2022", + "title": "Introduction to Next Generation Sequencing data", + "section": "Course material 2022", + "text": "Course material 2022\nHere you find a table with the instructor’s slides from 2022.\n\n\n\nTopic\nSlide\nNotebook\n\n\n\n\nSequencing technologies\nlink\n–\n\n\nMapping to reference\nlink\nNotebook\n\n\nData visualization\nlink\n–\n\n\nSNPs and structural variants\nlink\nNotebook\n\n\nRNA sequencing\nlink\nNotebook\n\n\nDe-novo assembly\nlink\n–\n\n\nMicrobiomes and metagenomics\nlink\n–\n\n\nSingle cell RNA sequencing\nlink\nNotebook" + }, + { + "objectID": "index.html#course-material-2024", + "href": "index.html#course-material-2024", + "title": "Introduction to Next Generation Sequencing data", + "section": "Course material 2024", + "text": "Course material 2024\nHere you find a table with the instructor’s slides and a link to the compiled notebooks, that you can also run on your own following the instructions in this webpage. Data alignment can also be performed on the Galaxy interactive webpage (see the galaxy exercise in this webpage)." + }, + { + "objectID": "news/past/2022-12-10-transcriptomics-launch.html", + "href": "news/past/2022-12-10-transcriptomics-launch.html", + "title": "Transcriptomics Sandbox app launched on UCloud!", + "section": "", + "text": "We have deployed our second standalone Sandbox app on UCloud! Please see the Access page for instructions on how to find our Sandbox apps on UCloud - This one is titled ‘Transcriptomics Sandbox’ and module documentation is linked from the UCloud app page as well as here in Modules." + }, + { + "objectID": "news/past/2023-01-08-platform-computerome.html", + "href": "news/past/2023-01-08-platform-computerome.html", + "title": "Soft launch of the new Course Platform at Computerome", + "section": "", + "text": "Sandbox data scientist Jesper Roy Christiansen has been integral to the development of a new ‘Course Platform’ at Computerome, the HPC platform at the Technical University of Denmark. Built as a collaboration between the Sandbox and Computerome, the Course Platform will host its first users, students in ‘Fra real-world data til personlig medicin’, a course of KU’s MS in Personlig Medicin. Sandbox coordinator Jennifer Bartell and Sandbox PI Martin Boegsted have also been involved in testing this new system during course setup. See the above link as well as HPC Access for more details on this platform and how you can also use this new platform to host courses (with or without Sandbox involvement!)." + }, + { + "objectID": "news/past/2022-04-22-basicpm-wrapup.html", + "href": "news/past/2022-04-22-basicpm-wrapup.html", + "title": "Basics of Personalized Medicine - final wrap-up", + "section": "", + "text": "Our first course, Basics of Personalized Medicine, wrapped up this month with student project presentations which described their approaches to analysis of the synthetic Chronic Lymphocytic Leukemia dataset created for the course. Course reviews highlighted the helpfulness of Sandbox staff in troubleshooting R problems and the tremendous amount that students learned about predictive modeling." + }, + { + "objectID": "news/past/2023-11-07-RDMtalk.html", + "href": "news/past/2023-11-07-RDMtalk.html", + "title": "From Data Chaos to Data Harmony", + "section": "", + "text": "Sandbox data scientist Jose Alejandro Romero Herrera gave a talk in the Data Management speaker track at the annual Danish E-Infrastructure Consortium (DeiC) conference in Kolding, Denmark. The talk was well received at the biggest DeiC conference ever (250 participants)." + }, + { + "objectID": "news/past/2023-09-07-workshop-conference.html", + "href": "news/past/2023-09-07-workshop-conference.html", + "title": "‘Digging into the Health Data Science Sandbox’ workshop", + "section": "", + "text": "The full team of Sandbox data scientists hosted a 4 hour workshop at the Danish Bioinformatics conference where they gave a taster session of each of our 3 omics apps. We learned that multi-omics analysis were a substantial draw for the crowd at the DBC and are making plans to address this interest in future events." + }, + { + "objectID": "news/past/2023-11-09-proteomics_biostat_SDU.html", + "href": "news/past/2023-11-09-proteomics_biostat_SDU.html", + "title": "Updates from SDU", + "section": "", + "text": "The Proteomics Sandbox Application has recently undergone a significant update, enhancing its security features to ensure safer usage for its users. In this latest iteration, Sandbox data scientist Jacob Fredegaard Hansen has expanded the app’s software suite by introducing two new tools: DIA-NN and MZmine, catering to the metabolomics field. Furthermore, the pre-existing software within the application has been refreshed and updated to the latest versions, ensuring that the Proteomics Sandbox Application remains at the cutting-edge of the field. Excitingly, this application will be actively utilized in the course “BMB831: Biostatistics in R II” at the University of Southern Denmark throughout this autumn, showcasing its relevance and applicability in academic settings." + }, + { + "objectID": "news/past/2022-01-04-basicpm.html", + "href": "news/past/2022-01-04-basicpm.html", + "title": "Basics of Personalized Medicine - MSc course", + "section": "", + "text": "The first course supported by the Sandbox is launching this month - ‘Basics of Personalized Medicine’ - where students in the new Master in Personal Medicine program at University of Copenhagen are introduced to predictive modeling using electronic health records." + }, + { + "objectID": "news/past/2024-02-01-DDSAD3A.html", + "href": "news/past/2024-02-01-DDSAD3A.html", + "title": "DDSA PhD meetup and D3A conference", + "section": "", + "text": "Several Sandbox staff represented the project at both the DDSA PhD Meetup with a practical presentation on research data management and with posters at D3A, the national data science meeting. It was nice to meet up in person and also make new connections with the excellent cadre of conference attendees. Thanks to the DDSA secretariat for their invitation and organizational efforts." + }, + { + "objectID": "news/past/2023-10-25-RDM_NGS.html", + "href": "news/past/2023-10-25-RDM_NGS.html", + "title": "A course on RDS for NGS data", + "section": "", + "text": "Sandbox data scientist Jose Alejandro Romero Herrera ran the first instance of a new module on research data management practices he developed specifically for NGS data. Twelve participants were hosted in conjunction with DeiC at DTU, and were exposed to tools like bash, conda, git, and cookie cutter in their quest to organize their omics data." + }, + { + "objectID": "news/past/2022-11-15-support-bioinf-sdu.html", + "href": "news/past/2022-11-15-support-bioinf-sdu.html", + "title": "Sandbox support within ‘Workshops in Applied Bioinformatics’ at SDU", + "section": "", + "text": "Sandbox data scientist Jacob Fredegaard Hansen created a tutorial on how to use ColabFold for a one day workshop as part of the ‘Workshops in Applied Bioinformatics’ series taught by Sandbox collaborator Veit Schwammle. The material is accessible on the Sandbox website (see Modules, Proteomics) for any UCloud user alongside the UCloud ColabFold App." + }, + { + "objectID": "news/past/2023-01-10-spring-support.html", + "href": "news/past/2023-01-10-spring-support.html", + "title": "Sandbox support for Spring 2023 courses", + "section": "", + "text": "The Health Data Science sandbox is working with the following courses during spring 2023:\n\nSandbox support for Population Genomics\n\nExercises for an MS course on Population Genomics taught by Prof. Kasper Munch at Aarhus University are being implemented on UCloud by Sandbox data scientist Samuele Soraggi. Students will explore the training materials on UCloud during the Spring 2023 semester, after which the materials will be accessible to any UCloud user via the Genomics Sandbox App.\n\nFra real-world data til personlig medicin with Course Platform & Sandbox support The second round of the course ‘Fra real-world data til personlig medicin’ in KU’s MS in Personlig Medicin begins in January with an introduction to CLL-TIM, a predictive model for chronic lymphocytic leukemia deployed by Prof. Carsten Niemann, an introduction by Sandbox coordinator Jennifer Bartell to the new Course Platform at Computerome built with Sandbox help for hosting courses with HPC resources, and an introduction to building predictive models using TidyModels in R by Prof. Rasmus Broendum. The course will run through April with 10 continuing education students building their own predictive models using a new and improved synthetic CLL dataset developed by Sandbox data scientist Sander Boisen Valentin. Jennifer and Rasmus are also manning the Sandbox Slack workspace to field student questions about the dataset and their model building.\nSandbox support for ‘Single-cell, Single-Molecule: The Next Level in Cell Biology’ An NNF-funded course, ‘Single-cell, Single-Molecule: The Next Level in Cell Biology’ combining experimental and computational approaches to RNA sequencing is starting at Aarhus University. In addition to course-responsible professor Stig Andersen and co-teachers Victoria Birkedal and Thomas Boesen, Sandbox PI Mikkel Schierup will be contributing along with Sandbox data scientist Samuele Soraggi. Samuele is adapting the Transcriptomics App material on UCloud to supply tutorials and exercises for this hefty course as well as serving as a teaching assistant. The course materials will be available to all users of the Transcriptomics Sandbox App on UCloud in the future." + }, + { + "objectID": "news/upcoming/2024-10-30-hpcLaunch.html", + "href": "news/upcoming/2024-10-30-hpcLaunch.html", + "title": "HPC launch", + "section": "", + "text": "Sign-up." + }, + { + "objectID": "news/upcoming/2024-11-15-hpcPipes.html", + "href": "news/upcoming/2024-11-15-hpcPipes.html", + "title": "HPC Pipes", + "section": "", + "text": "Sign-up." + }, + { + "objectID": "workshop/workshopAAU_2023.html", + "href": "workshop/workshopAAU_2023.html", + "title": "\nSandbox Workshop\n", + "section": "", + "text": "Sandbox Workshop\n!!! info “Upcoming Workshop at AAU” Intro to the Health Data Science Sandbox at Aalborg University" + }, + { + "objectID": "workshop/workshopAAU_2023.html#the-sandbox-concept", + "href": "workshop/workshopAAU_2023.html#the-sandbox-concept", + "title": "\nSandbox Workshop\n", + "section": "The Sandbox concept", + "text": "The Sandbox concept\nThe Health Data Science Sandbox aims to be a training resource for bioinformaticians, data scientists, and those generally curious about how to investigate large biomedical datasets. We are an active and developing project seeking interested users (both trainees and educators). All of our open-source materials are available on our Github page and much more information is available on the rest of the website you are currently visiting! We work with both UCloud and Computerome (major Danish academic supercomputers) - see our HPC Access page for more info on each set up." + }, + { + "objectID": "workshop/workshopAAU_2023.html#access-sandbox-resources", + "href": "workshop/workshopAAU_2023.html#access-sandbox-resources", + "title": "\nSandbox Workshop\n", + "section": "Access Sandbox resources", + "text": "Access Sandbox resources\nWe currently provide training materials and resources as topical apps on UCloud, the supercomputer located at the University of Southern Denmark. To use these resources, you’ll need the following:\n\nLog onto UCloud at the address http://cloud.sdu.dk using your university credentials.\nthe ability to navigate in linux / RStudio / Jupyter. You don’t need to be an expert, but it is beyond our ambitions (and course material) to teach you how to code and how to run analyses simultaneously. We recommend a basic R or Python course before diving in.\n\nNote:\n\nTo use Sandbox materials outside of the workshop, you can request a project by clicking on apply for resources in your uCloud dashboard.\nIf you are a BSc or MSc student, you need a supervisor to apply on your behalf, or you can try to apply yourself mentioning the supervisor approval in the application.\nRemember, however, that you have 1000Kr of computing credit, and around 50GB of free storage to work on uCLoud." + }, + { + "objectID": "workshop/workshopAAU_2023.html#try-out-our-transcriptomics-module", + "href": "workshop/workshopAAU_2023.html#try-out-our-transcriptomics-module", + "title": "\nSandbox Workshop\n", + "section": "Try out our transcriptomics module", + "text": "Try out our transcriptomics module\nSo our Sandbox data scientists have finished their intro at the workshop? Great, now the brave ones in the audience can try out one of our apps in a live session. Today we are demoing:\n ### Transcriptomics If you’re interested in bulk or single cell RNA sequencing analysis and visualization, join Sandbox Data Scientist Samuele Soraggi from Aarhus University in testing out our Transcriptomics Sandbox app.\nFollow these instructions to try our app:\n\nClick on the button below to join the project for today: <!DOCTYPE html>\n\n\n\n\n\n<p>Green Button</p>\n\n\n\n\n\nGo to Link\n\n\nYou should see a message on your browser where you have to accept the invitation to the project. This will add you to a project on uCloud, where we have data and extra computing credit for the course.\nBe sure you have joined the project. Check if you have the project OMICS workshop from the project menu (red circle). Afterwards, click on the App menu (green circle) \n\nFind the app Transcriptomics Sandbox (red circle), which is under the title Featured.\n\n\n\n\nClick on it. You will get into the settings window. Choose any Job Name (Nr 1 in the figure below), how many hours you want to use for the job (Nr 2; choose at least 3 hours, you can increase this later), and how many CPUs (Nr 3, choose at least 4 CPUs). Choose the course RNAseq in RStudio from the drop-down menu (Nr 4). Finally, click on the blue button Add Folder.\n\n\n\nNow, click on the browsing bar that appears (red circle).\n\n\n\nIn the appearing window, you should see already a folder called Intro_to_scRNAseq_R. Click on Use at its right (red circle)\n\n\n\nAfterwards, you should have something like this in the settings page:\n\n\n\nNow, click on Submit to start the app (the button is on the right side of the settings page)\nYou will now enter a waiting queue. When the session starts, the timer begins to count down (red circle), and you should be able to open the interface through the button (green circle). Note the buttons to add time to your session (blue circle) and the button to stop the session when you are done (pink circle)\n\n\n\nOpen the interface by clicking on the button (green circle of figure above). Sometimes you are warned of a missing connection: simply refresh the page. You will enter Rstudio, well-known interface to code in R.\nRun the following command to download the tutorial: download.file(\"https://raw.githubusercontent.com/hds-sandbox/ELIXIR-workshop/main/Notebooks/scRNAseq_Tutorial_R.Rmd\", \"tutorial_scrna.Rmd\")\nOpen the file tutorial_scrnaR.Rmd that should now appear in the file browser of Rstudio. Click now on visual (on the tool bar) if you need to see the tutorial in a more readable format.\nThe executable code is inside chunks (called cells) to be executed in order from the first to the last using the little green arrow appearing on the right side of each code cell.\nRead carefully through the tutorial and execute the code cells. You will see the outputs appearing as you proceed." + }, + { + "objectID": "workshop/workshopAAU_2023.html#discussion-and-feedback", + "href": "workshop/workshopAAU_2023.html#discussion-and-feedback", + "title": "\nSandbox Workshop\n", + "section": "Discussion and feedback", + "text": "Discussion and feedback\nWe hope you enjoyed the live demo. If you have broader questions, suggestions, or concerns, now is the time to raise them! If you are totally toast for the day, remember that you can check out longer versions of our tutorials as well as other topics and tools in each of the Sandbox modules or join us for a multi-day in person course.\nAs data scientists, we also would be really happy for some quantifiable info and feedback - we want to build things that the Danish health data science community is excited to use. Please answer these 5 questions for us before you head out for the day (link activated on day of the workshop).\n\nNice meeting you and we hope to see you again!" + } +] \ No newline at end of file diff --git a/search/search_index.json b/search/search_index.json deleted file mode 100644 index eb8dc7a..0000000 --- a/search/search_index.json +++ /dev/null @@ -1 +0,0 @@ -{"config":{"indexing":"full","lang":["en"],"min_search_length":3,"prebuild_index":false,"separator":"[\\s\\-]+"},"docs":[{"location":"index.html","text":"Introduction to Next Generation Sequencing data \u00b6 A course of the Summer School of Aarhus University \u00b6 Computing and didactical support from the Danish Health Data Science Sandbox The material for this course is organized in four separated jupyter notebooks in both bash , python and R where you will benefit of an interactive coding setup on jupyterlab . Overview After the course, you will have knowledge of bioinformatics methods for analyzing genomes using NGS data, including knowledge of the existing types of genome data, how the different types of data can be displayed and analyzed, the current methods for genome assembly and analysis, their accuracy and how they can be used. The course will enable you to devise and run a project that makes use of NGS data. \ud83d\udcda Prerequisites: This is an introductory course that needs a basic understanding of the biology behind sequencing, and not necessarily programming experience (though this would help!). \ud83d\udcac Syllabus: 1. Describe key challenges in the analysis of NGS data 2. Explain the theoretical foundation for methods that use NGS for assembly and analysis of genomes 3. Discuss the bioinformatic methods for genome analysis and hypothesize what drives the outcome of the methods 4. 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Useful functions \u00b6 You should continue to write your markdown document as normal. But here are some useful functions. You can find more in the Reference guide listed on the tab above. Be sure to delete the guide and the tips below when finished with them. Code \u00b6 Text will be highlighted appropriately when you include language abbreviation: import tensorflow as tf Admonitions \u00b6 The admonitions used for course/section overview and requirements should be consistent, though you can use any other admonitions freely. Examples (both drop-down and not): Quote Here is a quote What is the smallest country in the world? A: Vatican City Footnotes \u00b6 We can include footnotes like this one 1 . LaTeX \u00b6 You write an equation as normal: \\[ \\operatorname{ker} f=\\{g\\in G:f(g)=e_{H}\\}{\\mbox{.}} \\] Images \u00b6 Format is similar to links, but include an exclamation mark before: You can link to a URL or to somewhere locally. Remember to eat your vegetables. \u21a9","title":"General page"},{"location":"empty.html#general-page","text":"Section Overview \ud83d\udd70 Time Estimation: X minutes \ud83d\udcac Learning Objectives: 1. First item 2. Second item Write your introduction to the page here.","title":"General Page"},{"location":"empty.html#useful-functions","text":"You should continue to write your markdown document as normal. But here are some useful functions. You can find more in the Reference guide listed on the tab above. Be sure to delete the guide and the tips below when finished with them.","title":"Useful functions"},{"location":"empty.html#code","text":"Text will be highlighted appropriately when you include language abbreviation: import tensorflow as tf","title":"Code"},{"location":"empty.html#admonitions","text":"The admonitions used for course/section overview and requirements should be consistent, though you can use any other admonitions freely. Examples (both drop-down and not): Quote Here is a quote What is the smallest country in the world? A: Vatican City","title":"Admonitions"},{"location":"empty.html#footnotes","text":"We can include footnotes like this one 1 .","title":"Footnotes"},{"location":"empty.html#latex","text":"You write an equation as normal: \\[ \\operatorname{ker} f=\\{g\\in G:f(g)=e_{H}\\}{\\mbox{.}} \\]","title":"LaTeX"},{"location":"empty.html#images","text":"Format is similar to links, but include an exclamation mark before: You can link to a URL or to somewhere locally. Remember to eat your vegetables. \u21a9","title":"Images"},{"location":"filtering.html","text":"Data filtering \u00b6 Each person works on its own personal folder, which contains a dataset. As a reminder, these are the personal folders Name Sample folder Andersen, Albert Lund Gifu_ctr_1 Bagger, Andreas Gifu_ctr_2 Hansen, Mads W\u00fcrgler Gifu_ctr_ 3 Milo, Lasse Gifu_ctr_4 Reimick, Sebastian Haunstrup Gifu_R7A_1 Hemmingsen, Jonas Klejs Gifu_R7A_2 Skovm\u00f8ller, Emma Hvitfeldt Gifu_R7A_3 S\u00f8rensen, Emma Frasez Gifu_R7A_4 Agersnap, Simon N\u00f8rregaard HAR1_ctr_1 Schmidt, Alina HAR1_ctr_2 Henriksen, Frederik Oskar HAR1_ctr_3 Lundby, Josephine Marie HAR1_ctr_4 N\u00f8rholm, Anne HAR1_R7A_1 Odgaard, Louise Nyrup HAR1_R7A_2 S\u00f8rensen, Sara Sejer HAR1_R7A_3 L\u00f8nskov, Jonas HAR1_R7A_4 Niklassen, Jacob Hansen Gifu_ctr_1_bis \u00d8llgaard, Ann Mai Br\u00f8ndum Holm Gifu_ctr_2_bis Overgaard, Morten \u00d8gelund Gifu_R7A_1_bis S\u00f8rensen, Elisabeth Asta Gifu_R7A_2_bis Rey, Isabel HAR1_ctr_1_bis Instructions \u00b6 Open a new session of jupyterlab in the same way as in the tutorial session Find your way to your personal folder, which is inside 426401/Students_analysis Start filtering your data using the notebook filtering.ipynb . This is a copy of the first part of the tutorial, so be careful about small changes you have to made (e.g. condition name, thresholds). For the condition name created in the metadata at the beginning of the tutorial, here we use one of Gifu_Control , Gifu_Infected , HAR1_Control , HAR1_Infected (depending on the dataset you have assigned), so that it is easy to integrated all datasets at the end. When you are done and you saved your data at the end (keep the filename filtered.h5Seurat ), write when you are done at this google docs under the sheet Filtering , so we all know when we are ready to proceed to data integration.","title":"Data filtering"},{"location":"filtering.html#data-filtering","text":"Each person works on its own personal folder, which contains a dataset. As a reminder, these are the personal folders Name Sample folder Andersen, Albert Lund Gifu_ctr_1 Bagger, Andreas Gifu_ctr_2 Hansen, Mads W\u00fcrgler Gifu_ctr_ 3 Milo, Lasse Gifu_ctr_4 Reimick, Sebastian Haunstrup Gifu_R7A_1 Hemmingsen, Jonas Klejs Gifu_R7A_2 Skovm\u00f8ller, Emma Hvitfeldt Gifu_R7A_3 S\u00f8rensen, Emma Frasez Gifu_R7A_4 Agersnap, Simon N\u00f8rregaard HAR1_ctr_1 Schmidt, Alina HAR1_ctr_2 Henriksen, Frederik Oskar HAR1_ctr_3 Lundby, Josephine Marie HAR1_ctr_4 N\u00f8rholm, Anne HAR1_R7A_1 Odgaard, Louise Nyrup HAR1_R7A_2 S\u00f8rensen, Sara Sejer HAR1_R7A_3 L\u00f8nskov, Jonas HAR1_R7A_4 Niklassen, Jacob Hansen Gifu_ctr_1_bis \u00d8llgaard, Ann Mai Br\u00f8ndum Holm Gifu_ctr_2_bis Overgaard, Morten \u00d8gelund Gifu_R7A_1_bis S\u00f8rensen, Elisabeth Asta Gifu_R7A_2_bis Rey, Isabel HAR1_ctr_1_bis","title":"Data filtering"},{"location":"filtering.html#instructions","text":"Open a new session of jupyterlab in the same way as in the tutorial session Find your way to your personal folder, which is inside 426401/Students_analysis Start filtering your data using the notebook filtering.ipynb . This is a copy of the first part of the tutorial, so be careful about small changes you have to made (e.g. condition name, thresholds). For the condition name created in the metadata at the beginning of the tutorial, here we use one of Gifu_Control , Gifu_Infected , HAR1_Control , HAR1_Infected (depending on the dataset you have assigned), so that it is easy to integrated all datasets at the end. When you are done and you saved your data at the end (keep the filename filtered.h5Seurat ), write when you are done at this google docs under the sheet Filtering , so we all know when we are ready to proceed to data integration.","title":"Instructions"},{"location":"galaxy.html","text":"Quality Control and Alignment of raw reads \u00b6 This first exercise will be executed on Galaxy , an interactive platform to run bioinformatics workflows. We will replicate this lesson with computer code later in this course. Galaxy has the possibility of working with a free account. Biological introduction \u00b6 White clover ( Trifolium repens ) is an allotetraploid . This means that it contains genomes originating from two different species within the same nucleus. Normally, white clover is an outbreeding species, but a self-compatible line was used for sequencing the white clover genome . This line is designated S10 in your data, indicating that this is the 10 th self-fertilized generation. In addition, you have data from a wild clover accession (ecotype) called Tienshan ( Ti ), which is collected from Chinese mountains and is adapted to alpine conditions. Figure: Characterisation of the white clover population. T.Repens is a hybrid of T.Occidentale and T.Pallescens Exercise guide \u00b6 Prepare the tools and data \u00b6 Install IGV on your computer from here . This is a genome browser you will use to look at some files. Create an account at usegalaxy.org and log into galaxy. Find the course data by going to this web address and by clicking on Import this history (top left corner of the page). Note: If usegalaxy.org has availability problems, you can use the other server https://usegalaxy.eu/ and get the data at this link . You might need to create an account there as well. Data \u00b6 You will be working with two types of sequencing data. The first is PacBio Hifi reads , which are long and accurate. You can find them under Hifi_reads_white_clover.fastq. The second type is Illumina RNA-seq reads , which are short and accurate and should be aligned using a spliced aligner, such as STAR . There are 24 of these files, 12 for each of the two genotypes mentioned before. The files are named [genotype]_[treatment]_[replicate].fastq . Treatment 1 is before and treatment 2 is after exposure to frost, respectively. In addition to the sequencing data, there are also three reference files: one for homologous contig 1 (referencing T. occidentale-derived subgenome), one for contig 2 (T. pallescens-derived subgenome) and one for both Contigs 1 and 2. The reference files are in fasta format. The file white_clover_genes.gtf contains the gene annotations for the two contigs. Workflow illustration \u00b6 Through Galaxy , we build a workflow applying tools to the data. We will look at the quality of the raw reads for both PacBio HiFi and Illumina RNA-seq reads. Afterwards, we align to references, using two different tools for the two types of data. Finally, we will look at the alignments on a genome browser. We will work then on a computing cluster through uCloud to analyze the aligned data in some of the upcoming lessons of the course. Galaxy Workflow \u00b6 When you import the files, what you actually import is a History - a sequence of files and softwares applied on the data. You can see the history on the right side of your usegalaxy.org webpage with green panels. Here, we only have the starting data, and you will build the rest of your history through various tools. On the left side of the screen, you have a menu with various available tools organized by category. All those softwares are also available on a classical computing command line (we will try those as well). Quality control \u00b6 1 Run FastQC on the PacBio Hifi reads and on two of the Illumina RNA-seq libraries. FastQC does quality control of the raw sequence data, providing an overview of the data which can help identify if there are any problems that should be addressed before further analysis. In the tool menu, click on FASTQ quality control --> FASTQC read quality reports . You will see a window with tool parameters : for the first option (raw read data from history), choose multiple files and select Hifi_reads_white_clover.fastq plus other fastq files you want to see the quality of (example in figure below). Then click on the button Run Tool . You will notice that some new elements are added to your history. Part of them are FastQC producing a text file, while others are FastQC producing a webpage report. The reports are ready when coloured in green: click on the eye symbol of a history item to read a report. 2 FastQC provides a report for each sample. To have a better comparison between the Hifi and Illumina data, we would combine the three FastQC reports into one using MultiQC . Choose the MultiQC tool from FASTQ quality control --> MultiQC aggregate results from ... . In the options, select FastQC as the used tool for the logsselect FastQC as the tool used to generate the output, and then select the items of FastQC of your history producing RawData (Figure below). In this way, you build a pipeline from the previous reports to the new tool you are using. Now click on Run Tool . The tool will be now running in your history. When it is done, click on the eye symbol to see the report. select the three \u201cRawData\u201d outputs generated by FastQC. Visualize the Webpage generated by MultiQC. Hint: You can find a \u201cHelp\u201d button that offers additional information about the plots for each panel. Questions: Focus on the following panels: \u201cPer base sequence quality\u201d, \u201cPer sequence quality scores\u201d\u2026. (\u201cPer base sequence content\u201d always gives a FAIL for RNA-seq data). What do you notice with respect to the sequence quality scores? And are there any other quality issues worth noting? Hifi Data Alignment \u00b6 3 Map the PacBio Hifi reads ( Hifi_reads_white_clover.fastq ) to the white clover reference sequence (Contigs 1 and 2) using minimap2 (Map with minimap2). Find Genomics Analysis --> Mapping --> Map with minimap2 . In the options, do not leave Use a built-in genome index , but select the option for having a genome from history. Choose then DNA_Contig1_2.fasta as the reference sequence. Under the profile with preset options, choose PacBio/Oxford Nanopore read to reference mapping (map-pb) . Then click on Run Tool . 4 Run the same alignment, but choose as preset options Long assembly to reference mapping. Divergence is far below 20% (asm20) . Rename then the two alignments using the edit function ( pen symbol in the history). Use for example names Contig1_2_mappb and Contig1_2_asm20 , to distinguish alignment options and reference genome. 5 The aligned genomes are not sorted by coordinates. Sort the alignments using Samtools sort (Find the tool under Genomic file manipulation --> SAM/BAM --> Samtools sort ... ). In the options, choose the two aligned files with multiple selection. Then click on Run Tool . 6 Download the two alignments to your computer. To do so, click on the disk symbol of each file in your history, and for each download both the Dataset (alignments in bam format) and their index files (in bai format). Download as well the reference genome in fasta format ( DNA_Contig1_2.fasta from the history). 7 Open IGV on your computer. Load the reference first: go on Genome --> Load genome from file and select the fasta file you downloaded. Then load the two alignments: go on File --> Load from file and select the bam and bai files you downloaded, together. You can now visualize the alignments. Questions: Look at the alignments in IGV. What do you notice about the alignments? What is the difference between the two alignments? Do you think one of them is better than the other? Choose on of the two alignments for the next steps. 8 Repeat the alignment with Minimap2 (using the chosen alignment option from the question above) and the sorting, but using the reference genomes for Contig 1 and for Contig 2 searaately. Note: you can run all at once by choosing multiple reference genomes in the options! Questions: Download the two references for Contig 1 and 2, and the two sorted alignments. Load the references from the menu `Genomes` in IGV, and then open the two alignments using the menu `File` in IGV. - Why do you see fluctuations in coverage and large regions without any apparent subgenome SNPs? - What are the major differences between the stats for the reads mapped to Contigs1&2 versus contig1 and contig2? What is your interpretation of the differences? RNA Data Alignment \u00b6 9 First, group the 24 RNA-seq libraries into two dataset lists, one list of pairs for S10 libraries and another for Tienshan libraries. so we can work with multiple samples simultaneously. You can do this by selecting the libraries for each genotype and choosing Build Lists of Dataset Pairs . The grouping suggested by Galaxy is wrong, because the paired reads are paired according to _1 and _2 in their names. Change those two with R1 and R2 , click on Unpair all , and then click on the suggested corrected pairs with the buttons Pair these datasets . Your sequences will be substituted by two elements in your history. Here we chose for example to name them S10 and TI . 10 Do alignment of the RNA-seq lists of raw files to the reference DNA_Contig1_2.fasta using STAR . Go to Genomics analysis --> RNA-seq --> RNA STAR Gapped-read mapper for RNA-seq data . In the options use: as data, the parameter Paired-end (as collection) , and then choose one of the two collections (you cannot run them all at once) as reference, DNA_Contig1_2.fasta , with Length of SA pre-indexing string equal to 9 as index with gene-model, use white_clover_annotations.gtf as output, Per gene read counts (GeneCounts) . 11 Use MultiQC to see the quality of the output. The alignment of STAR produces log files which can be used for quality reports. Go on Genomic File Manipulation --> MultiQC . In the options select the tool STAR . Then Insert STAR output , as type of output the Log , and choose the two logs listing collections of STAR alignments. Then click on Run Tool . View the report to see the alignment statistics. Final note: `Galaxy can also be used to create an automatic workflow that will map the data. This workflow can be useful when running multiple samples. You can generate a workflow from the analysis already completed in a history, by going to Settings \u2192 Extract workflow. You can also create a workflow from scratch using the Workflow editor.","title":"1.Galaxy Exercise"},{"location":"galaxy.html#quality-control-and-alignment-of-raw-reads","text":"This first exercise will be executed on Galaxy , an interactive platform to run bioinformatics workflows. We will replicate this lesson with computer code later in this course. Galaxy has the possibility of working with a free account.","title":"Quality Control and Alignment of raw reads"},{"location":"galaxy.html#biological-introduction","text":"White clover ( Trifolium repens ) is an allotetraploid . This means that it contains genomes originating from two different species within the same nucleus. Normally, white clover is an outbreeding species, but a self-compatible line was used for sequencing the white clover genome . This line is designated S10 in your data, indicating that this is the 10 th self-fertilized generation. In addition, you have data from a wild clover accession (ecotype) called Tienshan ( Ti ), which is collected from Chinese mountains and is adapted to alpine conditions. Figure: Characterisation of the white clover population. T.Repens is a hybrid of T.Occidentale and T.Pallescens","title":"Biological introduction"},{"location":"galaxy.html#exercise-guide","text":"","title":"Exercise guide"},{"location":"galaxy.html#prepare-the-tools-and-data","text":"Install IGV on your computer from here . This is a genome browser you will use to look at some files. Create an account at usegalaxy.org and log into galaxy. Find the course data by going to this web address and by clicking on Import this history (top left corner of the page). Note: If usegalaxy.org has availability problems, you can use the other server https://usegalaxy.eu/ and get the data at this link . You might need to create an account there as well.","title":"Prepare the tools and data"},{"location":"galaxy.html#data","text":"You will be working with two types of sequencing data. The first is PacBio Hifi reads , which are long and accurate. You can find them under Hifi_reads_white_clover.fastq. The second type is Illumina RNA-seq reads , which are short and accurate and should be aligned using a spliced aligner, such as STAR . There are 24 of these files, 12 for each of the two genotypes mentioned before. The files are named [genotype]_[treatment]_[replicate].fastq . Treatment 1 is before and treatment 2 is after exposure to frost, respectively. In addition to the sequencing data, there are also three reference files: one for homologous contig 1 (referencing T. occidentale-derived subgenome), one for contig 2 (T. pallescens-derived subgenome) and one for both Contigs 1 and 2. The reference files are in fasta format. The file white_clover_genes.gtf contains the gene annotations for the two contigs.","title":"Data"},{"location":"galaxy.html#workflow-illustration","text":"Through Galaxy , we build a workflow applying tools to the data. We will look at the quality of the raw reads for both PacBio HiFi and Illumina RNA-seq reads. Afterwards, we align to references, using two different tools for the two types of data. Finally, we will look at the alignments on a genome browser. We will work then on a computing cluster through uCloud to analyze the aligned data in some of the upcoming lessons of the course.","title":"Workflow illustration"},{"location":"galaxy.html#galaxy-workflow","text":"When you import the files, what you actually import is a History - a sequence of files and softwares applied on the data. You can see the history on the right side of your usegalaxy.org webpage with green panels. Here, we only have the starting data, and you will build the rest of your history through various tools. On the left side of the screen, you have a menu with various available tools organized by category. All those softwares are also available on a classical computing command line (we will try those as well).","title":"Galaxy Workflow"},{"location":"galaxy.html#quality-control","text":"1 Run FastQC on the PacBio Hifi reads and on two of the Illumina RNA-seq libraries. FastQC does quality control of the raw sequence data, providing an overview of the data which can help identify if there are any problems that should be addressed before further analysis. In the tool menu, click on FASTQ quality control --> FASTQC read quality reports . You will see a window with tool parameters : for the first option (raw read data from history), choose multiple files and select Hifi_reads_white_clover.fastq plus other fastq files you want to see the quality of (example in figure below). Then click on the button Run Tool . You will notice that some new elements are added to your history. Part of them are FastQC producing a text file, while others are FastQC producing a webpage report. The reports are ready when coloured in green: click on the eye symbol of a history item to read a report. 2 FastQC provides a report for each sample. To have a better comparison between the Hifi and Illumina data, we would combine the three FastQC reports into one using MultiQC . Choose the MultiQC tool from FASTQ quality control --> MultiQC aggregate results from ... . In the options, select FastQC as the used tool for the logsselect FastQC as the tool used to generate the output, and then select the items of FastQC of your history producing RawData (Figure below). In this way, you build a pipeline from the previous reports to the new tool you are using. Now click on Run Tool . The tool will be now running in your history. When it is done, click on the eye symbol to see the report. select the three \u201cRawData\u201d outputs generated by FastQC. Visualize the Webpage generated by MultiQC. Hint: You can find a \u201cHelp\u201d button that offers additional information about the plots for each panel. Questions: Focus on the following panels: \u201cPer base sequence quality\u201d, \u201cPer sequence quality scores\u201d\u2026. (\u201cPer base sequence content\u201d always gives a FAIL for RNA-seq data). What do you notice with respect to the sequence quality scores? And are there any other quality issues worth noting?","title":"Quality control"},{"location":"galaxy.html#hifi-data-alignment","text":"3 Map the PacBio Hifi reads ( Hifi_reads_white_clover.fastq ) to the white clover reference sequence (Contigs 1 and 2) using minimap2 (Map with minimap2). Find Genomics Analysis --> Mapping --> Map with minimap2 . In the options, do not leave Use a built-in genome index , but select the option for having a genome from history. Choose then DNA_Contig1_2.fasta as the reference sequence. Under the profile with preset options, choose PacBio/Oxford Nanopore read to reference mapping (map-pb) . Then click on Run Tool . 4 Run the same alignment, but choose as preset options Long assembly to reference mapping. Divergence is far below 20% (asm20) . Rename then the two alignments using the edit function ( pen symbol in the history). Use for example names Contig1_2_mappb and Contig1_2_asm20 , to distinguish alignment options and reference genome. 5 The aligned genomes are not sorted by coordinates. Sort the alignments using Samtools sort (Find the tool under Genomic file manipulation --> SAM/BAM --> Samtools sort ... ). In the options, choose the two aligned files with multiple selection. Then click on Run Tool . 6 Download the two alignments to your computer. To do so, click on the disk symbol of each file in your history, and for each download both the Dataset (alignments in bam format) and their index files (in bai format). Download as well the reference genome in fasta format ( DNA_Contig1_2.fasta from the history). 7 Open IGV on your computer. Load the reference first: go on Genome --> Load genome from file and select the fasta file you downloaded. Then load the two alignments: go on File --> Load from file and select the bam and bai files you downloaded, together. You can now visualize the alignments. Questions: Look at the alignments in IGV. What do you notice about the alignments? What is the difference between the two alignments? Do you think one of them is better than the other? Choose on of the two alignments for the next steps. 8 Repeat the alignment with Minimap2 (using the chosen alignment option from the question above) and the sorting, but using the reference genomes for Contig 1 and for Contig 2 searaately. Note: you can run all at once by choosing multiple reference genomes in the options! Questions: Download the two references for Contig 1 and 2, and the two sorted alignments. Load the references from the menu `Genomes` in IGV, and then open the two alignments using the menu `File` in IGV. - Why do you see fluctuations in coverage and large regions without any apparent subgenome SNPs? - What are the major differences between the stats for the reads mapped to Contigs1&2 versus contig1 and contig2? What is your interpretation of the differences?","title":"Hifi Data Alignment"},{"location":"galaxy.html#rna-data-alignment","text":"9 First, group the 24 RNA-seq libraries into two dataset lists, one list of pairs for S10 libraries and another for Tienshan libraries. so we can work with multiple samples simultaneously. You can do this by selecting the libraries for each genotype and choosing Build Lists of Dataset Pairs . The grouping suggested by Galaxy is wrong, because the paired reads are paired according to _1 and _2 in their names. Change those two with R1 and R2 , click on Unpair all , and then click on the suggested corrected pairs with the buttons Pair these datasets . Your sequences will be substituted by two elements in your history. Here we chose for example to name them S10 and TI . 10 Do alignment of the RNA-seq lists of raw files to the reference DNA_Contig1_2.fasta using STAR . Go to Genomics analysis --> RNA-seq --> RNA STAR Gapped-read mapper for RNA-seq data . In the options use: as data, the parameter Paired-end (as collection) , and then choose one of the two collections (you cannot run them all at once) as reference, DNA_Contig1_2.fasta , with Length of SA pre-indexing string equal to 9 as index with gene-model, use white_clover_annotations.gtf as output, Per gene read counts (GeneCounts) . 11 Use MultiQC to see the quality of the output. The alignment of STAR produces log files which can be used for quality reports. Go on Genomic File Manipulation --> MultiQC . In the options select the tool STAR . Then Insert STAR output , as type of output the Log , and choose the two logs listing collections of STAR alignments. Then click on Run Tool . View the report to see the alignment statistics. Final note: `Galaxy can also be used to create an automatic workflow that will map the data. This workflow can be useful when running multiple samples. You can generate a workflow from the analysis already completed in a history, by going to Settings \u2192 Extract workflow. You can also create a workflow from scratch using the Workflow editor.","title":"RNA Data Alignment"},{"location":"instructions.html","text":"Instructions \u00b6 You have various options to run the course material. You can execute it on a supercomputing system or on your own computer. Access the material on uCloud \u00b6 Ucloud is an interactive online platform from the University of Southern Danmark eScience center that allows users to execute softwares and computer code directly from their browser. If you are enrolled in a danish university or hospital, you can access the platform for free and try the course. Please follow these instructions to access uCloud and get access to the course: To access uCloud for the first time, go to the ucloud webpage and log in by pressing on the green button, choosing your institution, and writing your institutional credentials. If you have a mail address from a danish institution or university, you should be able to login with your institutional credentials. If you are participating in the NGS Summer Course 2023 in Aarhus, click AFTER logging in on this link . This will add you to a project on uCloud, where we have data and extra computing credit for the course. You should see a message on your browser where you have to accept the invitation to the project. Click on the uCloud symbol on the top-left corner of the uCloud webpage. You should see a dashboard window similar to the one below. The dashboard is a home page you will always see when opening uCloud. You can use the menu on the left to navigate to different sections of uCloud (File explorer, applications, etc.) On top of the uCloud interface you have My Workspace . That is your private space where you have some free hundreds of CPU hours and GBs of memory to run different applications (that you can see by using the menu Apps on the left). Click on Apps and find the application called Genomics Courses . Here choose the course Intro to NGS data , and use the other options to choose, for example, how many resources you want to use (we suggest at least 8 vCPUs) Run the docker container \u00b6 With Docker , you can create containers that will work in the same way on all the machines. The results of the course are exactly reproducible if you use such a Docker container. We created a container for the course that already contains packages and course material installed. You need to download Docker Desktop at this link . We suggest you have at least 8GB of RAM and 20GB of hard disk space. When Docker Desktop is installed, you can use the command line to retrieve the container from the web: docker pull samuelesoraggi/ngs-summer-aarhus:2022.08.01 You can now execute the container. You will see a web address in the output of the command line: you need to copy that into your web browser to see jupyterlab . docker run --rm -it -p 8888:8888 samuelesoraggi/ngs-summer-aarhus:2022.08.01","title":"Instructions"},{"location":"instructions.html#instructions","text":"You have various options to run the course material. You can execute it on a supercomputing system or on your own computer.","title":"Instructions"},{"location":"instructions.html#access-the-material-on-ucloud","text":"Ucloud is an interactive online platform from the University of Southern Danmark eScience center that allows users to execute softwares and computer code directly from their browser. If you are enrolled in a danish university or hospital, you can access the platform for free and try the course. Please follow these instructions to access uCloud and get access to the course: To access uCloud for the first time, go to the ucloud webpage and log in by pressing on the green button, choosing your institution, and writing your institutional credentials. If you have a mail address from a danish institution or university, you should be able to login with your institutional credentials. If you are participating in the NGS Summer Course 2023 in Aarhus, click AFTER logging in on this link . This will add you to a project on uCloud, where we have data and extra computing credit for the course. You should see a message on your browser where you have to accept the invitation to the project. Click on the uCloud symbol on the top-left corner of the uCloud webpage. You should see a dashboard window similar to the one below. The dashboard is a home page you will always see when opening uCloud. You can use the menu on the left to navigate to different sections of uCloud (File explorer, applications, etc.) On top of the uCloud interface you have My Workspace . That is your private space where you have some free hundreds of CPU hours and GBs of memory to run different applications (that you can see by using the menu Apps on the left). Click on Apps and find the application called Genomics Courses . Here choose the course Intro to NGS data , and use the other options to choose, for example, how many resources you want to use (we suggest at least 8 vCPUs)","title":"Access the material on uCloud"},{"location":"instructions.html#run-the-docker-container","text":"With Docker , you can create containers that will work in the same way on all the machines. The results of the course are exactly reproducible if you use such a Docker container. We created a container for the course that already contains packages and course material installed. You need to download Docker Desktop at this link . We suggest you have at least 8GB of RAM and 20GB of hard disk space. When Docker Desktop is installed, you can use the command line to retrieve the container from the web: docker pull samuelesoraggi/ngs-summer-aarhus:2022.08.01 You can now execute the container. You will see a web address in the output of the command line: you need to copy that into your web browser to see jupyterlab . docker run --rm -it -p 8888:8888 samuelesoraggi/ngs-summer-aarhus:2022.08.01","title":"Run the docker container"},{"location":"ucloud.html","text":"Access through uCloud \u00b6 Ucloud is an interactive online platform from the University of Southern Danmark eScience center that allows users to execute softwares and computer code directly from their browser. If you have an account from a danish university, hospital, and other institutions, you can access the platform for free and try the course. Starting a session of the Introduction to NGS data analysis on uCloud \u00b6 Log onto ucloud at the address http://cloud.sdu.dk using the university/institution credentials you possess. If you are participating in the NGS Summer Course 2023 in Aarhus, click AFTER logging in on this link . You should see a message on your browser where you have to accept the invitation to the project. This will add you to a project on uCloud, where we have data and extra computing credit for the course. Be sure to be in the right project. If you are participating in the NGS Summer Course 2023 in Aarhus, choose NGS Summer Course from the project menu (red circle). Afterwards, click on the App menu (green circle) Note: The project My Workspace is instead your private space where you have some free hundreds of CPU hours and GBs of memory. Find the app Genomics Sandbox (red circle), which is under the title Featured . Click on it. You will get into the settings window. Choose any Job Name (Nr 1 in the figure below), how many hours you want to use for the job (Nr 2, choose at least 2 hours, you can increase this later), and how many CPUs (Nr 3, choose at least 4 CPUs for the first three exercises, but use at least 8 CPUs to run the single cell analysis). Select the Introduction to NGS Data Analysis as course (Nr 4). Then click on Submit (Nr 5). You will now enter a waiting queue. When the session starts, the timer begins to count down (red circle). In a couple of minutes you should be able to open the interface through the button (green circle). Note the buttons to add time to your session (blue circle) and the button to stop the session when you are done (pink circle) You will be able to see jupyterlab in your browser. On the left side of the screen you can see various folders. You can find the exercises inside the folder Notebooks . You can download any file by right-clicking on it and choosing Download . You can also upload files by clicking on the Upload button on the top left corner of the screen, if you want to experiment with your own data! Reuse your notebooks and data \u00b6 The first time you run the Genomics Sandbox, you download data and notebooks. You can reuse them! Open the Genomics Sandbox App and use the settings to run it. You can click on your previous job name to recycle the settings (red circle). Now click on Add Folder (red circle) and on the appearing browsing bar (green circle). You need to find a drive with your user name (red circle), written as Member Files: NameSurname#Number . Then, go into Jobs/Genomics Sandbox/JobID/Notebooks and choose the folder (green circle). JobID corresponds to the Job Name you used in the previous session, followed by some random number in parenthesis. Do the same procedure adding a folder again and finding Jobs/Genomics Sandbox/JobID/Data . At the end you should have two added folders like this: Click on Submit. Now you will be able to reuse data, results and exercises on which you worked before. Note: remember to recycle the settings of this session the next time, so you can actually reuse the data and notebooks without having to add folders.","title":"2.1.Ucloud Access"},{"location":"ucloud.html#access-through-ucloud","text":"Ucloud is an interactive online platform from the University of Southern Danmark eScience center that allows users to execute softwares and computer code directly from their browser. If you have an account from a danish university, hospital, and other institutions, you can access the platform for free and try the course.","title":"Access through uCloud"},{"location":"ucloud.html#starting-a-session-of-the-introduction-to-ngs-data-analysis-on-ucloud","text":"Log onto ucloud at the address http://cloud.sdu.dk using the university/institution credentials you possess. If you are participating in the NGS Summer Course 2023 in Aarhus, click AFTER logging in on this link . You should see a message on your browser where you have to accept the invitation to the project. This will add you to a project on uCloud, where we have data and extra computing credit for the course. Be sure to be in the right project. If you are participating in the NGS Summer Course 2023 in Aarhus, choose NGS Summer Course from the project menu (red circle). Afterwards, click on the App menu (green circle) Note: The project My Workspace is instead your private space where you have some free hundreds of CPU hours and GBs of memory. Find the app Genomics Sandbox (red circle), which is under the title Featured . Click on it. You will get into the settings window. Choose any Job Name (Nr 1 in the figure below), how many hours you want to use for the job (Nr 2, choose at least 2 hours, you can increase this later), and how many CPUs (Nr 3, choose at least 4 CPUs for the first three exercises, but use at least 8 CPUs to run the single cell analysis). Select the Introduction to NGS Data Analysis as course (Nr 4). Then click on Submit (Nr 5). You will now enter a waiting queue. When the session starts, the timer begins to count down (red circle). In a couple of minutes you should be able to open the interface through the button (green circle). Note the buttons to add time to your session (blue circle) and the button to stop the session when you are done (pink circle) You will be able to see jupyterlab in your browser. On the left side of the screen you can see various folders. You can find the exercises inside the folder Notebooks . You can download any file by right-clicking on it and choosing Download . You can also upload files by clicking on the Upload button on the top left corner of the screen, if you want to experiment with your own data!","title":"Starting a session of the Introduction to NGS data analysis on uCloud"},{"location":"ucloud.html#reuse-your-notebooks-and-data","text":"The first time you run the Genomics Sandbox, you download data and notebooks. You can reuse them! Open the Genomics Sandbox App and use the settings to run it. You can click on your previous job name to recycle the settings (red circle). Now click on Add Folder (red circle) and on the appearing browsing bar (green circle). You need to find a drive with your user name (red circle), written as Member Files: NameSurname#Number . Then, go into Jobs/Genomics Sandbox/JobID/Notebooks and choose the folder (green circle). JobID corresponds to the Job Name you used in the previous session, followed by some random number in parenthesis. Do the same procedure adding a folder again and finding Jobs/Genomics Sandbox/JobID/Data . At the end you should have two added folders like this: Click on Submit. Now you will be able to reuse data, results and exercises on which you worked before. Note: remember to recycle the settings of this session the next time, so you can actually reuse the data and notebooks without having to add folders.","title":"Reuse your notebooks and data"},{"location":"nb/align.html","text":"(function (global, factory) { typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory() : typeof define === 'function' && define.amd ? define(factory) : (global = global || self, global.ClipboardCopyElement = factory()); }(this, function () { 'use strict'; function createNode(text) { const node = document.createElement('pre'); node.style.width = '1px'; node.style.height = '1px'; node.style.position = 'fixed'; node.style.top = '5px'; node.textContent = text; return node; } function copyNode(node) { if ('clipboard' in navigator) { // eslint-disable-next-line flowtype/no-flow-fix-me-comments // $FlowFixMe Clipboard is not defined in Flow yet. return navigator.clipboard.writeText(node.textContent); } const selection = getSelection(); 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In a light * theme these would go from dark to light. */ --jp-inverse-layout-color0: #111111; --jp-inverse-layout-color1: var(--md-grey-900); --jp-inverse-layout-color2: var(--md-grey-800); --jp-inverse-layout-color3: var(--md-grey-700); --jp-inverse-layout-color4: var(--md-grey-600); /* Brand/accent */ --jp-brand-color0: var(--md-blue-900); --jp-brand-color1: var(--md-blue-700); --jp-brand-color2: var(--md-blue-300); --jp-brand-color3: var(--md-blue-100); --jp-brand-color4: var(--md-blue-50); --jp-accent-color0: var(--md-green-900); --jp-accent-color1: var(--md-green-700); --jp-accent-color2: var(--md-green-300); --jp-accent-color3: var(--md-green-100); /* State colors (warn, error, success, info) */ --jp-warn-color0: var(--md-orange-900); --jp-warn-color1: var(--md-orange-700); --jp-warn-color2: var(--md-orange-300); --jp-warn-color3: var(--md-orange-100); --jp-error-color0: var(--md-red-900); --jp-error-color1: var(--md-red-700); --jp-error-color2: var(--md-red-300); --jp-error-color3: var(--md-red-100); --jp-success-color0: var(--md-green-900); --jp-success-color1: var(--md-green-700); --jp-success-color2: var(--md-green-300); --jp-success-color3: var(--md-green-100); --jp-info-color0: var(--md-cyan-900); --jp-info-color1: var(--md-cyan-700); --jp-info-color2: var(--md-cyan-300); --jp-info-color3: var(--md-cyan-100); /* Cell specific styles */ --jp-cell-padding: 5px; --jp-cell-collapser-width: 8px; --jp-cell-collapser-min-height: 20px; --jp-cell-collapser-not-active-hover-opacity: 0.6; --jp-cell-editor-background: var(--md-grey-100); --jp-cell-editor-border-color: var(--md-grey-300); --jp-cell-editor-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-cell-editor-active-background: var(--jp-layout-color0); --jp-cell-editor-active-border-color: var(--jp-brand-color1); --jp-cell-prompt-width: 64px; --jp-cell-prompt-font-family: var(--jp-code-font-family-default); --jp-cell-prompt-letter-spacing: 0px; --jp-cell-prompt-opacity: 1; --jp-cell-prompt-not-active-opacity: 0.5; --jp-cell-prompt-not-active-font-color: var(--md-grey-700); /* A custom blend of MD grey and blue 600 * See https://meyerweb.com/eric/tools/color-blend/#546E7A:1E88E5:5:hex */ --jp-cell-inprompt-font-color: #307fc1; /* A custom blend of MD grey and orange 600 * https://meyerweb.com/eric/tools/color-blend/#546E7A:F4511E:5:hex */ --jp-cell-outprompt-font-color: #bf5b3d; /* Notebook specific styles */ --jp-notebook-padding: 10px; --jp-notebook-select-background: var(--jp-layout-color1); --jp-notebook-multiselected-color: var(--md-blue-50); /* The scroll padding is calculated to fill enough space at the bottom of the notebook to show one single-line cell (with appropriate padding) at the top when the notebook is scrolled all the way to the bottom. We also subtract one pixel so that no scrollbar appears if we have just one single-line cell in the notebook. This padding is to enable a 'scroll past end' feature in a notebook. */ --jp-notebook-scroll-padding: calc( 100% - var(--jp-code-font-size) * var(--jp-code-line-height) - var(--jp-code-padding) - var(--jp-cell-padding) - 1px ); /* Rendermime styles */ --jp-rendermime-error-background: #fdd; --jp-rendermime-table-row-background: var(--md-grey-100); --jp-rendermime-table-row-hover-background: var(--md-light-blue-50); /* Dialog specific styles */ --jp-dialog-background: rgba(0, 0, 0, 0.25); /* Console specific styles */ --jp-console-padding: 10px; /* Toolbar specific styles */ --jp-toolbar-border-color: var(--jp-border-color1); --jp-toolbar-micro-height: 8px; --jp-toolbar-background: var(--jp-layout-color1); --jp-toolbar-box-shadow: 0px 0px 2px 0px rgba(0, 0, 0, 0.24); --jp-toolbar-header-margin: 4px 4px 0px 4px; --jp-toolbar-active-background: var(--md-grey-300); /* Statusbar specific styles */ --jp-statusbar-height: 24px; /* Input field styles */ --jp-input-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-input-active-background: var(--jp-layout-color1); --jp-input-hover-background: var(--jp-layout-color1); --jp-input-background: var(--md-grey-100); --jp-input-border-color: var(--jp-border-color1); --jp-input-active-border-color: var(--jp-brand-color1); --jp-input-active-box-shadow-color: rgba(19, 124, 189, 0.3); /* General editor styles */ --jp-editor-selected-background: #d9d9d9; --jp-editor-selected-focused-background: #d7d4f0; --jp-editor-cursor-color: var(--jp-ui-font-color0); /* Code mirror specific styles */ --jp-mirror-editor-keyword-color: #008000; --jp-mirror-editor-atom-color: #88f; --jp-mirror-editor-number-color: #080; --jp-mirror-editor-def-color: #00f; --jp-mirror-editor-variable-color: var(--md-grey-900); --jp-mirror-editor-variable-2-color: #05a; --jp-mirror-editor-variable-3-color: #085; --jp-mirror-editor-punctuation-color: #05a; --jp-mirror-editor-property-color: #05a; --jp-mirror-editor-operator-color: #aa22ff; --jp-mirror-editor-comment-color: #408080; --jp-mirror-editor-string-color: #ba2121; --jp-mirror-editor-string-2-color: #708; --jp-mirror-editor-meta-color: #aa22ff; --jp-mirror-editor-qualifier-color: #555; --jp-mirror-editor-builtin-color: #008000; --jp-mirror-editor-bracket-color: #997; --jp-mirror-editor-tag-color: #170; --jp-mirror-editor-attribute-color: #00c; --jp-mirror-editor-header-color: blue; --jp-mirror-editor-quote-color: #090; --jp-mirror-editor-link-color: #00c; --jp-mirror-editor-error-color: #f00; --jp-mirror-editor-hr-color: #999; /* Vega extension styles */ --jp-vega-background: white; /* Sidebar-related styles */ --jp-sidebar-min-width: 250px; /* Search-related styles */ --jp-search-toggle-off-opacity: 0.5; --jp-search-toggle-hover-opacity: 0.8; --jp-search-toggle-on-opacity: 1; --jp-search-selected-match-background-color: rgb(245, 200, 0); --jp-search-selected-match-color: black; --jp-search-unselected-match-background-color: var( --jp-inverse-layout-color0 ); --jp-search-unselected-match-color: var(--jp-ui-inverse-font-color0); /* Icon colors that work well with light or dark backgrounds */ --jp-icon-contrast-color0: var(--md-purple-600); --jp-icon-contrast-color1: var(--md-green-600); --jp-icon-contrast-color2: var(--md-pink-600); --jp-icon-contrast-color3: var(--md-blue-600); } [data-md-color-scheme=\"slate\"] .jupyter-wrapper { /* Elevation * * We style box-shadows using Material Design's idea of elevation. These particular numbers are taken from here: * * https://github.com/material-components/material-components-web * https://material-components-web.appspot.com/elevation.html */ /* The dark theme shadows need a bit of work, but this will probably also require work on the core layout * colors used in the theme as well. */ --jp-shadow-base-lightness: 32; --jp-shadow-umbra-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.2 ); --jp-shadow-penumbra-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.14 ); --jp-shadow-ambient-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.12 ); --jp-elevation-z0: none; --jp-elevation-z1: 0px 2px 1px -1px var(--jp-shadow-umbra-color), 0px 1px 1px 0px var(--jp-shadow-penumbra-color), 0px 1px 3px 0px var(--jp-shadow-ambient-color); --jp-elevation-z2: 0px 3px 1px -2px var(--jp-shadow-umbra-color), 0px 2px 2px 0px var(--jp-shadow-penumbra-color), 0px 1px 5px 0px var(--jp-shadow-ambient-color); --jp-elevation-z4: 0px 2px 4px -1px var(--jp-shadow-umbra-color), 0px 4px 5px 0px var(--jp-shadow-penumbra-color), 0px 1px 10px 0px var(--jp-shadow-ambient-color); --jp-elevation-z6: 0px 3px 5px -1px var(--jp-shadow-umbra-color), 0px 6px 10px 0px var(--jp-shadow-penumbra-color), 0px 1px 18px 0px var(--jp-shadow-ambient-color); --jp-elevation-z8: 0px 5px 5px -3px var(--jp-shadow-umbra-color), 0px 8px 10px 1px var(--jp-shadow-penumbra-color), 0px 3px 14px 2px var(--jp-shadow-ambient-color); --jp-elevation-z12: 0px 7px 8px -4px var(--jp-shadow-umbra-color), 0px 12px 17px 2px var(--jp-shadow-penumbra-color), 0px 5px 22px 4px var(--jp-shadow-ambient-color); --jp-elevation-z16: 0px 8px 10px -5px var(--jp-shadow-umbra-color), 0px 16px 24px 2px var(--jp-shadow-penumbra-color), 0px 6px 30px 5px var(--jp-shadow-ambient-color); --jp-elevation-z20: 0px 10px 13px -6px var(--jp-shadow-umbra-color), 0px 20px 31px 3px var(--jp-shadow-penumbra-color), 0px 8px 38px 7px var(--jp-shadow-ambient-color); --jp-elevation-z24: 0px 11px 15px -7px var(--jp-shadow-umbra-color), 0px 24px 38px 3px var(--jp-shadow-penumbra-color), 0px 9px 46px 8px var(--jp-shadow-ambient-color); /* Borders * * The following variables, specify the visual styling of borders in JupyterLab. */ --jp-border-width: 1px; --jp-border-color0: var(--md-grey-700); --jp-border-color1: var(--md-grey-700); --jp-border-color2: var(--md-grey-800); --jp-border-color3: var(--md-grey-900); --jp-border-radius: 2px; /* UI Fonts * * The UI font CSS variables are used for the typography all of the JupyterLab * user interface elements that are not directly user generated content. * * The font sizing here is done assuming that the body font size of --jp-ui-font-size1 * is applied to a parent element. When children elements, such as headings, are sized * in em all things will be computed relative to that body size. */ --jp-ui-font-scale-factor: 1.2; --jp-ui-font-size0: 0.83333em; --jp-ui-font-size1: 13px; /* Base font size */ --jp-ui-font-size2: 1.2em; --jp-ui-font-size3: 1.44em; --jp-ui-font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\"; /* * Use these font colors against the corresponding main layout colors. * In a light theme, these go from dark to light. */ /* Defaults use Material Design specification */ --jp-ui-font-color0: rgba(255, 255, 255, 1); --jp-ui-font-color1: rgba(255, 255, 255, 0.87); --jp-ui-font-color2: rgba(255, 255, 255, 0.54); --jp-ui-font-color3: rgba(255, 255, 255, 0.38); /* * Use these against the brand/accent/warn/error colors. * These will typically go from light to darker, in both a dark and light theme. */ --jp-ui-inverse-font-color0: rgba(0, 0, 0, 1); --jp-ui-inverse-font-color1: rgba(0, 0, 0, 0.8); --jp-ui-inverse-font-color2: rgba(0, 0, 0, 0.5); --jp-ui-inverse-font-color3: rgba(0, 0, 0, 0.3); /* Content Fonts * * Content font variables are used for typography of user generated content. * * The font sizing here is done assuming that the body font size of --jp-content-font-size1 * is applied to a parent element. When children elements, such as headings, are sized * in em all things will be computed relative to that body size. */ --jp-content-line-height: 1.6; --jp-content-font-scale-factor: 1.2; --jp-content-font-size0: 0.83333em; --jp-content-font-size1: 14px; /* Base font size */ --jp-content-font-size2: 1.2em; --jp-content-font-size3: 1.44em; --jp-content-font-size4: 1.728em; --jp-content-font-size5: 2.0736em; /* This gives a magnification of about 125% in presentation mode over normal. */ --jp-content-presentation-font-size1: 17px; --jp-content-heading-line-height: 1; --jp-content-heading-margin-top: 1.2em; --jp-content-heading-margin-bottom: 0.8em; --jp-content-heading-font-weight: 500; /* Defaults use Material Design specification */ --jp-content-font-color0: rgba(255, 255, 255, 1); --jp-content-font-color1: rgba(255, 255, 255, 1); --jp-content-font-color2: rgba(255, 255, 255, 0.7); --jp-content-font-color3: rgba(255, 255, 255, 0.5); --jp-content-link-color: var(--md-blue-300); --jp-content-font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\"; /* * Code Fonts * * Code font variables are used for typography of code and other monospaces content. */ --jp-code-font-size: 13px; --jp-code-line-height: 1.3077; /* 17px for 13px base */ --jp-code-padding: 5px; /* 5px for 13px base, codemirror highlighting needs integer px value */ --jp-code-font-family-default: Menlo, Consolas, \"DejaVu Sans Mono\", monospace; --jp-code-font-family: var(--jp-code-font-family-default); /* This gives a magnification of about 125% in presentation mode over normal. */ --jp-code-presentation-font-size: 16px; /* may need to tweak cursor width if you change font size */ --jp-code-cursor-width0: 1.4px; --jp-code-cursor-width1: 2px; --jp-code-cursor-width2: 4px; /* Layout * * The following are the main layout colors use in JupyterLab. In a light * theme these would go from light to dark. */ --jp-layout-color0: #111111; --jp-layout-color1: var(--md-grey-900); --jp-layout-color2: var(--md-grey-800); --jp-layout-color3: var(--md-grey-700); --jp-layout-color4: var(--md-grey-600); /* Inverse Layout * * The following are the inverse layout colors use in JupyterLab. In a light * theme these would go from dark to light. */ --jp-inverse-layout-color0: white; --jp-inverse-layout-color1: white; --jp-inverse-layout-color2: var(--md-grey-200); --jp-inverse-layout-color3: var(--md-grey-400); --jp-inverse-layout-color4: var(--md-grey-600); /* Brand/accent */ --jp-brand-color0: var(--md-blue-700); --jp-brand-color1: var(--md-blue-500); --jp-brand-color2: var(--md-blue-300); --jp-brand-color3: var(--md-blue-100); --jp-brand-color4: var(--md-blue-50); --jp-accent-color0: var(--md-green-700); --jp-accent-color1: var(--md-green-500); --jp-accent-color2: var(--md-green-300); --jp-accent-color3: var(--md-green-100); /* State colors (warn, error, success, info) */ --jp-warn-color0: var(--md-orange-700); --jp-warn-color1: var(--md-orange-500); --jp-warn-color2: var(--md-orange-300); --jp-warn-color3: var(--md-orange-100); --jp-error-color0: var(--md-red-700); --jp-error-color1: var(--md-red-500); --jp-error-color2: var(--md-red-300); --jp-error-color3: var(--md-red-100); --jp-success-color0: var(--md-green-700); --jp-success-color1: var(--md-green-500); --jp-success-color2: var(--md-green-300); --jp-success-color3: var(--md-green-100); --jp-info-color0: var(--md-cyan-700); --jp-info-color1: var(--md-cyan-500); --jp-info-color2: var(--md-cyan-300); --jp-info-color3: var(--md-cyan-100); /* Cell specific styles */ --jp-cell-padding: 5px; --jp-cell-collapser-width: 8px; --jp-cell-collapser-min-height: 20px; --jp-cell-collapser-not-active-hover-opacity: 0.6; --jp-cell-editor-background: var(--jp-layout-color1); --jp-cell-editor-border-color: var(--md-grey-700); --jp-cell-editor-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-cell-editor-active-background: var(--jp-layout-color0); --jp-cell-editor-active-border-color: var(--jp-brand-color1); --jp-cell-prompt-width: 64px; --jp-cell-prompt-font-family: var(--jp-code-font-family-default); --jp-cell-prompt-letter-spacing: 0px; --jp-cell-prompt-opacity: 1; --jp-cell-prompt-not-active-opacity: 1; --jp-cell-prompt-not-active-font-color: var(--md-grey-300); /* A custom blend of MD grey and blue 600 * See https://meyerweb.com/eric/tools/color-blend/#546E7A:1E88E5:5:hex */ --jp-cell-inprompt-font-color: #307fc1; /* A custom blend of MD grey and orange 600 * https://meyerweb.com/eric/tools/color-blend/#546E7A:F4511E:5:hex */ --jp-cell-outprompt-font-color: #bf5b3d; /* Notebook specific styles */ --jp-notebook-padding: 10px; --jp-notebook-select-background: var(--jp-layout-color1); --jp-notebook-multiselected-color: rgba(33, 150, 243, 0.24); /* The scroll padding is calculated to fill enough space at the bottom of the notebook to show one single-line cell (with appropriate padding) at the top when the notebook is scrolled all the way to the bottom. We also subtract one pixel so that no scrollbar appears if we have just one single-line cell in the notebook. This padding is to enable a 'scroll past end' feature in a notebook. */ --jp-notebook-scroll-padding: calc( 100% - var(--jp-code-font-size) * var(--jp-code-line-height) - var(--jp-code-padding) - var(--jp-cell-padding) - 1px ); /* Rendermime styles */ --jp-rendermime-error-background: rgba(244, 67, 54, 0.28); --jp-rendermime-table-row-background: var(--md-grey-900); --jp-rendermime-table-row-hover-background: rgba(3, 169, 244, 0.2); /* Dialog specific styles */ --jp-dialog-background: rgba(0, 0, 0, 0.6); /* Console specific styles */ --jp-console-padding: 10px; /* Toolbar specific styles */ --jp-toolbar-border-color: var(--jp-border-color2); --jp-toolbar-micro-height: 8px; --jp-toolbar-background: var(--jp-layout-color1); --jp-toolbar-box-shadow: 0px 0px 2px 0px rgba(0, 0, 0, 0.8); --jp-toolbar-header-margin: 4px 4px 0px 4px; --jp-toolbar-active-background: var(--jp-layout-color0); /* Statusbar specific styles */ --jp-statusbar-height: 24px; /* Input field styles */ --jp-input-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-input-active-background: var(--jp-layout-color0); --jp-input-hover-background: var(--jp-layout-color2); --jp-input-background: var(--md-grey-800); --jp-input-border-color: var(--jp-border-color1); --jp-input-active-border-color: var(--jp-brand-color1); --jp-input-active-box-shadow-color: rgba(19, 124, 189, 0.3); /* General editor styles */ --jp-editor-selected-background: var(--jp-layout-color2); --jp-editor-selected-focused-background: rgba(33, 150, 243, 0.24); --jp-editor-cursor-color: var(--jp-ui-font-color0); /* Code mirror specific styles */ --jp-mirror-editor-keyword-color: var(--md-green-500); --jp-mirror-editor-atom-color: var(--md-blue-300); --jp-mirror-editor-number-color: var(--md-green-400); --jp-mirror-editor-def-color: var(--md-blue-600); --jp-mirror-editor-variable-color: var(--md-grey-300); --jp-mirror-editor-variable-2-color: var(--md-blue-400); --jp-mirror-editor-variable-3-color: var(--md-green-600); --jp-mirror-editor-punctuation-color: var(--md-blue-400); --jp-mirror-editor-property-color: var(--md-blue-400); --jp-mirror-editor-operator-color: #aa22ff; --jp-mirror-editor-comment-color: #408080; --jp-mirror-editor-string-color: #ff7070; --jp-mirror-editor-string-2-color: var(--md-purple-300); --jp-mirror-editor-meta-color: #aa22ff; --jp-mirror-editor-qualifier-color: #555; --jp-mirror-editor-builtin-color: var(--md-green-600); --jp-mirror-editor-bracket-color: #997; --jp-mirror-editor-tag-color: var(--md-green-700); --jp-mirror-editor-attribute-color: var(--md-blue-700); --jp-mirror-editor-header-color: var(--md-blue-500); --jp-mirror-editor-quote-color: var(--md-green-300); --jp-mirror-editor-link-color: var(--md-blue-700); --jp-mirror-editor-error-color: #f00; --jp-mirror-editor-hr-color: #999; /* Vega extension styles */ --jp-vega-background: var(--md-grey-400); /* Sidebar-related styles */ --jp-sidebar-min-width: 250px; /* Search-related styles */ --jp-search-toggle-off-opacity: 0.6; --jp-search-toggle-hover-opacity: 0.8; --jp-search-toggle-on-opacity: 1; --jp-search-selected-match-background-color: rgb(255, 225, 0); --jp-search-selected-match-color: black; --jp-search-unselected-match-background-color: var( --jp-inverse-layout-color0 ); --jp-search-unselected-match-color: var(--jp-ui-inverse-font-color0); /* scrollbar related styles. Supports every browser except Edge. */ /* colors based on JetBrain's Darcula theme */ --jp-scrollbar-background-color: #3f4244; --jp-scrollbar-thumb-color: 88, 96, 97; /* need to specify thumb color as an RGB triplet */ --jp-scrollbar-endpad: 3px; /* the minimum gap between the thumb and the ends of a scrollbar */ /* hacks for setting the thumb shape. These do nothing in Firefox */ --jp-scrollbar-thumb-margin: 3.5px; /* the space in between the sides of the thumb and the track */ --jp-scrollbar-thumb-radius: 9px; /* set to a large-ish value for rounded endcaps on the thumb */ /* Icon colors that work well with light or dark backgrounds */ --jp-icon-contrast-color0: var(--md-purple-600); --jp-icon-contrast-color1: var(--md-green-600); --jp-icon-contrast-color2: var(--md-pink-600); --jp-icon-contrast-color3: var(--md-blue-600); } :root{--md-red-50: #ffebee;--md-red-100: #ffcdd2;--md-red-200: #ef9a9a;--md-red-300: #e57373;--md-red-400: #ef5350;--md-red-500: #f44336;--md-red-600: #e53935;--md-red-700: #d32f2f;--md-red-800: #c62828;--md-red-900: #b71c1c;--md-red-A100: #ff8a80;--md-red-A200: #ff5252;--md-red-A400: #ff1744;--md-red-A700: #d50000;--md-pink-50: #fce4ec;--md-pink-100: #f8bbd0;--md-pink-200: #f48fb1;--md-pink-300: #f06292;--md-pink-400: #ec407a;--md-pink-500: #e91e63;--md-pink-600: #d81b60;--md-pink-700: #c2185b;--md-pink-800: #ad1457;--md-pink-900: #880e4f;--md-pink-A100: #ff80ab;--md-pink-A200: #ff4081;--md-pink-A400: #f50057;--md-pink-A700: #c51162;--md-purple-50: #f3e5f5;--md-purple-100: #e1bee7;--md-purple-200: #ce93d8;--md-purple-300: #ba68c8;--md-purple-400: #ab47bc;--md-purple-500: #9c27b0;--md-purple-600: #8e24aa;--md-purple-700: #7b1fa2;--md-purple-800: #6a1b9a;--md-purple-900: #4a148c;--md-purple-A100: #ea80fc;--md-purple-A200: #e040fb;--md-purple-A400: #d500f9;--md-purple-A700: #aa00ff;--md-deep-purple-50: #ede7f6;--md-deep-purple-100: #d1c4e9;--md-deep-purple-200: #b39ddb;--md-deep-purple-300: #9575cd;--md-deep-purple-400: #7e57c2;--md-deep-purple-500: #673ab7;--md-deep-purple-600: #5e35b1;--md-deep-purple-700: #512da8;--md-deep-purple-800: #4527a0;--md-deep-purple-900: #311b92;--md-deep-purple-A100: #b388ff;--md-deep-purple-A200: #7c4dff;--md-deep-purple-A400: #651fff;--md-deep-purple-A700: #6200ea;--md-indigo-50: #e8eaf6;--md-indigo-100: #c5cae9;--md-indigo-200: #9fa8da;--md-indigo-300: 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sourceMappingURL=mkdocs-jupyter.css.map*/ init_mathjax = function() { if (window.MathJax) { // MathJax loaded MathJax.Hub.Config({ TeX: { equationNumbers: { autoNumber: \"AMS\", useLabelIds: true } }, tex2jax: { inlineMath: [ ['$','$'], [\"\\\\(\",\"\\\\)\"] ], displayMath: [ ['$$','$$'], [\"\\\\[\",\"\\\\]\"] ], processEscapes: true, processEnvironments: true }, displayAlign: 'center', CommonHTML: { linebreaks: { automatic: true } } }); MathJax.Hub.Queue([\"Typeset\", MathJax.Hub]); } } init_mathjax(); Raw data alignment This tutorial will cover the steps for performing the alignment of raw RNA- and HiFi-sequencing data. You will need to use the software IGV on your computer to visualize some of the output files, which can be easily downloaded once they are produced. At the end of this tutorial you will be able to: perform and discuss quality control on raw data in fastq format using FastQC and MultiQC align HiFi and RNA sequencing data with dedicated tools such as MiniMap2 and STAR analyze the quality the alignment with qualimap The output of this notebook will be used for the Variant calling analysis and the bulk RNA-sequencing analysis. If you do not want to run this notebook, you can alternatively use the free interactive tool Galaxy to perform the alignment steps. We have uploaded the data on Galaxy, and the manual to perform the exercise is found at the course webpage . The present tutorial, like the rest of the course material, is available at our open-source github repository . A few introductory points to run this notebook (click to show): To use this notebook, use the NGS (python) kernel that contains the packages. Choose it by selecting Kernel -> Change Kernel in the menu on top of the window. In this notebook you will use only bash commands as you would do in the command line (this is why you read %%bash at the beginning of each piece of code). Those commands can be replicated in the command line, but we thought of integrating them in a notebook to make the tutorial understandable. The bash commands can also be marked with an ! sign at the beginning of the line On some computers, you might see the result of the commands once they are done running. This means you will wait some time while the computer is crunching, and only afterwards you will see the result of the command you have executed You can run the code in each cell by clicking on the run cell button, or by pressing Shift + Enter . When the code is done running, a small green check sign will appear on the left side You need to run the cells in sequential order, please do not run a cell until the one above finished running and do not skip any cells Each cell contains a short description of the code and the output you should get. Please try not to focus on understanding the code for each command in too much detail, but rather try to focus on the output You can create new code cells by pressing + in the Menu bar above.
    Biological background \u00b6 White clover (Trifolium repens) is an allotetraploid. It is a relatively young, outcrossing species, which originated during the most recent glaciation around 20,000 years ago by hybridisation of two diploid species, T. occidentale and T. pallescens (see figure below). This means that it contains genomes originating from two different species within the same nucleus. Normally, white clover is an outbreeding species, but a self-compatible line was used for sequencing the white clover genome (Griffiths et al, 2019) . This line will be designated as S10 in the data, indicating that this is the 10th self-fertilized generation. In addition, we have data from a wild clover accession (ecotype) called Tienshan ( Ti ), which is collected from the Chinese mountains and is adapted to alpine conditions. We will perform alignment of the data to the white clover's reference genome containing both T. occidentale and T. pallescens (called contig 1 and contig 2 in the data). We will also perform alignment to each subgenome, and see which are the differences with the quality control tools. Quality control and mapping \u00b6 Quality Control \u00b6 We run FastQC on the PacBio Hifi reads and on two of the Illumina RNA-seq libraries. FastQC does quality control of the raw sequence data, providing an overview of the data which can help identify if there are any problems that should be addressed before further analysis. You can find the report for each file into the folder results/fastqc_output/ . The output is in HTML format and can be opened in any browser or in jupyterlab . It is however not easy to compare the various libraries by opening separate reports. To aggregate all the results, we apply the MultiQC software to the reports' folder. The output of MultiQC is in the directory results/multiqc_output/fastqc_data . In [1]: Copied! %% bash #run fastqc mkdir - p results / fastqc_output fastqc - q - o results / fastqc_output ../ Data / Clover_Data /*. fastq > / dev / null 2 >& 1 %%bash #run fastqc mkdir -p results/fastqc_output fastqc -q -o results/fastqc_output ../Data/Clover_Data/*.fastq > /dev/null 2>&1 Note: fastqc prints a lot of output conisting of a simple confirmation of execution without error, even when using the option -q , which means quiet . Therefore we added > /dev/null 2>&1 to the command to mute the printing of that output. In [2]: Copied! %% bash #run multiqc multiqc -- outdir results / multiqc_output / fastqc_data results / fastqc_output %%bash #run multiqc multiqc --outdir results/multiqc_output/fastqc_data results/fastqc_output / / / \u001b]8;id=903972;https://multiqc.info\u001b\\ MultiQC \u001b]8;;\u001b\\ \ud83d\udd0d | v1.14 | multiqc | Search path : /work/SamueleSoraggi/Notebooks/results/fastqc_output | searching | \u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501 100% 50/50 .html | fastqc | Found 25 reports | multiqc | Compressing plot data | multiqc | Report : results/multiqc_output/fastqc_data/multiqc_report.html | multiqc | Data : results/multiqc_output/fastqc_data/multiqc_data | multiqc | MultiQC complete Questions Visualize the Webpage generated by MultiQC. Hint: You can find a Help button that offers additional information about the plots for each panel. Focus on the following panels: \u201cPer base sequence quality\u201d, \u201cPer sequence quality scores\u201d.... (\u201cPer base sequence content\u201d always gives a FAIL for RNA-seq data). What do you notice with respect to the sequence quality scores? Are there any other quality issues worth noting? Hifi data mapping \u00b6 We map the PacBio Hifi reads ( Hifi_reads_white_clover.fastq ) to the white clover reference sequence (Contig1&2) using minimap2 . We run two mapping rounds, using two different preset options ( -x in the command) for the technology: PacBio/Oxford Nanopore read to reference mapping: map-pb Long assembly to reference mapping. Divergence is below 20%\u201d settings asm20 . Next, we create reports of the mapping results by running QualiMap on the two obtained SAM files. We first need to index the reference fasta files using samtools faidx . This produces files in .fai format containing informations about length of the reference sequence, offset for the quality scores, name of the reference sequence. Click here for a detailed overview. In [3]: Copied! %% bash #copy the reference data in the folder reference_data, so that you can write the indexing files mkdir - p reference_data cp ../ Data / Clover_Data / DNA_Contig1_2 . fasta ../ Data / Clover_Data / DNA_Contig1 . fasta ../ Data / Clover_Data / DNA_Contig2 . fasta reference_data %%bash #copy the reference data in the folder reference_data, so that you can write the indexing files mkdir -p reference_data cp ../Data/Clover_Data/DNA_Contig1_2.fasta ../Data/Clover_Data/DNA_Contig1.fasta ../Data/Clover_Data/DNA_Contig2.fasta reference_data In [4]: Copied! %% bash samtools faidx reference_data / DNA_Contig1_2 . fasta samtools faidx reference_data / DNA_Contig1 . fasta samtools faidx reference_data / DNA_Contig2 . fasta %%bash samtools faidx reference_data/DNA_Contig1_2.fasta samtools faidx reference_data/DNA_Contig1.fasta samtools faidx reference_data/DNA_Contig2.fasta we create an output folder for the HIFI alignment, and run minimap2 with the settings explained before. In [5]: Copied! %% bash mkdir - p results / HIFI_alignment / minimap2 - a - x map - pb - o results / HIFI_alignment / PacBio_clover_alignment_1_2_mappb . sam \\ reference_data / DNA_Contig1_2 . fasta \\ ../ Data / Clover_Data / Hifi_reads_white_clover . fastq minimap2 - a - x asm20 - o results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sam \\ reference_data / DNA_Contig1_2 . fasta \\ ../ Data / Clover_Data / Hifi_reads_white_clover . fastq %%bash mkdir -p results/HIFI_alignment/ minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sam \\ reference_data/DNA_Contig1_2.fasta \\ ../Data/Clover_Data/Hifi_reads_white_clover.fastq minimap2 -a -x asm20 -o results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sam \\ reference_data/DNA_Contig1_2.fasta \\ ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::mm_idx_gen::0.075*1.04] collected minimizers [M::mm_idx_gen::0.099*1.52] sorted minimizers [M::main::0.099*1.52] loaded/built the index for 2 target sequence(s) [M::mm_mapopt_update::0.114*1.45] mid_occ = 11 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 2 [M::mm_idx_stat::0.118*1.43] distinct minimizers: 203943 (79.05% are singletons); average occurrences: 1.273; average spacing: 8.047; total length: 2089554 [M::worker_pipeline::11.859*2.89] mapped 4395 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sam reference_data/DNA_Contig1_2.fasta ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::main] Real time: 11.873 sec; CPU: 34.246 sec; Peak RSS: 1.186 GB [M::mm_idx_gen::0.084*1.04] collected minimizers [M::mm_idx_gen::0.121*1.62] sorted minimizers [M::main::0.121*1.62] loaded/built the index for 2 target sequence(s) [M::mm_mapopt_update::0.138*1.54] mid_occ = 50 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 2 [M::mm_idx_stat::0.143*1.52] distinct minimizers: 298340 (78.21% are singletons); average occurrences: 1.277; average spacing: 5.484; total length: 2089554 [M::worker_pipeline::18.366*2.88] mapped 4395 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a -x asm20 -o results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sam reference_data/DNA_Contig1_2.fasta ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::main] Real time: 18.394 sec; CPU: 52.932 sec; Peak RSS: 1.692 GB samtools sort is used to sort the alignment with left-to-right coordinates. The output is in .bam format, with .sam files in input (Note that you could have gotten .bam files from minimap2 with a specific option). In [6]: Copied! %% bash samtools sort results / HIFI_alignment / PacBio_clover_alignment_1_2_mappb . sam \\ - o results / HIFI_alignment / PacBio_clover_alignment_1_2_mappb . sort . bam samtools sort results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sam \\ - o results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sort . bam %%bash samtools sort results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sam \\ -o results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sort.bam samtools sort results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sam \\ -o results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sort.bam samtools index creates the index for the bam file, stored in .bai format. The index file lets programs access any position into the aligned data without reading the whole file, which would take too much time. In [7]: Copied! %% bash samtools index results / HIFI_alignment / PacBio_clover_alignment_1_2_mappb . sort . bam samtools index results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sort . bam %%bash samtools index results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sort.bam samtools index results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sort.bam Run quality control on both files In [8]: Copied! %% bash qualimap bamqc - bam results / HIFI_alignment / PacBio_clover_alignment_1_2_mappb . sort . bam \\ - outdir results / qualimap_output / PacBio_clover_alignment_1_2_mappb qualimap bamqc - bam results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sort . bam \\ - outdir results / qualimap_output / PacBio_clover_alignment_1_2_asm20 %%bash qualimap bamqc -bam results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sort.bam \\ -outdir results/qualimap_output/PacBio_clover_alignment_1_2_mappb qualimap bamqc -bam results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sort.bam \\ -outdir results/qualimap_output/PacBio_clover_alignment_1_2_asm20 Java memory size is set to 1200M Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 1258 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 401 Chunk of reads size: 1000 Number of threads: 8 Processed 50 out of 401 windows... Processed 100 out of 401 windows... Processed 150 out of 401 windows... Processed 200 out of 401 windows... Processed 250 out of 401 windows... Processed 300 out of 401 windows... Processed 350 out of 401 windows... Processed 400 out of 401 windows... Total processed windows:401 Number of reads: 4395 Number of valid reads: 4696 Number of correct strand reads:0 Inside of regions... Num mapped reads: 4395 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 12 Computing descriptors... numberOfMappedBases: 70274383 referenceSize: 2089554 numberOfSequencedBases: 70039397 numberOfAs: 23621784 Computing per chromosome statistics... Computing histograms... Overall analysis time: 12 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished Java memory size is set to 1200M Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 1258 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 401 Chunk of reads size: 1000 Number of threads: 8 Processed 50 out of 401 windows... Processed 100 out of 401 windows... Processed 150 out of 401 windows... Processed 200 out of 401 windows... Processed 250 out of 401 windows... Processed 300 out of 401 windows... Processed 350 out of 401 windows... Processed 400 out of 401 windows... Total processed windows:401 Number of reads: 4395 Number of valid reads: 4747 Number of correct strand reads:0 Inside of regions... Num mapped reads: 4395 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 12 Computing descriptors... numberOfMappedBases: 69947563 referenceSize: 2089554 numberOfSequencedBases: 69812688 numberOfAs: 23541478 Computing per chromosome statistics... Computing histograms... Overall analysis time: 12 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished For easier comparison, we can again collapse the two reports into a single one using MultiQC , in the same way we did for putting together the other reports from fastQC . In [9]: Copied! %% bash #run multiqc multiqc -- outdir results / qualimap_output results / qualimap_output %%bash #run multiqc multiqc --outdir results/qualimap_output results/qualimap_output / / / \u001b]8;id=941002;https://multiqc.info\u001b\\ MultiQC \u001b]8;;\u001b\\ \ud83d\udd0d | v1.14 | multiqc | Search path : /work/SamueleSoraggi/Notebooks/results/qualimap_output | searching | \u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501 100% 93/93 nt.t\u2026 | qualimap | Found 2 BamQC reports | multiqc | Compressing plot data | multiqc | Report : results/qualimap_output/multiqc_report.html | multiqc | Data : results/qualimap_output/multiqc_data | multiqc | MultiQC complete Now you can visualize the report generated, which is in results/qualimap_output/multiqc_report.html . Next, we map the white clover PacBio Hifi reads to contig1 and contig2 separately, using the setting you selected at the previous step (let's say map-pb was chosen, but you are free to change this setting in the commands). As the two contigs represent the two white clover subgenomes, this mapping will allow you to see the two subgenome haplotypes and call subgenome SNPs. In [10]: Copied! %% bash minimap2 - a - x map - pb - o results / HIFI_alignment / PacBio_clover_alignment_1 . sam \\ reference_data / DNA_Contig1 . fasta \\ ../ Data / Clover_Data / Hifi_reads_white_clover . fastq %%bash minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_1.sam \\ reference_data/DNA_Contig1.fasta \\ ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::mm_idx_gen::0.050*0.96] collected minimizers [M::mm_idx_gen::0.071*1.55] sorted minimizers [M::main::0.071*1.55] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.079*1.50] mid_occ = 10 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 1 [M::mm_idx_stat::0.082*1.48] distinct minimizers: 112547 (91.45% are singletons); average occurrences: 1.141; average spacing: 8.031; total length: 1031631 [M::worker_pipeline::27.024*2.90] mapped 4395 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_1.sam reference_data/DNA_Contig1.fasta ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::main] Real time: 27.035 sec; CPU: 78.431 sec; Peak RSS: 2.258 GB In [11]: Copied! %% bash minimap2 - a - x map - pb - o results / HIFI_alignment / PacBio_clover_alignment_2 . sam \\ reference_data / DNA_Contig2 . fasta \\ ../ Data / Clover_Data / Hifi_reads_white_clover . fastq %%bash minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_2.sam \\ reference_data/DNA_Contig2.fasta \\ ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::mm_idx_gen::0.048*1.04] collected minimizers [M::mm_idx_gen::0.069*1.61] sorted minimizers [M::main::0.069*1.61] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.076*1.55] mid_occ = 10 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 1 [M::mm_idx_stat::0.080*1.53] distinct minimizers: 120722 (93.18% are singletons); average occurrences: 1.087; average spacing: 8.062; total length: 1057923 [M::worker_pipeline::27.150*2.94] mapped 4395 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_2.sam reference_data/DNA_Contig2.fasta ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::main] Real time: 27.162 sec; CPU: 79.819 sec; Peak RSS: 2.058 GB Sort the bam files and create their index using samtools In [12]: Copied! %% bash samtools sort results / HIFI_alignment / PacBio_clover_alignment_1 . sam - o results / HIFI_alignment / PacBio_clover_alignment_1 . sort . bam samtools sort results / HIFI_alignment / PacBio_clover_alignment_2 . sam - o results / HIFI_alignment / PacBio_clover_alignment_2 . sort . bam %%bash samtools sort results/HIFI_alignment/PacBio_clover_alignment_1.sam -o results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam samtools sort results/HIFI_alignment/PacBio_clover_alignment_2.sam -o results/HIFI_alignment/PacBio_clover_alignment_2.sort.bam In [13]: Copied! %% bash samtools index results / HIFI_alignment / PacBio_clover_alignment_1 . sort . bam samtools index results / HIFI_alignment / PacBio_clover_alignment_2 . sort . bam %%bash samtools index results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam samtools index results/HIFI_alignment/PacBio_clover_alignment_2.sort.bam Perform quality control In [14]: Copied! %% bash mkdir - p results / qualimap_output qualimap bamqc - bam results / HIFI_alignment / PacBio_clover_alignment_1 . sort . bam - outdir results / qualimap_output / PacBio_clover_alignment_1 %%bash mkdir -p results/qualimap_output qualimap bamqc -bam results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam -outdir results/qualimap_output/PacBio_clover_alignment_1 Java memory size is set to 1200M Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 1258 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 400 Chunk of reads size: 1000 Number of threads: 8 Processed 50 out of 400 windows... Processed 100 out of 400 windows... Processed 150 out of 400 windows... Processed 200 out of 400 windows... Processed 250 out of 400 windows... Processed 300 out of 400 windows... Processed 350 out of 400 windows... Processed 400 out of 400 windows... Total processed windows:400 Number of reads: 4395 Number of valid reads: 9070 Number of correct strand reads:0 Inside of regions... Num mapped reads: 4356 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 10 Computing descriptors... numberOfMappedBases: 59058058 referenceSize: 1031631 numberOfSequencedBases: 54917933 numberOfAs: 18508479 Computing per chromosome statistics... Computing histograms... Overall analysis time: 11 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished In [15]: Copied! %% bash qualimap bamqc - bam results / HIFI_alignment / PacBio_clover_alignment_2 . sort . bam - outdir results / qualimap_output / PacBio_clover_alignment_2 %%bash qualimap bamqc -bam results/HIFI_alignment/PacBio_clover_alignment_2.sort.bam -outdir results/qualimap_output/PacBio_clover_alignment_2 Java memory size is set to 1200M Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 1258 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 400 Chunk of reads size: 1000 Number of threads: 8 Processed 50 out of 400 windows... Processed 100 out of 400 windows... Processed 150 out of 400 windows... Processed 200 out of 400 windows... Processed 250 out of 400 windows... Processed 300 out of 400 windows... Processed 350 out of 400 windows... Processed 400 out of 400 windows... Total processed windows:400 Number of reads: 4395 Number of valid reads: 9462 Number of correct strand reads:0 Inside of regions... Num mapped reads: 4394 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 13 Computing descriptors... numberOfMappedBases: 59388453 referenceSize: 1057923 numberOfSequencedBases: 55867300 numberOfAs: 18822184 Computing per chromosome statistics... Computing histograms... Overall analysis time: 13 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished In [16]: Copied! %% bash #run multiqc multiqc -- outdir results / qualimap_output results / qualimap_output %%bash #run multiqc multiqc --outdir results/qualimap_output results/qualimap_output / / / \u001b]8;id=999624;https://multiqc.info\u001b\\ MultiQC \u001b]8;;\u001b\\ \ud83d\udd0d | v1.14 | multiqc | Search path : /work/SamueleSoraggi/Notebooks/results/qualimap_output | searching | \u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501 100% 187/187 .t\u2026 | qualimap | Found 4 BamQC reports | multiqc | Compressing plot data | multiqc | Previous MultiQC output found! Adjusting filenames.. | multiqc | Use -f or --force to overwrite existing reports instead | multiqc | Report : results/qualimap_output/multiqc_report_1.html | multiqc | Data : results/qualimap_output/multiqc_data_1 | multiqc | MultiQC complete Task: IGV visualization and Questions Now you can inspect the alignment files in IGV . First, you will need to download the reference fasta sequence in ../Data/Clover_Data/DNA_Contig1_2.fasta and import it into IGV. You can do the same for the files DNA_Contig1.fasta and DNA_Contig2.fasta that you might need later. In IGV, this is done with the menu Genomes --> Load Genome from file menu and by selecting the relevant fasta file. Then, choose the reference you need from the drop-down menu (see figure below). You will not yet see much, but you can choose one of the two subgenomes (contig 1 or 2) and double click on a chromosome position to inspect the reference sequence. The next step will visualize the mapped files on IGV. Each mapped genome can be seen in IGV against the reference file of choice. To load an aligned file, first download it together with the index file in .bai format. For example, you need to download both results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam and results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam.bai to see this alignment (you need to open only the .bam file with IGV). If you open more files, their alignments will be distributed in the IGV interface, and you can change the size of each visualization yourself (below shown with only one opened alignment). Now compare in IGV the two bam files PacBio_clover_alignment_1.sort.bam and PacBio_clover_alignment_2.sort.bam . What do you observe when comparing the two BAM files? Have a look at the polymorphic regions in IGV. Are they true polymorphisms? Add to the visualization the third alignment PacBio_clover_alignment_1_2_mappb.sort.bam in IGV. Why do you see fluctuations in coverage and large regions without any apparent subgenome SNPs? What are the major differences between the stats for the reads mapped to Contigs1&2 versus contig1 and contig2? What is your interpretation of the differences? RNA-seq mapping \u00b6 In the ../Data folder you will find 24 RNA-seq libraries, 12 S10 libraries and 12 Tienshan libraries. Each library is paired-end, which is denoted by R1 and R2 at the end of two files having the same name, such as S10_1_1.R1.fastq and S10_1_1.R2.fastq . We will align each library separately and then merge the alignments to create two final samples for S10 and Tienshan . First, we need to create a genome file for the reference fasta file of contigs 1 and 2 . This is done with STAR , using the option --runMode genomeGenerate . We also need to convert the gene annotation from gff to gtf format with gffread to allow counting gene transcripts. STAR is a very complex tool with many options, so it is always useful to have a reference manual . In [17]: Copied! %% bash gffread - T - o reference_data / white_clover_genes . gtf ../ Data / Clover_Data / white_clover_genes . gff %%bash gffread -T -o reference_data/white_clover_genes.gtf ../Data/Clover_Data/white_clover_genes.gff In [18]: Copied! %% bash STAR -- runThreadN 8 \\ -- runMode genomeGenerate \\ -- genomeDir results / STAR_output / indexing_contigs_1_2 \\ -- genomeFastaFiles reference_data / DNA_Contig1_2 . fasta \\ -- sjdbGTFfile reference_data / white_clover_genes . gtf %%bash STAR --runThreadN 8 \\ --runMode genomeGenerate \\ --genomeDir results/STAR_output/indexing_contigs_1_2 \\ --genomeFastaFiles reference_data/DNA_Contig1_2.fasta \\ --sjdbGTFfile reference_data/white_clover_genes.gtf STAR --runThreadN 8 --runMode genomeGenerate --genomeDir results/STAR_output/indexing_contigs_1_2 --genomeFastaFiles reference_data/DNA_Contig1_2.fasta --sjdbGTFfile reference_data/white_clover_genes.gtf STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:23:03 ..... started STAR run Jun 19 10:23:03 ... starting to generate Genome files Jun 19 10:23:03 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 14 is too large for the genome size=2089554, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 9 Jun 19 10:23:03 ... starting to sort Suffix Array. This may take a long time... Jun 19 10:23:03 ... sorting Suffix Array chunks and saving them to disk... Jun 19 10:23:04 ... loading chunks from disk, packing SA... Jun 19 10:23:04 ... finished generating suffix array Jun 19 10:23:04 ... generating Suffix Array index Jun 19 10:23:08 ... completed Suffix Array index Jun 19 10:23:08 ..... inserting junctions into the genome indices Jun 19 10:23:16 ... writing Genome to disk ... Jun 19 10:23:16 ... writing Suffix Array to disk ... Jun 19 10:23:17 ... writing SAindex to disk Jun 19 10:23:18 ..... finished successfully We got a warning saying !!!!! WARNING: --genomeSAindexNbases 14 is too large for the genome size=2089554, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 9 meaning we need shorter strings of bases (9 bases instead of 14) to be indexed, as our reference genome is very short, and too long strings would cause many alignment errors. So we rerun the command with the suggested option. In [19]: Copied! %% bash STAR -- runThreadN 8 \\ -- runMode genomeGenerate \\ -- genomeDir results / STAR_output / indexing_contigs_1_2 \\ -- genomeFastaFiles reference_data / DNA_Contig1_2 . fasta \\ -- sjdbGTFfile reference_data / white_clover_genes . gtf \\ -- genomeSAindexNbases 9 %%bash STAR --runThreadN 8 \\ --runMode genomeGenerate \\ --genomeDir results/STAR_output/indexing_contigs_1_2 \\ --genomeFastaFiles reference_data/DNA_Contig1_2.fasta \\ --sjdbGTFfile reference_data/white_clover_genes.gtf \\ --genomeSAindexNbases 9 STAR --runThreadN 8 --runMode genomeGenerate --genomeDir results/STAR_output/indexing_contigs_1_2 --genomeFastaFiles reference_data/DNA_Contig1_2.fasta --sjdbGTFfile reference_data/white_clover_genes.gtf --genomeSAindexNbases 9 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:23:18 ..... started STAR run Jun 19 10:23:18 ... starting to generate Genome files Jun 19 10:23:18 ..... processing annotations GTF Jun 19 10:23:20 ... starting to sort Suffix Array. This may take a long time... Jun 19 10:23:20 ... sorting Suffix Array chunks and saving them to disk... Jun 19 10:23:21 ... loading chunks from disk, packing SA... Jun 19 10:23:21 ... finished generating suffix array Jun 19 10:23:21 ... generating Suffix Array index Jun 19 10:23:21 ... completed Suffix Array index Jun 19 10:23:22 ..... inserting junctions into the genome indices Jun 19 10:23:23 ... writing Genome to disk ... Jun 19 10:23:23 ... writing Suffix Array to disk ... Jun 19 10:23:23 ... writing SAindex to disk Jun 19 10:23:24 ..... finished successfully We use again STAR to align every single library for S10 . We extract the library name of each file and run STAR through each pair of files. Note that plant introns are very rarely more than 5000 bp and that you are mapping to two homoeologous contigs that show high similarity, especially in genic regions. We set the maximum size to 5000 using --alignIntronMax 5000 . In [20]: Copied! %% bash for i in ` ls ../ Data / Clover_Data / S10 *. R1 . fastq ` do PREFIXNAME = ` basename $ i . R1 . fastq ` echo \"###############################################\" echo \"##### ALIGNING PAIRED-END READS \" $ PREFIXNAME echo \"###############################################\" STAR -- genomeDir results / STAR_output / indexing_contigs_1_2 / \\ -- runThreadN 8 \\ -- runMode alignReads \\ -- readFilesIn ../ Data / Clover_Data / $ PREFIXNAME . R1 . fastq ../ Data / Clover_Data / $ PREFIXNAME . R2 . fastq \\ -- outFileNamePrefix results / STAR_output / S10_align_contigs_1_2 / $ PREFIXNAME \\ -- outSAMtype BAM SortedByCoordinate \\ -- outSAMattributes Standard \\ -- quantMode GeneCounts \\ -- alignIntronMax 5000 done %%bash for i in `ls ../Data/Clover_Data/S10*.R1.fastq` do PREFIXNAME=`basename $i .R1.fastq` echo \"###############################################\" echo \"##### ALIGNING PAIRED-END READS \"$PREFIXNAME echo \"###############################################\" STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ \\ --runThreadN 8 \\ --runMode alignReads \\ --readFilesIn ../Data/Clover_Data/$PREFIXNAME.R1.fastq ../Data/Clover_Data/$PREFIXNAME.R2.fastq \\ --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/$PREFIXNAME \\ --outSAMtype BAM SortedByCoordinate \\ --outSAMattributes Standard \\ --quantMode GeneCounts \\ --alignIntronMax 5000 done ############################################### ##### ALIGNING PAIRED-END READS S10_1_1 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_1_1.R1.fastq ../Data/Clover_Data/S10_1_1.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_1_1 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:23:24 ..... started STAR run Jun 19 10:23:24 ..... loading genome Jun 19 10:23:24 ..... started mapping Jun 19 10:23:35 ..... finished mapping Jun 19 10:23:35 ..... started sorting BAM Jun 19 10:23:37 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS S10_1_2 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_1_2.R1.fastq ../Data/Clover_Data/S10_1_2.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_1_2 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:23:38 ..... started STAR run Jun 19 10:23:38 ..... loading genome Jun 19 10:23:38 ..... started mapping Jun 19 10:23:48 ..... finished mapping Jun 19 10:23:48 ..... started sorting BAM Jun 19 10:23:51 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS S10_1_3 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_1_3.R1.fastq ../Data/Clover_Data/S10_1_3.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_1_3 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:23:52 ..... started STAR run Jun 19 10:23:52 ..... loading genome Jun 19 10:23:52 ..... started mapping Jun 19 10:24:03 ..... finished mapping Jun 19 10:24:03 ..... started sorting BAM Jun 19 10:24:06 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS S10_2_1 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_2_1.R1.fastq ../Data/Clover_Data/S10_2_1.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_2_1 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:24:06 ..... started STAR run Jun 19 10:24:06 ..... loading genome Jun 19 10:24:06 ..... started mapping Jun 19 10:24:16 ..... finished mapping Jun 19 10:24:16 ..... started sorting BAM Jun 19 10:24:18 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS S10_2_2 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_2_2.R1.fastq ../Data/Clover_Data/S10_2_2.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_2_2 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:24:20 ..... started STAR run Jun 19 10:24:20 ..... loading genome Jun 19 10:24:20 ..... started mapping Jun 19 10:24:31 ..... finished mapping Jun 19 10:24:31 ..... started sorting BAM Jun 19 10:24:33 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS S10_2_3 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_2_3.R1.fastq ../Data/Clover_Data/S10_2_3.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_2_3 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:24:33 ..... started STAR run Jun 19 10:24:33 ..... loading genome Jun 19 10:24:33 ..... started mapping Jun 19 10:24:45 ..... finished mapping Jun 19 10:24:45 ..... started sorting BAM Jun 19 10:24:48 ..... finished successfully Do the same alignment for Tienshan libraries In [21]: Copied! %% bash for i in ` ls ../ Data / Clover_Data / TI *. R1 . fastq ` do PREFIXNAME = ` basename $ i . R1 . fastq ` echo \"###############################################\" echo \"##### ALIGNING PAIRED-END READS \" $ PREFIXNAME echo \"###############################################\" STAR -- genomeDir results / STAR_output / indexing_contigs_1_2 / \\ -- runThreadN 8 \\ -- readFilesIn ../ Data / Clover_Data / $ PREFIXNAME . R1 . fastq ../ Data / Clover_Data / $ PREFIXNAME . R2 . fastq \\ -- outFileNamePrefix results / STAR_output / TI_align_contigs_1_2 / $ PREFIXNAME \\ -- outSAMtype BAM SortedByCoordinate \\ -- outSAMattributes Standard \\ -- quantMode GeneCounts \\ -- alignIntronMax 5000 done %%bash for i in `ls ../Data/Clover_Data/TI*.R1.fastq` do PREFIXNAME=`basename $i .R1.fastq` echo \"###############################################\" echo \"##### ALIGNING PAIRED-END READS \"$PREFIXNAME echo \"###############################################\" STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ \\ --runThreadN 8 \\ --readFilesIn ../Data/Clover_Data/$PREFIXNAME.R1.fastq ../Data/Clover_Data/$PREFIXNAME.R2.fastq \\ --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/$PREFIXNAME \\ --outSAMtype BAM SortedByCoordinate \\ --outSAMattributes Standard \\ --quantMode GeneCounts \\ --alignIntronMax 5000 done ############################################### ##### ALIGNING PAIRED-END READS TI_1_1 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_1_1.R1.fastq ../Data/Clover_Data/TI_1_1.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_1_1 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:24:50 ..... started STAR run Jun 19 10:24:50 ..... loading genome Jun 19 10:24:50 ..... started mapping Jun 19 10:25:03 ..... finished mapping Jun 19 10:25:04 ..... started sorting BAM Jun 19 10:25:18 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS TI_1_2 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_1_2.R1.fastq ../Data/Clover_Data/TI_1_2.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_1_2 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:25:18 ..... started STAR run Jun 19 10:25:18 ..... loading genome Jun 19 10:25:18 ..... started mapping Jun 19 10:25:30 ..... finished mapping Jun 19 10:25:30 ..... started sorting BAM Jun 19 10:25:33 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS TI_1_3 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_1_3.R1.fastq ../Data/Clover_Data/TI_1_3.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_1_3 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:25:36 ..... started STAR run Jun 19 10:25:36 ..... loading genome Jun 19 10:25:36 ..... started mapping Jun 19 10:25:50 ..... finished mapping Jun 19 10:25:50 ..... started sorting BAM Jun 19 10:25:51 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS TI_2_1 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_2_1.R1.fastq ../Data/Clover_Data/TI_2_1.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_2_1 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:25:51 ..... started STAR run Jun 19 10:25:51 ..... loading genome Jun 19 10:25:52 ..... started mapping Jun 19 10:26:06 ..... finished mapping Jun 19 10:26:06 ..... started sorting BAM Jun 19 10:26:09 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS TI_2_2 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_2_2.R1.fastq ../Data/Clover_Data/TI_2_2.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_2_2 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:26:09 ..... started STAR run Jun 19 10:26:09 ..... loading genome Jun 19 10:26:09 ..... started mapping Jun 19 10:26:23 ..... finished mapping Jun 19 10:26:23 ..... started sorting BAM Jun 19 10:26:31 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS TI_2_3 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_2_3.R1.fastq ../Data/Clover_Data/TI_2_3.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_2_3 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:26:31 ..... started STAR run Jun 19 10:26:31 ..... loading genome Jun 19 10:26:31 ..... started mapping Jun 19 10:26:46 ..... finished mapping Jun 19 10:26:46 ..... started sorting BAM Jun 19 10:26:49 ..... finished successfully Run quality control on each aligned library with MultiQC . In this way there will be a whole report to compare S10 files and Tienshan files. In [22]: Copied! %% bash multiqc -- outdir results / multiqc_output / TI_STAR_align_1_2 \\ results / STAR_output / TI_align_contigs_1_2 / %%bash multiqc --outdir results/multiqc_output/TI_STAR_align_1_2 \\ results/STAR_output/TI_align_contigs_1_2/ / / / \u001b]8;id=121575;https://multiqc.info\u001b\\ MultiQC \u001b]8;;\u001b\\ \ud83d\udd0d | v1.14 | multiqc | Search path : /work/SamueleSoraggi/Notebooks/results/STAR_output/TI_align_contigs_1_2 | searching | \u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501 100% 36/36 og.o\u2026 | star | Found 6 reports and 6 gene count files | multiqc | Compressing plot data | multiqc | Report : results/multiqc_output/TI_STAR_align_1_2/multiqc_report.html | multiqc | Data : results/multiqc_output/TI_STAR_align_1_2/multiqc_data | multiqc | MultiQC complete In [23]: Copied! %% bash multiqc -- outdir results / multiqc_output / S10_STAR_align_1_2 \\ results / STAR_output / S10_align_contigs_1_2 / %%bash multiqc --outdir results/multiqc_output/S10_STAR_align_1_2 \\ results/STAR_output/S10_align_contigs_1_2/ / / / \u001b]8;id=596946;https://multiqc.info\u001b\\ MultiQC \u001b]8;;\u001b\\ \ud83d\udd0d | v1.14 | multiqc | Search path : /work/SamueleSoraggi/Notebooks/results/STAR_output/S10_align_contigs_1_2 | searching | \u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501 100% 36/36 ut.t\u2026 | star | Found 6 reports and 6 gene count files | multiqc | Compressing plot data | multiqc | Report : results/multiqc_output/S10_STAR_align_1_2/multiqc_report.html | multiqc | Data : results/multiqc_output/S10_STAR_align_1_2/multiqc_data | multiqc | MultiQC complete We merge the outputs of each group of aligned libraries. Here is how the files look like for the Tienshan . In [24]: Copied! ! ls - lh results / STAR_output / TI_align_contigs_1_2 / TI_ *. sortedByCoord . out . bam !ls -lh results/STAR_output/TI_align_contigs_1_2/TI_*.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 6.6M Jun 19 10:25 results/STAR_output/TI_align_contigs_1_2/TI_1_1Aligned.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 6.0M Jun 19 10:25 results/STAR_output/TI_align_contigs_1_2/TI_1_2Aligned.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 7.1M Jun 19 10:25 results/STAR_output/TI_align_contigs_1_2/TI_1_3Aligned.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 9.6M Jun 19 10:26 results/STAR_output/TI_align_contigs_1_2/TI_2_1Aligned.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 7.2M Jun 19 10:26 results/STAR_output/TI_align_contigs_1_2/TI_2_2Aligned.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 8.2M Jun 19 10:26 results/STAR_output/TI_align_contigs_1_2/TI_2_3Aligned.sortedByCoord.out.bam Apply samtools merge In [25]: Copied! %% bash mkdir - p results / STAR_output / TI_align_contigs_1_2_merge / samtools merge - f results / STAR_output / TI_align_contigs_1_2_merge / TI . sorted . bam results / STAR_output / TI_align_contigs_1_2 / TI_ *. sortedByCoord . out . bam %%bash mkdir -p results/STAR_output/TI_align_contigs_1_2_merge/ samtools merge -f results/STAR_output/TI_align_contigs_1_2_merge/TI.sorted.bam results/STAR_output/TI_align_contigs_1_2/TI_*.sortedByCoord.out.bam In [26]: Copied! %% bash mkdir - p results / STAR_output / S10_align_contigs_1_2_merge / samtools merge - f results / STAR_output / S10_align_contigs_1_2_merge / S10 . sorted . bam results / STAR_output / S10_align_contigs_1_2 / S10_ *. sortedByCoord . out . bam %%bash mkdir -p results/STAR_output/S10_align_contigs_1_2_merge/ samtools merge -f results/STAR_output/S10_align_contigs_1_2_merge/S10.sorted.bam results/STAR_output/S10_align_contigs_1_2/S10_*.sortedByCoord.out.bam Index both merging outputs. A file in format bam.bai will appear in their respective folders. In [27]: Copied! %% bash samtools index results / STAR_output / S10_align_contigs_1_2_merge / S10 . sorted . bam %%bash samtools index results/STAR_output/S10_align_contigs_1_2_merge/S10.sorted.bam In [28]: Copied! %% bash samtools index results / STAR_output / TI_align_contigs_1_2_merge / TI . sorted . bam %%bash samtools index results/STAR_output/TI_align_contigs_1_2_merge/TI.sorted.bam Wrapping up \ud83c\udf89 \ud83c\udf89 \ud83c\udf89 \u00b6 In this exercise, you learnt to align various types of data after performing quality control for raw data. We looked at some of the options for the aligners and at how to use some of the basic samtools manipulation programs. The outputs from the RNA alignments will be used for the VCF file analysis in the next notebook, and the RNA alignments will be use for the bulk RNA data analysis.","title":"3.1.Alignment of raw data"},{"location":"nb/align.html#biological-background","text":"White clover (Trifolium repens) is an allotetraploid. It is a relatively young, outcrossing species, which originated during the most recent glaciation around 20,000 years ago by hybridisation of two diploid species, T. occidentale and T. pallescens (see figure below). This means that it contains genomes originating from two different species within the same nucleus. Normally, white clover is an outbreeding species, but a self-compatible line was used for sequencing the white clover genome (Griffiths et al, 2019) . This line will be designated as S10 in the data, indicating that this is the 10th self-fertilized generation. In addition, we have data from a wild clover accession (ecotype) called Tienshan ( Ti ), which is collected from the Chinese mountains and is adapted to alpine conditions. We will perform alignment of the data to the white clover's reference genome containing both T. occidentale and T. pallescens (called contig 1 and contig 2 in the data). We will also perform alignment to each subgenome, and see which are the differences with the quality control tools.","title":"Biological background"},{"location":"nb/align.html#quality-control-and-mapping","text":"","title":"Quality control and mapping"},{"location":"nb/align.html#quality-control","text":"We run FastQC on the PacBio Hifi reads and on two of the Illumina RNA-seq libraries. FastQC does quality control of the raw sequence data, providing an overview of the data which can help identify if there are any problems that should be addressed before further analysis. You can find the report for each file into the folder results/fastqc_output/ . The output is in HTML format and can be opened in any browser or in jupyterlab . It is however not easy to compare the various libraries by opening separate reports. To aggregate all the results, we apply the MultiQC software to the reports' folder. The output of MultiQC is in the directory results/multiqc_output/fastqc_data . In [1]: Copied! %% bash #run fastqc mkdir - p results / fastqc_output fastqc - q - o results / fastqc_output ../ Data / Clover_Data /*. fastq > / dev / null 2 >& 1 %%bash #run fastqc mkdir -p results/fastqc_output fastqc -q -o results/fastqc_output ../Data/Clover_Data/*.fastq > /dev/null 2>&1 Note: fastqc prints a lot of output conisting of a simple confirmation of execution without error, even when using the option -q , which means quiet . Therefore we added > /dev/null 2>&1 to the command to mute the printing of that output. In [2]: Copied! %% bash #run multiqc multiqc -- outdir results / multiqc_output / fastqc_data results / fastqc_output %%bash #run multiqc multiqc --outdir results/multiqc_output/fastqc_data results/fastqc_output / / / \u001b]8;id=903972;https://multiqc.info\u001b\\ MultiQC \u001b]8;;\u001b\\ \ud83d\udd0d | v1.14 | multiqc | Search path : /work/SamueleSoraggi/Notebooks/results/fastqc_output | searching | \u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501 100% 50/50 .html | fastqc | Found 25 reports | multiqc | Compressing plot data | multiqc | Report : results/multiqc_output/fastqc_data/multiqc_report.html | multiqc | Data : results/multiqc_output/fastqc_data/multiqc_data | multiqc | MultiQC complete Questions Visualize the Webpage generated by MultiQC. Hint: You can find a Help button that offers additional information about the plots for each panel. Focus on the following panels: \u201cPer base sequence quality\u201d, \u201cPer sequence quality scores\u201d.... (\u201cPer base sequence content\u201d always gives a FAIL for RNA-seq data). What do you notice with respect to the sequence quality scores? Are there any other quality issues worth noting?","title":"Quality Control"},{"location":"nb/align.html#hifi-data-mapping","text":"We map the PacBio Hifi reads ( Hifi_reads_white_clover.fastq ) to the white clover reference sequence (Contig1&2) using minimap2 . We run two mapping rounds, using two different preset options ( -x in the command) for the technology: PacBio/Oxford Nanopore read to reference mapping: map-pb Long assembly to reference mapping. Divergence is below 20%\u201d settings asm20 . Next, we create reports of the mapping results by running QualiMap on the two obtained SAM files. We first need to index the reference fasta files using samtools faidx . This produces files in .fai format containing informations about length of the reference sequence, offset for the quality scores, name of the reference sequence. Click here for a detailed overview. In [3]: Copied! %% bash #copy the reference data in the folder reference_data, so that you can write the indexing files mkdir - p reference_data cp ../ Data / Clover_Data / DNA_Contig1_2 . fasta ../ Data / Clover_Data / DNA_Contig1 . fasta ../ Data / Clover_Data / DNA_Contig2 . fasta reference_data %%bash #copy the reference data in the folder reference_data, so that you can write the indexing files mkdir -p reference_data cp ../Data/Clover_Data/DNA_Contig1_2.fasta ../Data/Clover_Data/DNA_Contig1.fasta ../Data/Clover_Data/DNA_Contig2.fasta reference_data In [4]: Copied! %% bash samtools faidx reference_data / DNA_Contig1_2 . fasta samtools faidx reference_data / DNA_Contig1 . fasta samtools faidx reference_data / DNA_Contig2 . fasta %%bash samtools faidx reference_data/DNA_Contig1_2.fasta samtools faidx reference_data/DNA_Contig1.fasta samtools faidx reference_data/DNA_Contig2.fasta we create an output folder for the HIFI alignment, and run minimap2 with the settings explained before. In [5]: Copied! %% bash mkdir - p results / HIFI_alignment / minimap2 - a - x map - pb - o results / HIFI_alignment / PacBio_clover_alignment_1_2_mappb . sam \\ reference_data / DNA_Contig1_2 . fasta \\ ../ Data / Clover_Data / Hifi_reads_white_clover . fastq minimap2 - a - x asm20 - o results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sam \\ reference_data / DNA_Contig1_2 . fasta \\ ../ Data / Clover_Data / Hifi_reads_white_clover . fastq %%bash mkdir -p results/HIFI_alignment/ minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sam \\ reference_data/DNA_Contig1_2.fasta \\ ../Data/Clover_Data/Hifi_reads_white_clover.fastq minimap2 -a -x asm20 -o results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sam \\ reference_data/DNA_Contig1_2.fasta \\ ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::mm_idx_gen::0.075*1.04] collected minimizers [M::mm_idx_gen::0.099*1.52] sorted minimizers [M::main::0.099*1.52] loaded/built the index for 2 target sequence(s) [M::mm_mapopt_update::0.114*1.45] mid_occ = 11 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 2 [M::mm_idx_stat::0.118*1.43] distinct minimizers: 203943 (79.05% are singletons); average occurrences: 1.273; average spacing: 8.047; total length: 2089554 [M::worker_pipeline::11.859*2.89] mapped 4395 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sam reference_data/DNA_Contig1_2.fasta ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::main] Real time: 11.873 sec; CPU: 34.246 sec; Peak RSS: 1.186 GB [M::mm_idx_gen::0.084*1.04] collected minimizers [M::mm_idx_gen::0.121*1.62] sorted minimizers [M::main::0.121*1.62] loaded/built the index for 2 target sequence(s) [M::mm_mapopt_update::0.138*1.54] mid_occ = 50 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 0; #seq: 2 [M::mm_idx_stat::0.143*1.52] distinct minimizers: 298340 (78.21% are singletons); average occurrences: 1.277; average spacing: 5.484; total length: 2089554 [M::worker_pipeline::18.366*2.88] mapped 4395 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a -x asm20 -o results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sam reference_data/DNA_Contig1_2.fasta ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::main] Real time: 18.394 sec; CPU: 52.932 sec; Peak RSS: 1.692 GB samtools sort is used to sort the alignment with left-to-right coordinates. The output is in .bam format, with .sam files in input (Note that you could have gotten .bam files from minimap2 with a specific option). In [6]: Copied! %% bash samtools sort results / HIFI_alignment / PacBio_clover_alignment_1_2_mappb . sam \\ - o results / HIFI_alignment / PacBio_clover_alignment_1_2_mappb . sort . bam samtools sort results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sam \\ - o results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sort . bam %%bash samtools sort results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sam \\ -o results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sort.bam samtools sort results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sam \\ -o results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sort.bam samtools index creates the index for the bam file, stored in .bai format. The index file lets programs access any position into the aligned data without reading the whole file, which would take too much time. In [7]: Copied! %% bash samtools index results / HIFI_alignment / PacBio_clover_alignment_1_2_mappb . sort . bam samtools index results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sort . bam %%bash samtools index results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sort.bam samtools index results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sort.bam Run quality control on both files In [8]: Copied! %% bash qualimap bamqc - bam results / HIFI_alignment / PacBio_clover_alignment_1_2_mappb . sort . bam \\ - outdir results / qualimap_output / PacBio_clover_alignment_1_2_mappb qualimap bamqc - bam results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sort . bam \\ - outdir results / qualimap_output / PacBio_clover_alignment_1_2_asm20 %%bash qualimap bamqc -bam results/HIFI_alignment/PacBio_clover_alignment_1_2_mappb.sort.bam \\ -outdir results/qualimap_output/PacBio_clover_alignment_1_2_mappb qualimap bamqc -bam results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sort.bam \\ -outdir results/qualimap_output/PacBio_clover_alignment_1_2_asm20 Java memory size is set to 1200M Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 1258 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 401 Chunk of reads size: 1000 Number of threads: 8 Processed 50 out of 401 windows... Processed 100 out of 401 windows... Processed 150 out of 401 windows... Processed 200 out of 401 windows... Processed 250 out of 401 windows... Processed 300 out of 401 windows... Processed 350 out of 401 windows... Processed 400 out of 401 windows... Total processed windows:401 Number of reads: 4395 Number of valid reads: 4696 Number of correct strand reads:0 Inside of regions... Num mapped reads: 4395 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 12 Computing descriptors... numberOfMappedBases: 70274383 referenceSize: 2089554 numberOfSequencedBases: 70039397 numberOfAs: 23621784 Computing per chromosome statistics... Computing histograms... Overall analysis time: 12 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished Java memory size is set to 1200M Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 1258 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 401 Chunk of reads size: 1000 Number of threads: 8 Processed 50 out of 401 windows... Processed 100 out of 401 windows... Processed 150 out of 401 windows... Processed 200 out of 401 windows... Processed 250 out of 401 windows... Processed 300 out of 401 windows... Processed 350 out of 401 windows... Processed 400 out of 401 windows... Total processed windows:401 Number of reads: 4395 Number of valid reads: 4747 Number of correct strand reads:0 Inside of regions... Num mapped reads: 4395 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 12 Computing descriptors... numberOfMappedBases: 69947563 referenceSize: 2089554 numberOfSequencedBases: 69812688 numberOfAs: 23541478 Computing per chromosome statistics... Computing histograms... Overall analysis time: 12 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished For easier comparison, we can again collapse the two reports into a single one using MultiQC , in the same way we did for putting together the other reports from fastQC . In [9]: Copied! %% bash #run multiqc multiqc -- outdir results / qualimap_output results / qualimap_output %%bash #run multiqc multiqc --outdir results/qualimap_output results/qualimap_output / / / \u001b]8;id=941002;https://multiqc.info\u001b\\ MultiQC \u001b]8;;\u001b\\ \ud83d\udd0d | v1.14 | multiqc | Search path : /work/SamueleSoraggi/Notebooks/results/qualimap_output | searching | \u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501 100% 93/93 nt.t\u2026 | qualimap | Found 2 BamQC reports | multiqc | Compressing plot data | multiqc | Report : results/qualimap_output/multiqc_report.html | multiqc | Data : results/qualimap_output/multiqc_data | multiqc | MultiQC complete Now you can visualize the report generated, which is in results/qualimap_output/multiqc_report.html . Next, we map the white clover PacBio Hifi reads to contig1 and contig2 separately, using the setting you selected at the previous step (let's say map-pb was chosen, but you are free to change this setting in the commands). As the two contigs represent the two white clover subgenomes, this mapping will allow you to see the two subgenome haplotypes and call subgenome SNPs. In [10]: Copied! %% bash minimap2 - a - x map - pb - o results / HIFI_alignment / PacBio_clover_alignment_1 . sam \\ reference_data / DNA_Contig1 . fasta \\ ../ Data / Clover_Data / Hifi_reads_white_clover . fastq %%bash minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_1.sam \\ reference_data/DNA_Contig1.fasta \\ ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::mm_idx_gen::0.050*0.96] collected minimizers [M::mm_idx_gen::0.071*1.55] sorted minimizers [M::main::0.071*1.55] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.079*1.50] mid_occ = 10 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 1 [M::mm_idx_stat::0.082*1.48] distinct minimizers: 112547 (91.45% are singletons); average occurrences: 1.141; average spacing: 8.031; total length: 1031631 [M::worker_pipeline::27.024*2.90] mapped 4395 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_1.sam reference_data/DNA_Contig1.fasta ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::main] Real time: 27.035 sec; CPU: 78.431 sec; Peak RSS: 2.258 GB In [11]: Copied! %% bash minimap2 - a - x map - pb - o results / HIFI_alignment / PacBio_clover_alignment_2 . sam \\ reference_data / DNA_Contig2 . fasta \\ ../ Data / Clover_Data / Hifi_reads_white_clover . fastq %%bash minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_2.sam \\ reference_data/DNA_Contig2.fasta \\ ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::mm_idx_gen::0.048*1.04] collected minimizers [M::mm_idx_gen::0.069*1.61] sorted minimizers [M::main::0.069*1.61] loaded/built the index for 1 target sequence(s) [M::mm_mapopt_update::0.076*1.55] mid_occ = 10 [M::mm_idx_stat] kmer size: 19; skip: 10; is_hpc: 1; #seq: 1 [M::mm_idx_stat::0.080*1.53] distinct minimizers: 120722 (93.18% are singletons); average occurrences: 1.087; average spacing: 8.062; total length: 1057923 [M::worker_pipeline::27.150*2.94] mapped 4395 sequences [M::main] Version: 2.24-r1122 [M::main] CMD: minimap2 -a -x map-pb -o results/HIFI_alignment/PacBio_clover_alignment_2.sam reference_data/DNA_Contig2.fasta ../Data/Clover_Data/Hifi_reads_white_clover.fastq [M::main] Real time: 27.162 sec; CPU: 79.819 sec; Peak RSS: 2.058 GB Sort the bam files and create their index using samtools In [12]: Copied! %% bash samtools sort results / HIFI_alignment / PacBio_clover_alignment_1 . sam - o results / HIFI_alignment / PacBio_clover_alignment_1 . sort . bam samtools sort results / HIFI_alignment / PacBio_clover_alignment_2 . sam - o results / HIFI_alignment / PacBio_clover_alignment_2 . sort . bam %%bash samtools sort results/HIFI_alignment/PacBio_clover_alignment_1.sam -o results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam samtools sort results/HIFI_alignment/PacBio_clover_alignment_2.sam -o results/HIFI_alignment/PacBio_clover_alignment_2.sort.bam In [13]: Copied! %% bash samtools index results / HIFI_alignment / PacBio_clover_alignment_1 . sort . bam samtools index results / HIFI_alignment / PacBio_clover_alignment_2 . sort . bam %%bash samtools index results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam samtools index results/HIFI_alignment/PacBio_clover_alignment_2.sort.bam Perform quality control In [14]: Copied! %% bash mkdir - p results / qualimap_output qualimap bamqc - bam results / HIFI_alignment / PacBio_clover_alignment_1 . sort . bam - outdir results / qualimap_output / PacBio_clover_alignment_1 %%bash mkdir -p results/qualimap_output qualimap bamqc -bam results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam -outdir results/qualimap_output/PacBio_clover_alignment_1 Java memory size is set to 1200M Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 1258 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 400 Chunk of reads size: 1000 Number of threads: 8 Processed 50 out of 400 windows... Processed 100 out of 400 windows... Processed 150 out of 400 windows... Processed 200 out of 400 windows... Processed 250 out of 400 windows... Processed 300 out of 400 windows... Processed 350 out of 400 windows... Processed 400 out of 400 windows... Total processed windows:400 Number of reads: 4395 Number of valid reads: 9070 Number of correct strand reads:0 Inside of regions... Num mapped reads: 4356 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 10 Computing descriptors... numberOfMappedBases: 59058058 referenceSize: 1031631 numberOfSequencedBases: 54917933 numberOfAs: 18508479 Computing per chromosome statistics... Computing histograms... Overall analysis time: 11 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished In [15]: Copied! %% bash qualimap bamqc - bam results / HIFI_alignment / PacBio_clover_alignment_2 . sort . bam - outdir results / qualimap_output / PacBio_clover_alignment_2 %%bash qualimap bamqc -bam results/HIFI_alignment/PacBio_clover_alignment_2.sort.bam -outdir results/qualimap_output/PacBio_clover_alignment_2 Java memory size is set to 1200M Launching application... QualiMap v.2.2.2-dev Built on 2019-11-11 14:05 Selected tool: bamqc Available memory (Mb): 33 Max memory (Mb): 1258 Starting bam qc.... Loading sam header... Loading locator... Loading reference... Number of windows: 400, effective number of windows: 400 Chunk of reads size: 1000 Number of threads: 8 Processed 50 out of 400 windows... Processed 100 out of 400 windows... Processed 150 out of 400 windows... Processed 200 out of 400 windows... Processed 250 out of 400 windows... Processed 300 out of 400 windows... Processed 350 out of 400 windows... Processed 400 out of 400 windows... Total processed windows:400 Number of reads: 4395 Number of valid reads: 9462 Number of correct strand reads:0 Inside of regions... Num mapped reads: 4394 Num mapped first of pair: 0 Num mapped second of pair: 0 Num singletons: 0 Time taken to analyze reads: 13 Computing descriptors... numberOfMappedBases: 59388453 referenceSize: 1057923 numberOfSequencedBases: 55867300 numberOfAs: 18822184 Computing per chromosome statistics... Computing histograms... Overall analysis time: 13 end of bam qc Computing report... Writing HTML report... HTML report created successfully Finished In [16]: Copied! %% bash #run multiqc multiqc -- outdir results / qualimap_output results / qualimap_output %%bash #run multiqc multiqc --outdir results/qualimap_output results/qualimap_output / / / \u001b]8;id=999624;https://multiqc.info\u001b\\ MultiQC \u001b]8;;\u001b\\ \ud83d\udd0d | v1.14 | multiqc | Search path : /work/SamueleSoraggi/Notebooks/results/qualimap_output | searching | \u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501 100% 187/187 .t\u2026 | qualimap | Found 4 BamQC reports | multiqc | Compressing plot data | multiqc | Previous MultiQC output found! Adjusting filenames.. | multiqc | Use -f or --force to overwrite existing reports instead | multiqc | Report : results/qualimap_output/multiqc_report_1.html | multiqc | Data : results/qualimap_output/multiqc_data_1 | multiqc | MultiQC complete Task: IGV visualization and Questions Now you can inspect the alignment files in IGV . First, you will need to download the reference fasta sequence in ../Data/Clover_Data/DNA_Contig1_2.fasta and import it into IGV. You can do the same for the files DNA_Contig1.fasta and DNA_Contig2.fasta that you might need later. In IGV, this is done with the menu Genomes --> Load Genome from file menu and by selecting the relevant fasta file. Then, choose the reference you need from the drop-down menu (see figure below). You will not yet see much, but you can choose one of the two subgenomes (contig 1 or 2) and double click on a chromosome position to inspect the reference sequence. The next step will visualize the mapped files on IGV. Each mapped genome can be seen in IGV against the reference file of choice. To load an aligned file, first download it together with the index file in .bai format. For example, you need to download both results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam and results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam.bai to see this alignment (you need to open only the .bam file with IGV). If you open more files, their alignments will be distributed in the IGV interface, and you can change the size of each visualization yourself (below shown with only one opened alignment). Now compare in IGV the two bam files PacBio_clover_alignment_1.sort.bam and PacBio_clover_alignment_2.sort.bam . What do you observe when comparing the two BAM files? Have a look at the polymorphic regions in IGV. Are they true polymorphisms? Add to the visualization the third alignment PacBio_clover_alignment_1_2_mappb.sort.bam in IGV. Why do you see fluctuations in coverage and large regions without any apparent subgenome SNPs? What are the major differences between the stats for the reads mapped to Contigs1&2 versus contig1 and contig2? What is your interpretation of the differences?","title":"Hifi data mapping"},{"location":"nb/align.html#rna-seq-mapping","text":"In the ../Data folder you will find 24 RNA-seq libraries, 12 S10 libraries and 12 Tienshan libraries. Each library is paired-end, which is denoted by R1 and R2 at the end of two files having the same name, such as S10_1_1.R1.fastq and S10_1_1.R2.fastq . We will align each library separately and then merge the alignments to create two final samples for S10 and Tienshan . First, we need to create a genome file for the reference fasta file of contigs 1 and 2 . This is done with STAR , using the option --runMode genomeGenerate . We also need to convert the gene annotation from gff to gtf format with gffread to allow counting gene transcripts. STAR is a very complex tool with many options, so it is always useful to have a reference manual . In [17]: Copied! %% bash gffread - T - o reference_data / white_clover_genes . gtf ../ Data / Clover_Data / white_clover_genes . gff %%bash gffread -T -o reference_data/white_clover_genes.gtf ../Data/Clover_Data/white_clover_genes.gff In [18]: Copied! %% bash STAR -- runThreadN 8 \\ -- runMode genomeGenerate \\ -- genomeDir results / STAR_output / indexing_contigs_1_2 \\ -- genomeFastaFiles reference_data / DNA_Contig1_2 . fasta \\ -- sjdbGTFfile reference_data / white_clover_genes . gtf %%bash STAR --runThreadN 8 \\ --runMode genomeGenerate \\ --genomeDir results/STAR_output/indexing_contigs_1_2 \\ --genomeFastaFiles reference_data/DNA_Contig1_2.fasta \\ --sjdbGTFfile reference_data/white_clover_genes.gtf STAR --runThreadN 8 --runMode genomeGenerate --genomeDir results/STAR_output/indexing_contigs_1_2 --genomeFastaFiles reference_data/DNA_Contig1_2.fasta --sjdbGTFfile reference_data/white_clover_genes.gtf STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:23:03 ..... started STAR run Jun 19 10:23:03 ... starting to generate Genome files Jun 19 10:23:03 ..... processing annotations GTF !!!!! WARNING: --genomeSAindexNbases 14 is too large for the genome size=2089554, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 9 Jun 19 10:23:03 ... starting to sort Suffix Array. This may take a long time... Jun 19 10:23:03 ... sorting Suffix Array chunks and saving them to disk... Jun 19 10:23:04 ... loading chunks from disk, packing SA... Jun 19 10:23:04 ... finished generating suffix array Jun 19 10:23:04 ... generating Suffix Array index Jun 19 10:23:08 ... completed Suffix Array index Jun 19 10:23:08 ..... inserting junctions into the genome indices Jun 19 10:23:16 ... writing Genome to disk ... Jun 19 10:23:16 ... writing Suffix Array to disk ... Jun 19 10:23:17 ... writing SAindex to disk Jun 19 10:23:18 ..... finished successfully We got a warning saying !!!!! WARNING: --genomeSAindexNbases 14 is too large for the genome size=2089554, which may cause seg-fault at the mapping step. Re-run genome generation with recommended --genomeSAindexNbases 9 meaning we need shorter strings of bases (9 bases instead of 14) to be indexed, as our reference genome is very short, and too long strings would cause many alignment errors. So we rerun the command with the suggested option. In [19]: Copied! %% bash STAR -- runThreadN 8 \\ -- runMode genomeGenerate \\ -- genomeDir results / STAR_output / indexing_contigs_1_2 \\ -- genomeFastaFiles reference_data / DNA_Contig1_2 . fasta \\ -- sjdbGTFfile reference_data / white_clover_genes . gtf \\ -- genomeSAindexNbases 9 %%bash STAR --runThreadN 8 \\ --runMode genomeGenerate \\ --genomeDir results/STAR_output/indexing_contigs_1_2 \\ --genomeFastaFiles reference_data/DNA_Contig1_2.fasta \\ --sjdbGTFfile reference_data/white_clover_genes.gtf \\ --genomeSAindexNbases 9 STAR --runThreadN 8 --runMode genomeGenerate --genomeDir results/STAR_output/indexing_contigs_1_2 --genomeFastaFiles reference_data/DNA_Contig1_2.fasta --sjdbGTFfile reference_data/white_clover_genes.gtf --genomeSAindexNbases 9 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:23:18 ..... started STAR run Jun 19 10:23:18 ... starting to generate Genome files Jun 19 10:23:18 ..... processing annotations GTF Jun 19 10:23:20 ... starting to sort Suffix Array. This may take a long time... Jun 19 10:23:20 ... sorting Suffix Array chunks and saving them to disk... Jun 19 10:23:21 ... loading chunks from disk, packing SA... Jun 19 10:23:21 ... finished generating suffix array Jun 19 10:23:21 ... generating Suffix Array index Jun 19 10:23:21 ... completed Suffix Array index Jun 19 10:23:22 ..... inserting junctions into the genome indices Jun 19 10:23:23 ... writing Genome to disk ... Jun 19 10:23:23 ... writing Suffix Array to disk ... Jun 19 10:23:23 ... writing SAindex to disk Jun 19 10:23:24 ..... finished successfully We use again STAR to align every single library for S10 . We extract the library name of each file and run STAR through each pair of files. Note that plant introns are very rarely more than 5000 bp and that you are mapping to two homoeologous contigs that show high similarity, especially in genic regions. We set the maximum size to 5000 using --alignIntronMax 5000 . In [20]: Copied! %% bash for i in ` ls ../ Data / Clover_Data / S10 *. R1 . fastq ` do PREFIXNAME = ` basename $ i . R1 . fastq ` echo \"###############################################\" echo \"##### ALIGNING PAIRED-END READS \" $ PREFIXNAME echo \"###############################################\" STAR -- genomeDir results / STAR_output / indexing_contigs_1_2 / \\ -- runThreadN 8 \\ -- runMode alignReads \\ -- readFilesIn ../ Data / Clover_Data / $ PREFIXNAME . R1 . fastq ../ Data / Clover_Data / $ PREFIXNAME . R2 . fastq \\ -- outFileNamePrefix results / STAR_output / S10_align_contigs_1_2 / $ PREFIXNAME \\ -- outSAMtype BAM SortedByCoordinate \\ -- outSAMattributes Standard \\ -- quantMode GeneCounts \\ -- alignIntronMax 5000 done %%bash for i in `ls ../Data/Clover_Data/S10*.R1.fastq` do PREFIXNAME=`basename $i .R1.fastq` echo \"###############################################\" echo \"##### ALIGNING PAIRED-END READS \"$PREFIXNAME echo \"###############################################\" STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ \\ --runThreadN 8 \\ --runMode alignReads \\ --readFilesIn ../Data/Clover_Data/$PREFIXNAME.R1.fastq ../Data/Clover_Data/$PREFIXNAME.R2.fastq \\ --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/$PREFIXNAME \\ --outSAMtype BAM SortedByCoordinate \\ --outSAMattributes Standard \\ --quantMode GeneCounts \\ --alignIntronMax 5000 done ############################################### ##### ALIGNING PAIRED-END READS S10_1_1 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_1_1.R1.fastq ../Data/Clover_Data/S10_1_1.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_1_1 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:23:24 ..... started STAR run Jun 19 10:23:24 ..... loading genome Jun 19 10:23:24 ..... started mapping Jun 19 10:23:35 ..... finished mapping Jun 19 10:23:35 ..... started sorting BAM Jun 19 10:23:37 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS S10_1_2 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_1_2.R1.fastq ../Data/Clover_Data/S10_1_2.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_1_2 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:23:38 ..... started STAR run Jun 19 10:23:38 ..... loading genome Jun 19 10:23:38 ..... started mapping Jun 19 10:23:48 ..... finished mapping Jun 19 10:23:48 ..... started sorting BAM Jun 19 10:23:51 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS S10_1_3 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_1_3.R1.fastq ../Data/Clover_Data/S10_1_3.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_1_3 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:23:52 ..... started STAR run Jun 19 10:23:52 ..... loading genome Jun 19 10:23:52 ..... started mapping Jun 19 10:24:03 ..... finished mapping Jun 19 10:24:03 ..... started sorting BAM Jun 19 10:24:06 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS S10_2_1 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_2_1.R1.fastq ../Data/Clover_Data/S10_2_1.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_2_1 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:24:06 ..... started STAR run Jun 19 10:24:06 ..... loading genome Jun 19 10:24:06 ..... started mapping Jun 19 10:24:16 ..... finished mapping Jun 19 10:24:16 ..... started sorting BAM Jun 19 10:24:18 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS S10_2_2 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_2_2.R1.fastq ../Data/Clover_Data/S10_2_2.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_2_2 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:24:20 ..... started STAR run Jun 19 10:24:20 ..... loading genome Jun 19 10:24:20 ..... started mapping Jun 19 10:24:31 ..... finished mapping Jun 19 10:24:31 ..... started sorting BAM Jun 19 10:24:33 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS S10_2_3 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --runMode alignReads --readFilesIn ../Data/Clover_Data/S10_2_3.R1.fastq ../Data/Clover_Data/S10_2_3.R2.fastq --outFileNamePrefix results/STAR_output/S10_align_contigs_1_2/S10_2_3 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:24:33 ..... started STAR run Jun 19 10:24:33 ..... loading genome Jun 19 10:24:33 ..... started mapping Jun 19 10:24:45 ..... finished mapping Jun 19 10:24:45 ..... started sorting BAM Jun 19 10:24:48 ..... finished successfully Do the same alignment for Tienshan libraries In [21]: Copied! %% bash for i in ` ls ../ Data / Clover_Data / TI *. R1 . fastq ` do PREFIXNAME = ` basename $ i . R1 . fastq ` echo \"###############################################\" echo \"##### ALIGNING PAIRED-END READS \" $ PREFIXNAME echo \"###############################################\" STAR -- genomeDir results / STAR_output / indexing_contigs_1_2 / \\ -- runThreadN 8 \\ -- readFilesIn ../ Data / Clover_Data / $ PREFIXNAME . R1 . fastq ../ Data / Clover_Data / $ PREFIXNAME . R2 . fastq \\ -- outFileNamePrefix results / STAR_output / TI_align_contigs_1_2 / $ PREFIXNAME \\ -- outSAMtype BAM SortedByCoordinate \\ -- outSAMattributes Standard \\ -- quantMode GeneCounts \\ -- alignIntronMax 5000 done %%bash for i in `ls ../Data/Clover_Data/TI*.R1.fastq` do PREFIXNAME=`basename $i .R1.fastq` echo \"###############################################\" echo \"##### ALIGNING PAIRED-END READS \"$PREFIXNAME echo \"###############################################\" STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ \\ --runThreadN 8 \\ --readFilesIn ../Data/Clover_Data/$PREFIXNAME.R1.fastq ../Data/Clover_Data/$PREFIXNAME.R2.fastq \\ --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/$PREFIXNAME \\ --outSAMtype BAM SortedByCoordinate \\ --outSAMattributes Standard \\ --quantMode GeneCounts \\ --alignIntronMax 5000 done ############################################### ##### ALIGNING PAIRED-END READS TI_1_1 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_1_1.R1.fastq ../Data/Clover_Data/TI_1_1.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_1_1 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:24:50 ..... started STAR run Jun 19 10:24:50 ..... loading genome Jun 19 10:24:50 ..... started mapping Jun 19 10:25:03 ..... finished mapping Jun 19 10:25:04 ..... started sorting BAM Jun 19 10:25:18 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS TI_1_2 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_1_2.R1.fastq ../Data/Clover_Data/TI_1_2.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_1_2 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:25:18 ..... started STAR run Jun 19 10:25:18 ..... loading genome Jun 19 10:25:18 ..... started mapping Jun 19 10:25:30 ..... finished mapping Jun 19 10:25:30 ..... started sorting BAM Jun 19 10:25:33 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS TI_1_3 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_1_3.R1.fastq ../Data/Clover_Data/TI_1_3.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_1_3 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:25:36 ..... started STAR run Jun 19 10:25:36 ..... loading genome Jun 19 10:25:36 ..... started mapping Jun 19 10:25:50 ..... finished mapping Jun 19 10:25:50 ..... started sorting BAM Jun 19 10:25:51 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS TI_2_1 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_2_1.R1.fastq ../Data/Clover_Data/TI_2_1.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_2_1 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:25:51 ..... started STAR run Jun 19 10:25:51 ..... loading genome Jun 19 10:25:52 ..... started mapping Jun 19 10:26:06 ..... finished mapping Jun 19 10:26:06 ..... started sorting BAM Jun 19 10:26:09 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS TI_2_2 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_2_2.R1.fastq ../Data/Clover_Data/TI_2_2.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_2_2 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:26:09 ..... started STAR run Jun 19 10:26:09 ..... loading genome Jun 19 10:26:09 ..... started mapping Jun 19 10:26:23 ..... finished mapping Jun 19 10:26:23 ..... started sorting BAM Jun 19 10:26:31 ..... finished successfully ############################################### ##### ALIGNING PAIRED-END READS TI_2_3 ############################################### STAR --genomeDir results/STAR_output/indexing_contigs_1_2/ --runThreadN 8 --readFilesIn ../Data/Clover_Data/TI_2_3.R1.fastq ../Data/Clover_Data/TI_2_3.R2.fastq --outFileNamePrefix results/STAR_output/TI_align_contigs_1_2/TI_2_3 --outSAMtype BAM SortedByCoordinate --outSAMattributes Standard --quantMode GeneCounts --alignIntronMax 5000 STAR version: 2.7.10a compiled: 2022-01-14T18:50:00-05:00 :/home/dobin/data/STAR/STARcode/STAR.master/source Jun 19 10:26:31 ..... started STAR run Jun 19 10:26:31 ..... loading genome Jun 19 10:26:31 ..... started mapping Jun 19 10:26:46 ..... finished mapping Jun 19 10:26:46 ..... started sorting BAM Jun 19 10:26:49 ..... finished successfully Run quality control on each aligned library with MultiQC . In this way there will be a whole report to compare S10 files and Tienshan files. In [22]: Copied! %% bash multiqc -- outdir results / multiqc_output / TI_STAR_align_1_2 \\ results / STAR_output / TI_align_contigs_1_2 / %%bash multiqc --outdir results/multiqc_output/TI_STAR_align_1_2 \\ results/STAR_output/TI_align_contigs_1_2/ / / / \u001b]8;id=121575;https://multiqc.info\u001b\\ MultiQC \u001b]8;;\u001b\\ \ud83d\udd0d | v1.14 | multiqc | Search path : /work/SamueleSoraggi/Notebooks/results/STAR_output/TI_align_contigs_1_2 | searching | \u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501 100% 36/36 og.o\u2026 | star | Found 6 reports and 6 gene count files | multiqc | Compressing plot data | multiqc | Report : results/multiqc_output/TI_STAR_align_1_2/multiqc_report.html | multiqc | Data : results/multiqc_output/TI_STAR_align_1_2/multiqc_data | multiqc | MultiQC complete In [23]: Copied! %% bash multiqc -- outdir results / multiqc_output / S10_STAR_align_1_2 \\ results / STAR_output / S10_align_contigs_1_2 / %%bash multiqc --outdir results/multiqc_output/S10_STAR_align_1_2 \\ results/STAR_output/S10_align_contigs_1_2/ / / / \u001b]8;id=596946;https://multiqc.info\u001b\\ MultiQC \u001b]8;;\u001b\\ \ud83d\udd0d | v1.14 | multiqc | Search path : /work/SamueleSoraggi/Notebooks/results/STAR_output/S10_align_contigs_1_2 | searching | \u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501\u2501 100% 36/36 ut.t\u2026 | star | Found 6 reports and 6 gene count files | multiqc | Compressing plot data | multiqc | Report : results/multiqc_output/S10_STAR_align_1_2/multiqc_report.html | multiqc | Data : results/multiqc_output/S10_STAR_align_1_2/multiqc_data | multiqc | MultiQC complete We merge the outputs of each group of aligned libraries. Here is how the files look like for the Tienshan . In [24]: Copied! ! ls - lh results / STAR_output / TI_align_contigs_1_2 / TI_ *. sortedByCoord . out . bam !ls -lh results/STAR_output/TI_align_contigs_1_2/TI_*.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 6.6M Jun 19 10:25 results/STAR_output/TI_align_contigs_1_2/TI_1_1Aligned.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 6.0M Jun 19 10:25 results/STAR_output/TI_align_contigs_1_2/TI_1_2Aligned.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 7.1M Jun 19 10:25 results/STAR_output/TI_align_contigs_1_2/TI_1_3Aligned.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 9.6M Jun 19 10:26 results/STAR_output/TI_align_contigs_1_2/TI_2_1Aligned.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 7.2M Jun 19 10:26 results/STAR_output/TI_align_contigs_1_2/TI_2_2Aligned.sortedByCoord.out.bam -rw-r--r--. 1 ucloud users 8.2M Jun 19 10:26 results/STAR_output/TI_align_contigs_1_2/TI_2_3Aligned.sortedByCoord.out.bam Apply samtools merge In [25]: Copied! %% bash mkdir - p results / STAR_output / TI_align_contigs_1_2_merge / samtools merge - f results / STAR_output / TI_align_contigs_1_2_merge / TI . sorted . bam results / STAR_output / TI_align_contigs_1_2 / TI_ *. sortedByCoord . out . bam %%bash mkdir -p results/STAR_output/TI_align_contigs_1_2_merge/ samtools merge -f results/STAR_output/TI_align_contigs_1_2_merge/TI.sorted.bam results/STAR_output/TI_align_contigs_1_2/TI_*.sortedByCoord.out.bam In [26]: Copied! %% bash mkdir - p results / STAR_output / S10_align_contigs_1_2_merge / samtools merge - f results / STAR_output / S10_align_contigs_1_2_merge / S10 . sorted . bam results / STAR_output / S10_align_contigs_1_2 / S10_ *. sortedByCoord . out . bam %%bash mkdir -p results/STAR_output/S10_align_contigs_1_2_merge/ samtools merge -f results/STAR_output/S10_align_contigs_1_2_merge/S10.sorted.bam results/STAR_output/S10_align_contigs_1_2/S10_*.sortedByCoord.out.bam Index both merging outputs. A file in format bam.bai will appear in their respective folders. In [27]: Copied! %% bash samtools index results / STAR_output / S10_align_contigs_1_2_merge / S10 . sorted . bam %%bash samtools index results/STAR_output/S10_align_contigs_1_2_merge/S10.sorted.bam In [28]: Copied! %% bash samtools index results / STAR_output / TI_align_contigs_1_2_merge / TI . sorted . bam %%bash samtools index results/STAR_output/TI_align_contigs_1_2_merge/TI.sorted.bam","title":"RNA-seq mapping"},{"location":"nb/align.html#wrapping-up","text":"In this exercise, you learnt to align various types of data after performing quality control for raw data. We looked at some of the options for the aligners and at how to use some of the basic samtools manipulation programs. 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padding-left: 5px; padding-right: 5px; } td.linenos .special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } span.linenos.special { color: #000000; background-color: #ffffc0; padding-left: 5px; padding-right: 5px; } .highlight-ipynb .hll { background-color: var(--jp-cell-editor-active-background) } .highlight-ipynb { background: var(--jp-cell-editor-background); color: var(--jp-mirror-editor-variable-color) } .highlight-ipynb .c { color: var(--jp-mirror-editor-comment-color); font-style: italic } /* Comment */ .highlight-ipynb .err { color: var(--jp-mirror-editor-error-color) } /* Error */ .highlight-ipynb .k { color: var(--jp-mirror-editor-keyword-color); font-weight: bold } /* Keyword */ .highlight-ipynb .o { color: var(--jp-mirror-editor-operator-color); font-weight: bold } /* Operator */ .highlight-ipynb .p { color: var(--jp-mirror-editor-punctuation-color) } /* Punctuation */ .highlight-ipynb .ch { color: var(--jp-mirror-editor-comment-color); font-style: italic } /* Comment.Hashbang */ .highlight-ipynb .cm { color: var(--jp-mirror-editor-comment-color); font-style: italic } /* Comment.Multiline */ .highlight-ipynb .cp { color: var(--jp-mirror-editor-comment-color); font-style: italic } /* Comment.Preproc */ .highlight-ipynb .cpf { color: var(--jp-mirror-editor-comment-color); font-style: italic } /* Comment.PreprocFile */ .highlight-ipynb .c1 { color: var(--jp-mirror-editor-comment-color); font-style: italic } /* Comment.Single */ .highlight-ipynb .cs { color: var(--jp-mirror-editor-comment-color); font-style: italic } /* Comment.Special */ .highlight-ipynb .kc { color: var(--jp-mirror-editor-keyword-color); font-weight: bold } /* Keyword.Constant */ .highlight-ipynb .kd { color: var(--jp-mirror-editor-keyword-color); font-weight: bold } /* Keyword.Declaration */ .highlight-ipynb .kn { color: var(--jp-mirror-editor-keyword-color); font-weight: bold } /* Keyword.Namespace */ .highlight-ipynb .kp { color: var(--jp-mirror-editor-keyword-color); font-weight: bold } /* Keyword.Pseudo */ .highlight-ipynb .kr { color: var(--jp-mirror-editor-keyword-color); font-weight: bold } /* Keyword.Reserved */ .highlight-ipynb .kt { color: var(--jp-mirror-editor-keyword-color); font-weight: bold } /* Keyword.Type */ .highlight-ipynb .m { color: var(--jp-mirror-editor-number-color) } /* Literal.Number */ .highlight-ipynb .s { color: var(--jp-mirror-editor-string-color) } /* Literal.String */ .highlight-ipynb .ow { color: var(--jp-mirror-editor-operator-color); font-weight: bold } /* Operator.Word */ .highlight-ipynb .w { color: var(--jp-mirror-editor-variable-color) } /* Text.Whitespace */ .highlight-ipynb .mb { color: var(--jp-mirror-editor-number-color) } /* Literal.Number.Bin */ .highlight-ipynb .mf { color: var(--jp-mirror-editor-number-color) } /* Literal.Number.Float */ .highlight-ipynb .mh { color: var(--jp-mirror-editor-number-color) } /* Literal.Number.Hex */ .highlight-ipynb .mi { color: var(--jp-mirror-editor-number-color) } /* Literal.Number.Integer */ .highlight-ipynb .mo { color: var(--jp-mirror-editor-number-color) } /* Literal.Number.Oct */ .highlight-ipynb .sa { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Affix */ .highlight-ipynb .sb { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Backtick */ .highlight-ipynb .sc { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Char */ .highlight-ipynb .dl { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Delimiter */ .highlight-ipynb .sd { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Doc */ .highlight-ipynb .s2 { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Double */ .highlight-ipynb .se { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Escape */ .highlight-ipynb .sh { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Heredoc */ .highlight-ipynb .si { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Interpol */ .highlight-ipynb .sx { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Other */ .highlight-ipynb .sr { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Regex */ .highlight-ipynb .s1 { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Single */ .highlight-ipynb .ss { color: var(--jp-mirror-editor-string-color) } /* Literal.String.Symbol */ .highlight-ipynb .il { color: var(--jp-mirror-editor-number-color) } /* Literal.Number.Integer.Long */ /* This file is taken from the built JupyterLab theme.css Found on share/nbconvert/templates/lab/static Some changes have been made and marked with CHANGE */ .jupyter-wrapper { /* Elevation * * We style box-shadows using Material Design's idea of elevation. These particular numbers are taken from here: * * https://github.com/material-components/material-components-web * https://material-components-web.appspot.com/elevation.html */ --jp-shadow-base-lightness: 0; --jp-shadow-umbra-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.2 ); --jp-shadow-penumbra-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.14 ); --jp-shadow-ambient-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.12 ); --jp-elevation-z0: none; --jp-elevation-z1: 0px 2px 1px -1px var(--jp-shadow-umbra-color), 0px 1px 1px 0px var(--jp-shadow-penumbra-color), 0px 1px 3px 0px var(--jp-shadow-ambient-color); --jp-elevation-z2: 0px 3px 1px -2px var(--jp-shadow-umbra-color), 0px 2px 2px 0px var(--jp-shadow-penumbra-color), 0px 1px 5px 0px var(--jp-shadow-ambient-color); --jp-elevation-z4: 0px 2px 4px -1px var(--jp-shadow-umbra-color), 0px 4px 5px 0px var(--jp-shadow-penumbra-color), 0px 1px 10px 0px var(--jp-shadow-ambient-color); --jp-elevation-z6: 0px 3px 5px -1px var(--jp-shadow-umbra-color), 0px 6px 10px 0px var(--jp-shadow-penumbra-color), 0px 1px 18px 0px var(--jp-shadow-ambient-color); --jp-elevation-z8: 0px 5px 5px -3px var(--jp-shadow-umbra-color), 0px 8px 10px 1px var(--jp-shadow-penumbra-color), 0px 3px 14px 2px var(--jp-shadow-ambient-color); --jp-elevation-z12: 0px 7px 8px -4px var(--jp-shadow-umbra-color), 0px 12px 17px 2px var(--jp-shadow-penumbra-color), 0px 5px 22px 4px var(--jp-shadow-ambient-color); --jp-elevation-z16: 0px 8px 10px -5px var(--jp-shadow-umbra-color), 0px 16px 24px 2px var(--jp-shadow-penumbra-color), 0px 6px 30px 5px var(--jp-shadow-ambient-color); --jp-elevation-z20: 0px 10px 13px -6px var(--jp-shadow-umbra-color), 0px 20px 31px 3px var(--jp-shadow-penumbra-color), 0px 8px 38px 7px var(--jp-shadow-ambient-color); --jp-elevation-z24: 0px 11px 15px -7px var(--jp-shadow-umbra-color), 0px 24px 38px 3px var(--jp-shadow-penumbra-color), 0px 9px 46px 8px var(--jp-shadow-ambient-color); /* Borders * * The following variables, specify the visual styling of borders in JupyterLab. */ --jp-border-width: 1px; --jp-border-color0: var(--md-grey-400); --jp-border-color1: var(--md-grey-400); --jp-border-color2: var(--md-grey-300); --jp-border-color3: var(--md-grey-200); --jp-border-radius: 2px; /* UI Fonts * * The UI font CSS variables are used for the typography all of the JupyterLab * user interface elements that are not directly user generated content. * * The font sizing here is done assuming that the body font size of --jp-ui-font-size1 * is applied to a parent element. When children elements, such as headings, are sized * in em all things will be computed relative to that body size. */ --jp-ui-font-scale-factor: 1.2; --jp-ui-font-size0: 0.83333em; --jp-ui-font-size1: 13px; /* Base font size */ --jp-ui-font-size2: 1.2em; --jp-ui-font-size3: 1.44em; --jp-ui-font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\"; /* * Use these font colors against the corresponding main layout colors. * In a light theme, these go from dark to light. */ /* Defaults use Material Design specification */ --jp-ui-font-color0: rgba(0, 0, 0, 1); --jp-ui-font-color1: rgba(0, 0, 0, 0.87); --jp-ui-font-color2: rgba(0, 0, 0, 0.54); --jp-ui-font-color3: rgba(0, 0, 0, 0.38); /* * Use these against the brand/accent/warn/error colors. * These will typically go from light to darker, in both a dark and light theme. */ --jp-ui-inverse-font-color0: rgba(255, 255, 255, 1); --jp-ui-inverse-font-color1: rgba(255, 255, 255, 1); --jp-ui-inverse-font-color2: rgba(255, 255, 255, 0.7); --jp-ui-inverse-font-color3: rgba(255, 255, 255, 0.5); /* Content Fonts * * Content font variables are used for typography of user generated content. * * The font sizing here is done assuming that the body font size of --jp-content-font-size1 * is applied to a parent element. When children elements, such as headings, are sized * in em all things will be computed relative to that body size. */ --jp-content-line-height: 1.6; --jp-content-font-scale-factor: 1.2; --jp-content-font-size0: 0.83333em; --jp-content-font-size1: 14px; /* Base font size */ --jp-content-font-size2: 1.2em; --jp-content-font-size3: 1.44em; --jp-content-font-size4: 1.728em; --jp-content-font-size5: 2.0736em; /* This gives a magnification of about 125% in presentation mode over normal. */ --jp-content-presentation-font-size1: 17px; --jp-content-heading-line-height: 1; --jp-content-heading-margin-top: 1.2em; --jp-content-heading-margin-bottom: 0.8em; --jp-content-heading-font-weight: 500; /* Defaults use Material Design specification */ --jp-content-font-color0: rgba(0, 0, 0, 1); --jp-content-font-color1: rgba(0, 0, 0, 0.87); --jp-content-font-color2: rgba(0, 0, 0, 0.54); --jp-content-font-color3: rgba(0, 0, 0, 0.38); --jp-content-link-color: var(--md-blue-700); --jp-content-font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\"; /* * Code Fonts * * Code font variables are used for typography of code and other monospaces content. */ --jp-code-font-size: 13px; --jp-code-line-height: 1.3077; /* 17px for 13px base */ --jp-code-padding: 5px; /* 5px for 13px base, codemirror highlighting needs integer px value */ --jp-code-font-family-default: Menlo, Consolas, \"DejaVu Sans Mono\", monospace; --jp-code-font-family: var(--jp-code-font-family-default); /* This gives a magnification of about 125% in presentation mode over normal. */ --jp-code-presentation-font-size: 16px; /* may need to tweak cursor width if you change font size */ --jp-code-cursor-width0: 1.4px; --jp-code-cursor-width1: 2px; --jp-code-cursor-width2: 4px; /* Layout * * The following are the main layout colors use in JupyterLab. In a light * theme these would go from light to dark. */ --jp-layout-color0: white; --jp-layout-color1: white; --jp-layout-color2: var(--md-grey-200); --jp-layout-color3: var(--md-grey-400); --jp-layout-color4: var(--md-grey-600); /* Inverse Layout * * The following are the inverse layout colors use in JupyterLab. In a light * theme these would go from dark to light. */ --jp-inverse-layout-color0: #111111; --jp-inverse-layout-color1: var(--md-grey-900); --jp-inverse-layout-color2: var(--md-grey-800); --jp-inverse-layout-color3: var(--md-grey-700); --jp-inverse-layout-color4: var(--md-grey-600); /* Brand/accent */ --jp-brand-color0: var(--md-blue-900); --jp-brand-color1: var(--md-blue-700); --jp-brand-color2: var(--md-blue-300); --jp-brand-color3: var(--md-blue-100); --jp-brand-color4: var(--md-blue-50); --jp-accent-color0: var(--md-green-900); --jp-accent-color1: var(--md-green-700); --jp-accent-color2: var(--md-green-300); --jp-accent-color3: var(--md-green-100); /* State colors (warn, error, success, info) */ --jp-warn-color0: var(--md-orange-900); --jp-warn-color1: var(--md-orange-700); --jp-warn-color2: var(--md-orange-300); --jp-warn-color3: var(--md-orange-100); --jp-error-color0: var(--md-red-900); --jp-error-color1: var(--md-red-700); --jp-error-color2: var(--md-red-300); --jp-error-color3: var(--md-red-100); --jp-success-color0: var(--md-green-900); --jp-success-color1: var(--md-green-700); --jp-success-color2: var(--md-green-300); --jp-success-color3: var(--md-green-100); --jp-info-color0: var(--md-cyan-900); --jp-info-color1: var(--md-cyan-700); --jp-info-color2: var(--md-cyan-300); --jp-info-color3: var(--md-cyan-100); /* Cell specific styles */ --jp-cell-padding: 5px; --jp-cell-collapser-width: 8px; --jp-cell-collapser-min-height: 20px; --jp-cell-collapser-not-active-hover-opacity: 0.6; --jp-cell-editor-background: var(--md-grey-100); --jp-cell-editor-border-color: var(--md-grey-300); --jp-cell-editor-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-cell-editor-active-background: var(--jp-layout-color0); --jp-cell-editor-active-border-color: var(--jp-brand-color1); --jp-cell-prompt-width: 64px; --jp-cell-prompt-font-family: var(--jp-code-font-family-default); --jp-cell-prompt-letter-spacing: 0px; --jp-cell-prompt-opacity: 1; --jp-cell-prompt-not-active-opacity: 0.5; --jp-cell-prompt-not-active-font-color: var(--md-grey-700); /* A custom blend of MD grey and blue 600 * See https://meyerweb.com/eric/tools/color-blend/#546E7A:1E88E5:5:hex */ --jp-cell-inprompt-font-color: #307fc1; /* A custom blend of MD grey and orange 600 * https://meyerweb.com/eric/tools/color-blend/#546E7A:F4511E:5:hex */ --jp-cell-outprompt-font-color: #bf5b3d; /* Notebook specific styles */ --jp-notebook-padding: 10px; --jp-notebook-select-background: var(--jp-layout-color1); --jp-notebook-multiselected-color: var(--md-blue-50); /* The scroll padding is calculated to fill enough space at the bottom of the notebook to show one single-line cell (with appropriate padding) at the top when the notebook is scrolled all the way to the bottom. We also subtract one pixel so that no scrollbar appears if we have just one single-line cell in the notebook. This padding is to enable a 'scroll past end' feature in a notebook. */ --jp-notebook-scroll-padding: calc( 100% - var(--jp-code-font-size) * var(--jp-code-line-height) - var(--jp-code-padding) - var(--jp-cell-padding) - 1px ); /* Rendermime styles */ --jp-rendermime-error-background: #fdd; --jp-rendermime-table-row-background: var(--md-grey-100); --jp-rendermime-table-row-hover-background: var(--md-light-blue-50); /* Dialog specific styles */ --jp-dialog-background: rgba(0, 0, 0, 0.25); /* Console specific styles */ --jp-console-padding: 10px; /* Toolbar specific styles */ --jp-toolbar-border-color: var(--jp-border-color1); --jp-toolbar-micro-height: 8px; --jp-toolbar-background: var(--jp-layout-color1); --jp-toolbar-box-shadow: 0px 0px 2px 0px rgba(0, 0, 0, 0.24); --jp-toolbar-header-margin: 4px 4px 0px 4px; --jp-toolbar-active-background: var(--md-grey-300); /* Statusbar specific styles */ --jp-statusbar-height: 24px; /* Input field styles */ --jp-input-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-input-active-background: var(--jp-layout-color1); --jp-input-hover-background: var(--jp-layout-color1); --jp-input-background: var(--md-grey-100); --jp-input-border-color: var(--jp-border-color1); --jp-input-active-border-color: var(--jp-brand-color1); --jp-input-active-box-shadow-color: rgba(19, 124, 189, 0.3); /* General editor styles */ --jp-editor-selected-background: #d9d9d9; --jp-editor-selected-focused-background: #d7d4f0; --jp-editor-cursor-color: var(--jp-ui-font-color0); /* Code mirror specific styles */ --jp-mirror-editor-keyword-color: #008000; --jp-mirror-editor-atom-color: #88f; --jp-mirror-editor-number-color: #080; --jp-mirror-editor-def-color: #00f; --jp-mirror-editor-variable-color: var(--md-grey-900); --jp-mirror-editor-variable-2-color: #05a; --jp-mirror-editor-variable-3-color: #085; --jp-mirror-editor-punctuation-color: #05a; --jp-mirror-editor-property-color: #05a; --jp-mirror-editor-operator-color: #aa22ff; --jp-mirror-editor-comment-color: #408080; --jp-mirror-editor-string-color: #ba2121; --jp-mirror-editor-string-2-color: #708; --jp-mirror-editor-meta-color: #aa22ff; --jp-mirror-editor-qualifier-color: #555; --jp-mirror-editor-builtin-color: #008000; --jp-mirror-editor-bracket-color: #997; --jp-mirror-editor-tag-color: #170; --jp-mirror-editor-attribute-color: #00c; --jp-mirror-editor-header-color: blue; --jp-mirror-editor-quote-color: #090; --jp-mirror-editor-link-color: #00c; --jp-mirror-editor-error-color: #f00; --jp-mirror-editor-hr-color: #999; /* Vega extension styles */ --jp-vega-background: white; /* Sidebar-related styles */ --jp-sidebar-min-width: 250px; /* Search-related styles */ --jp-search-toggle-off-opacity: 0.5; --jp-search-toggle-hover-opacity: 0.8; --jp-search-toggle-on-opacity: 1; --jp-search-selected-match-background-color: rgb(245, 200, 0); --jp-search-selected-match-color: black; --jp-search-unselected-match-background-color: var( --jp-inverse-layout-color0 ); --jp-search-unselected-match-color: var(--jp-ui-inverse-font-color0); /* Icon colors that work well with light or dark backgrounds */ --jp-icon-contrast-color0: var(--md-purple-600); --jp-icon-contrast-color1: var(--md-green-600); --jp-icon-contrast-color2: var(--md-pink-600); --jp-icon-contrast-color3: var(--md-blue-600); } [data-md-color-scheme=\"slate\"] .jupyter-wrapper { /* Elevation * * We style box-shadows using Material Design's idea of elevation. These particular numbers are taken from here: * * https://github.com/material-components/material-components-web * https://material-components-web.appspot.com/elevation.html */ /* The dark theme shadows need a bit of work, but this will probably also require work on the core layout * colors used in the theme as well. */ --jp-shadow-base-lightness: 32; --jp-shadow-umbra-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.2 ); --jp-shadow-penumbra-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.14 ); --jp-shadow-ambient-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.12 ); --jp-elevation-z0: none; --jp-elevation-z1: 0px 2px 1px -1px var(--jp-shadow-umbra-color), 0px 1px 1px 0px var(--jp-shadow-penumbra-color), 0px 1px 3px 0px var(--jp-shadow-ambient-color); --jp-elevation-z2: 0px 3px 1px -2px var(--jp-shadow-umbra-color), 0px 2px 2px 0px var(--jp-shadow-penumbra-color), 0px 1px 5px 0px var(--jp-shadow-ambient-color); --jp-elevation-z4: 0px 2px 4px -1px var(--jp-shadow-umbra-color), 0px 4px 5px 0px var(--jp-shadow-penumbra-color), 0px 1px 10px 0px var(--jp-shadow-ambient-color); --jp-elevation-z6: 0px 3px 5px -1px var(--jp-shadow-umbra-color), 0px 6px 10px 0px var(--jp-shadow-penumbra-color), 0px 1px 18px 0px var(--jp-shadow-ambient-color); --jp-elevation-z8: 0px 5px 5px -3px var(--jp-shadow-umbra-color), 0px 8px 10px 1px var(--jp-shadow-penumbra-color), 0px 3px 14px 2px var(--jp-shadow-ambient-color); --jp-elevation-z12: 0px 7px 8px -4px var(--jp-shadow-umbra-color), 0px 12px 17px 2px var(--jp-shadow-penumbra-color), 0px 5px 22px 4px var(--jp-shadow-ambient-color); --jp-elevation-z16: 0px 8px 10px -5px var(--jp-shadow-umbra-color), 0px 16px 24px 2px var(--jp-shadow-penumbra-color), 0px 6px 30px 5px var(--jp-shadow-ambient-color); --jp-elevation-z20: 0px 10px 13px -6px var(--jp-shadow-umbra-color), 0px 20px 31px 3px var(--jp-shadow-penumbra-color), 0px 8px 38px 7px var(--jp-shadow-ambient-color); --jp-elevation-z24: 0px 11px 15px -7px var(--jp-shadow-umbra-color), 0px 24px 38px 3px var(--jp-shadow-penumbra-color), 0px 9px 46px 8px var(--jp-shadow-ambient-color); /* Borders * * The following variables, specify the visual styling of borders in JupyterLab. */ --jp-border-width: 1px; --jp-border-color0: var(--md-grey-700); --jp-border-color1: var(--md-grey-700); --jp-border-color2: var(--md-grey-800); --jp-border-color3: var(--md-grey-900); --jp-border-radius: 2px; /* UI Fonts * * The UI font CSS variables are used for the typography all of the JupyterLab * user interface elements that are not directly user generated content. * * The font sizing here is done assuming that the body font size of --jp-ui-font-size1 * is applied to a parent element. When children elements, such as headings, are sized * in em all things will be computed relative to that body size. */ --jp-ui-font-scale-factor: 1.2; --jp-ui-font-size0: 0.83333em; --jp-ui-font-size1: 13px; /* Base font size */ --jp-ui-font-size2: 1.2em; --jp-ui-font-size3: 1.44em; --jp-ui-font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\"; /* * Use these font colors against the corresponding main layout colors. * In a light theme, these go from dark to light. */ /* Defaults use Material Design specification */ --jp-ui-font-color0: rgba(255, 255, 255, 1); --jp-ui-font-color1: rgba(255, 255, 255, 0.87); --jp-ui-font-color2: rgba(255, 255, 255, 0.54); --jp-ui-font-color3: rgba(255, 255, 255, 0.38); /* * Use these against the brand/accent/warn/error colors. * These will typically go from light to darker, in both a dark and light theme. */ --jp-ui-inverse-font-color0: rgba(0, 0, 0, 1); --jp-ui-inverse-font-color1: rgba(0, 0, 0, 0.8); --jp-ui-inverse-font-color2: rgba(0, 0, 0, 0.5); --jp-ui-inverse-font-color3: rgba(0, 0, 0, 0.3); /* Content Fonts * * Content font variables are used for typography of user generated content. * * The font sizing here is done assuming that the body font size of --jp-content-font-size1 * is applied to a parent element. When children elements, such as headings, are sized * in em all things will be computed relative to that body size. */ --jp-content-line-height: 1.6; --jp-content-font-scale-factor: 1.2; --jp-content-font-size0: 0.83333em; --jp-content-font-size1: 14px; /* Base font size */ --jp-content-font-size2: 1.2em; --jp-content-font-size3: 1.44em; --jp-content-font-size4: 1.728em; --jp-content-font-size5: 2.0736em; /* This gives a magnification of about 125% in presentation mode over normal. */ --jp-content-presentation-font-size1: 17px; --jp-content-heading-line-height: 1; --jp-content-heading-margin-top: 1.2em; --jp-content-heading-margin-bottom: 0.8em; --jp-content-heading-font-weight: 500; /* Defaults use Material Design specification */ --jp-content-font-color0: rgba(255, 255, 255, 1); --jp-content-font-color1: rgba(255, 255, 255, 1); --jp-content-font-color2: rgba(255, 255, 255, 0.7); --jp-content-font-color3: rgba(255, 255, 255, 0.5); --jp-content-link-color: var(--md-blue-300); --jp-content-font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\"; /* * Code Fonts * * Code font variables are used for typography of code and other monospaces content. */ --jp-code-font-size: 13px; --jp-code-line-height: 1.3077; /* 17px for 13px base */ --jp-code-padding: 5px; /* 5px for 13px base, codemirror highlighting needs integer px value */ --jp-code-font-family-default: Menlo, Consolas, \"DejaVu Sans Mono\", monospace; --jp-code-font-family: var(--jp-code-font-family-default); /* This gives a magnification of about 125% in presentation mode over normal. */ --jp-code-presentation-font-size: 16px; /* may need to tweak cursor width if you change font size */ --jp-code-cursor-width0: 1.4px; --jp-code-cursor-width1: 2px; --jp-code-cursor-width2: 4px; /* Layout * * The following are the main layout colors use in JupyterLab. In a light * theme these would go from light to dark. */ --jp-layout-color0: #111111; --jp-layout-color1: var(--md-grey-900); --jp-layout-color2: var(--md-grey-800); --jp-layout-color3: var(--md-grey-700); --jp-layout-color4: var(--md-grey-600); /* Inverse Layout * * The following are the inverse layout colors use in JupyterLab. In a light * theme these would go from dark to light. */ --jp-inverse-layout-color0: white; --jp-inverse-layout-color1: white; --jp-inverse-layout-color2: var(--md-grey-200); --jp-inverse-layout-color3: var(--md-grey-400); --jp-inverse-layout-color4: var(--md-grey-600); /* Brand/accent */ --jp-brand-color0: var(--md-blue-700); --jp-brand-color1: var(--md-blue-500); --jp-brand-color2: var(--md-blue-300); --jp-brand-color3: var(--md-blue-100); --jp-brand-color4: var(--md-blue-50); --jp-accent-color0: var(--md-green-700); --jp-accent-color1: var(--md-green-500); --jp-accent-color2: var(--md-green-300); --jp-accent-color3: var(--md-green-100); /* State colors (warn, error, success, info) */ --jp-warn-color0: var(--md-orange-700); --jp-warn-color1: var(--md-orange-500); --jp-warn-color2: var(--md-orange-300); --jp-warn-color3: var(--md-orange-100); --jp-error-color0: var(--md-red-700); --jp-error-color1: var(--md-red-500); --jp-error-color2: var(--md-red-300); --jp-error-color3: var(--md-red-100); --jp-success-color0: var(--md-green-700); --jp-success-color1: var(--md-green-500); --jp-success-color2: var(--md-green-300); --jp-success-color3: var(--md-green-100); --jp-info-color0: var(--md-cyan-700); --jp-info-color1: var(--md-cyan-500); --jp-info-color2: var(--md-cyan-300); --jp-info-color3: var(--md-cyan-100); /* Cell specific styles */ --jp-cell-padding: 5px; --jp-cell-collapser-width: 8px; --jp-cell-collapser-min-height: 20px; --jp-cell-collapser-not-active-hover-opacity: 0.6; --jp-cell-editor-background: var(--jp-layout-color1); --jp-cell-editor-border-color: var(--md-grey-700); --jp-cell-editor-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-cell-editor-active-background: var(--jp-layout-color0); --jp-cell-editor-active-border-color: var(--jp-brand-color1); --jp-cell-prompt-width: 64px; --jp-cell-prompt-font-family: var(--jp-code-font-family-default); --jp-cell-prompt-letter-spacing: 0px; --jp-cell-prompt-opacity: 1; --jp-cell-prompt-not-active-opacity: 1; --jp-cell-prompt-not-active-font-color: var(--md-grey-300); /* A custom blend of MD grey and blue 600 * See https://meyerweb.com/eric/tools/color-blend/#546E7A:1E88E5:5:hex */ --jp-cell-inprompt-font-color: #307fc1; /* A custom blend of MD grey and orange 600 * https://meyerweb.com/eric/tools/color-blend/#546E7A:F4511E:5:hex */ --jp-cell-outprompt-font-color: #bf5b3d; /* Notebook specific styles */ --jp-notebook-padding: 10px; --jp-notebook-select-background: var(--jp-layout-color1); --jp-notebook-multiselected-color: rgba(33, 150, 243, 0.24); /* The scroll padding is calculated to fill enough space at the bottom of the notebook to show one single-line cell (with appropriate padding) at the top when the notebook is scrolled all the way to the bottom. We also subtract one pixel so that no scrollbar appears if we have just one single-line cell in the notebook. This padding is to enable a 'scroll past end' feature in a notebook. */ --jp-notebook-scroll-padding: calc( 100% - var(--jp-code-font-size) * var(--jp-code-line-height) - var(--jp-code-padding) - var(--jp-cell-padding) - 1px ); /* Rendermime styles */ --jp-rendermime-error-background: rgba(244, 67, 54, 0.28); --jp-rendermime-table-row-background: var(--md-grey-900); --jp-rendermime-table-row-hover-background: rgba(3, 169, 244, 0.2); /* Dialog specific styles */ --jp-dialog-background: rgba(0, 0, 0, 0.6); /* Console specific styles */ --jp-console-padding: 10px; /* Toolbar specific styles */ --jp-toolbar-border-color: var(--jp-border-color2); --jp-toolbar-micro-height: 8px; --jp-toolbar-background: var(--jp-layout-color1); --jp-toolbar-box-shadow: 0px 0px 2px 0px rgba(0, 0, 0, 0.8); --jp-toolbar-header-margin: 4px 4px 0px 4px; --jp-toolbar-active-background: var(--jp-layout-color0); /* Statusbar specific styles */ --jp-statusbar-height: 24px; /* Input field styles */ --jp-input-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-input-active-background: var(--jp-layout-color0); --jp-input-hover-background: var(--jp-layout-color2); --jp-input-background: var(--md-grey-800); --jp-input-border-color: var(--jp-border-color1); --jp-input-active-border-color: var(--jp-brand-color1); --jp-input-active-box-shadow-color: rgba(19, 124, 189, 0.3); /* General editor styles */ --jp-editor-selected-background: var(--jp-layout-color2); --jp-editor-selected-focused-background: rgba(33, 150, 243, 0.24); --jp-editor-cursor-color: var(--jp-ui-font-color0); /* Code mirror specific styles */ --jp-mirror-editor-keyword-color: var(--md-green-500); --jp-mirror-editor-atom-color: var(--md-blue-300); --jp-mirror-editor-number-color: var(--md-green-400); --jp-mirror-editor-def-color: var(--md-blue-600); --jp-mirror-editor-variable-color: var(--md-grey-300); --jp-mirror-editor-variable-2-color: var(--md-blue-400); --jp-mirror-editor-variable-3-color: var(--md-green-600); --jp-mirror-editor-punctuation-color: var(--md-blue-400); --jp-mirror-editor-property-color: var(--md-blue-400); --jp-mirror-editor-operator-color: #aa22ff; --jp-mirror-editor-comment-color: #408080; --jp-mirror-editor-string-color: #ff7070; --jp-mirror-editor-string-2-color: var(--md-purple-300); --jp-mirror-editor-meta-color: #aa22ff; --jp-mirror-editor-qualifier-color: #555; --jp-mirror-editor-builtin-color: var(--md-green-600); --jp-mirror-editor-bracket-color: #997; --jp-mirror-editor-tag-color: var(--md-green-700); --jp-mirror-editor-attribute-color: var(--md-blue-700); --jp-mirror-editor-header-color: var(--md-blue-500); --jp-mirror-editor-quote-color: var(--md-green-300); --jp-mirror-editor-link-color: var(--md-blue-700); --jp-mirror-editor-error-color: #f00; --jp-mirror-editor-hr-color: #999; /* Vega extension styles */ --jp-vega-background: var(--md-grey-400); /* Sidebar-related styles */ --jp-sidebar-min-width: 250px; /* Search-related styles */ --jp-search-toggle-off-opacity: 0.6; --jp-search-toggle-hover-opacity: 0.8; --jp-search-toggle-on-opacity: 1; --jp-search-selected-match-background-color: rgb(255, 225, 0); --jp-search-selected-match-color: black; --jp-search-unselected-match-background-color: var( --jp-inverse-layout-color0 ); --jp-search-unselected-match-color: var(--jp-ui-inverse-font-color0); /* scrollbar related styles. Supports every browser except Edge. */ /* colors based on JetBrain's Darcula theme */ --jp-scrollbar-background-color: #3f4244; --jp-scrollbar-thumb-color: 88, 96, 97; /* need to specify thumb color as an RGB triplet */ --jp-scrollbar-endpad: 3px; /* the minimum gap between the thumb and the ends of a scrollbar */ /* hacks for setting the thumb shape. These do nothing in Firefox */ --jp-scrollbar-thumb-margin: 3.5px; /* the space in between the sides of the thumb and the track */ --jp-scrollbar-thumb-radius: 9px; /* set to a large-ish value for rounded endcaps on the thumb */ /* Icon colors that work well with light or dark backgrounds */ --jp-icon-contrast-color0: var(--md-purple-600); --jp-icon-contrast-color1: var(--md-green-600); --jp-icon-contrast-color2: var(--md-pink-600); --jp-icon-contrast-color3: var(--md-blue-600); } :root{--md-red-50: #ffebee;--md-red-100: #ffcdd2;--md-red-200: #ef9a9a;--md-red-300: #e57373;--md-red-400: #ef5350;--md-red-500: #f44336;--md-red-600: #e53935;--md-red-700: #d32f2f;--md-red-800: #c62828;--md-red-900: #b71c1c;--md-red-A100: #ff8a80;--md-red-A200: #ff5252;--md-red-A400: #ff1744;--md-red-A700: #d50000;--md-pink-50: #fce4ec;--md-pink-100: #f8bbd0;--md-pink-200: #f48fb1;--md-pink-300: #f06292;--md-pink-400: #ec407a;--md-pink-500: #e91e63;--md-pink-600: #d81b60;--md-pink-700: #c2185b;--md-pink-800: #ad1457;--md-pink-900: #880e4f;--md-pink-A100: #ff80ab;--md-pink-A200: #ff4081;--md-pink-A400: #f50057;--md-pink-A700: #c51162;--md-purple-50: #f3e5f5;--md-purple-100: #e1bee7;--md-purple-200: #ce93d8;--md-purple-300: #ba68c8;--md-purple-400: #ab47bc;--md-purple-500: #9c27b0;--md-purple-600: #8e24aa;--md-purple-700: #7b1fa2;--md-purple-800: #6a1b9a;--md-purple-900: #4a148c;--md-purple-A100: #ea80fc;--md-purple-A200: #e040fb;--md-purple-A400: #d500f9;--md-purple-A700: #aa00ff;--md-deep-purple-50: #ede7f6;--md-deep-purple-100: #d1c4e9;--md-deep-purple-200: #b39ddb;--md-deep-purple-300: #9575cd;--md-deep-purple-400: #7e57c2;--md-deep-purple-500: #673ab7;--md-deep-purple-600: #5e35b1;--md-deep-purple-700: #512da8;--md-deep-purple-800: #4527a0;--md-deep-purple-900: #311b92;--md-deep-purple-A100: #b388ff;--md-deep-purple-A200: #7c4dff;--md-deep-purple-A400: #651fff;--md-deep-purple-A700: #6200ea;--md-indigo-50: #e8eaf6;--md-indigo-100: #c5cae9;--md-indigo-200: #9fa8da;--md-indigo-300: #7986cb;--md-indigo-400: #5c6bc0;--md-indigo-500: #3f51b5;--md-indigo-600: #3949ab;--md-indigo-700: #303f9f;--md-indigo-800: #283593;--md-indigo-900: #1a237e;--md-indigo-A100: #8c9eff;--md-indigo-A200: #536dfe;--md-indigo-A400: #3d5afe;--md-indigo-A700: #304ffe;--md-blue-50: #e3f2fd;--md-blue-100: #bbdefb;--md-blue-200: #90caf9;--md-blue-300: #64b5f6;--md-blue-400: #42a5f5;--md-blue-500: #2196f3;--md-blue-600: #1e88e5;--md-blue-700: #1976d2;--md-blue-800: #1565c0;--md-blue-900: #0d47a1;--md-blue-A100: #82b1ff;--md-blue-A200: #448aff;--md-blue-A400: #2979ff;--md-blue-A700: #2962ff;--md-light-blue-50: #e1f5fe;--md-light-blue-100: #b3e5fc;--md-light-blue-200: #81d4fa;--md-light-blue-300: #4fc3f7;--md-light-blue-400: #29b6f6;--md-light-blue-500: #03a9f4;--md-light-blue-600: #039be5;--md-light-blue-700: #0288d1;--md-light-blue-800: #0277bd;--md-light-blue-900: #01579b;--md-light-blue-A100: #80d8ff;--md-light-blue-A200: #40c4ff;--md-light-blue-A400: #00b0ff;--md-light-blue-A700: #0091ea;--md-cyan-50: #e0f7fa;--md-cyan-100: #b2ebf2;--md-cyan-200: #80deea;--md-cyan-300: #4dd0e1;--md-cyan-400: #26c6da;--md-cyan-500: #00bcd4;--md-cyan-600: #00acc1;--md-cyan-700: #0097a7;--md-cyan-800: #00838f;--md-cyan-900: #006064;--md-cyan-A100: #84ffff;--md-cyan-A200: #18ffff;--md-cyan-A400: #00e5ff;--md-cyan-A700: #00b8d4;--md-teal-50: #e0f2f1;--md-teal-100: #b2dfdb;--md-teal-200: #80cbc4;--md-teal-300: #4db6ac;--md-teal-400: #26a69a;--md-teal-500: #009688;--md-teal-600: #00897b;--md-teal-700: #00796b;--md-teal-800: #00695c;--md-teal-900: #004d40;--md-teal-A100: #a7ffeb;--md-teal-A200: #64ffda;--md-teal-A400: #1de9b6;--md-teal-A700: #00bfa5;--md-green-50: #e8f5e9;--md-green-100: #c8e6c9;--md-green-200: #a5d6a7;--md-green-300: #81c784;--md-green-400: #66bb6a;--md-green-500: #4caf50;--md-green-600: #43a047;--md-green-700: #388e3c;--md-green-800: #2e7d32;--md-green-900: #1b5e20;--md-green-A100: #b9f6ca;--md-green-A200: #69f0ae;--md-green-A400: #00e676;--md-green-A700: #00c853;--md-light-green-50: #f1f8e9;--md-light-green-100: #dcedc8;--md-light-green-200: #c5e1a5;--md-light-green-300: #aed581;--md-light-green-400: #9ccc65;--md-light-green-500: #8bc34a;--md-light-green-600: #7cb342;--md-light-green-700: #689f38;--md-light-green-800: #558b2f;--md-light-green-900: #33691e;--md-light-green-A100: #ccff90;--md-light-green-A200: #b2ff59;--md-light-green-A400: #76ff03;--md-light-green-A700: #64dd17;--md-lime-50: #f9fbe7;--md-lime-100: #f0f4c3;--md-lime-200: #e6ee9c;--md-lime-300: #dce775;--md-lime-400: #d4e157;--md-lime-500: #cddc39;--md-lime-600: #c0ca33;--md-lime-700: #afb42b;--md-lime-800: #9e9d24;--md-lime-900: #827717;--md-lime-A100: #f4ff81;--md-lime-A200: #eeff41;--md-lime-A400: #c6ff00;--md-lime-A700: #aeea00;--md-yellow-50: #fffde7;--md-yellow-100: #fff9c4;--md-yellow-200: #fff59d;--md-yellow-300: #fff176;--md-yellow-400: #ffee58;--md-yellow-500: #ffeb3b;--md-yellow-600: #fdd835;--md-yellow-700: #fbc02d;--md-yellow-800: #f9a825;--md-yellow-900: #f57f17;--md-yellow-A100: #ffff8d;--md-yellow-A200: #ffff00;--md-yellow-A400: #ffea00;--md-yellow-A700: #ffd600;--md-amber-50: #fff8e1;--md-amber-100: #ffecb3;--md-amber-200: #ffe082;--md-amber-300: #ffd54f;--md-amber-400: #ffca28;--md-amber-500: #ffc107;--md-amber-600: #ffb300;--md-amber-700: #ffa000;--md-amber-800: #ff8f00;--md-amber-900: #ff6f00;--md-amber-A100: #ffe57f;--md-amber-A200: #ffd740;--md-amber-A400: #ffc400;--md-amber-A700: #ffab00;--md-orange-50: #fff3e0;--md-orange-100: #ffe0b2;--md-orange-200: #ffcc80;--md-orange-300: #ffb74d;--md-orange-400: #ffa726;--md-orange-500: #ff9800;--md-orange-600: #fb8c00;--md-orange-700: #f57c00;--md-orange-800: #ef6c00;--md-orange-900: #e65100;--md-orange-A100: #ffd180;--md-orange-A200: #ffab40;--md-orange-A400: #ff9100;--md-orange-A700: #ff6d00;--md-deep-orange-50: #fbe9e7;--md-deep-orange-100: #ffccbc;--md-deep-orange-200: #ffab91;--md-deep-orange-300: #ff8a65;--md-deep-orange-400: #ff7043;--md-deep-orange-500: 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sourceMappingURL=mkdocs-jupyter.css.map*/ init_mathjax = function() { if (window.MathJax) { // MathJax loaded MathJax.Hub.Config({ TeX: { equationNumbers: { autoNumber: \"AMS\", useLabelIds: true } }, tex2jax: { inlineMath: [ ['$','$'], [\"\\\\(\",\"\\\\)\"] ], displayMath: [ ['$$','$$'], [\"\\\\[\",\"\\\\]\"] ], processEscapes: true, processEnvironments: true }, displayAlign: 'center', CommonHTML: { linebreaks: { automatic: true } } }); MathJax.Hub.Queue([\"Typeset\", MathJax.Hub]); } } init_mathjax(); RNA-seq differential gene expression This tutorial will cover the steps for performing Differential Gene Expression on the RNA-seq data obtained from Galaxy. At the end of this tutorial you will be able to use R to Perform preliminary analyses of the RNA-seq results Find differentially expressed genes between two conditions using edgeR The present tutorial, like the rest of the course material, is available at our open-source github repository . To use this notebook, use the NGS (R) kernel that contains the packages. Choose it by selecting Kernel -> Change Kernel in the menu on top of the window. A few introductory points to run this notebook (click to show): To use this notebook, use the NGS (R) kernel that contains the packages. Choose it by selecting Kernel -> Change Kernel in the menu on top of the window. In this notebook you will use only R commands On some computers, you might see the result of the commands once they are done running. This means you will wait some time while the computer is crunching, and only afterwards you will see the result of the command you have executed You can run the code in each cell by clicking on the run cell button, or by pressing Shift + Enter . When the code is done running, a small green check sign will appear on the left side You need to run the cells in sequential order, please do not run a cell until the one above finished running and do not skip any cells Each cell contains a short description of the code and the output you should get. Please try not to focus on understanding the code for each command in too much detail, but rather try to focus on the output You can create new code cells by pressing + in the Menu bar above.
    Load the necessary R libraries In [1]: Copied! library ( VennDiagram ) library ( dplyr ) library ( tibble ) library ( formattable ) library ( mixOmics ) library ( pheatmap ) library ( edgeR ) library(VennDiagram) library(dplyr) library(tibble) library(formattable) library(mixOmics) library(pheatmap) library(edgeR) Warning message: \u201cpackage \u2018VennDiagram\u2019 was built under R version 4.1.3\u201d Loading required package: grid Loading required package: futile.logger Warning message: \u201cpackage \u2018futile.logger\u2019 was built under R version 4.1.3\u201d Warning message: \u201cpackage \u2018dplyr\u2019 was built under R version 4.1.3\u201d Attaching package: \u2018dplyr\u2019 The following objects are masked from \u2018package:stats\u2019: filter, lag The following objects are masked from \u2018package:base\u2019: intersect, setdiff, setequal, union Warning message: \u201cpackage \u2018tibble\u2019 was built under R version 4.1.3\u201d Warning message: \u201cpackage \u2018formattable\u2019 was built under R version 4.1.3\u201d Loading required package: MASS Warning message: \u201cpackage \u2018MASS\u2019 was built under R version 4.1.3\u201d Attaching package: \u2018MASS\u2019 The following object is masked from \u2018package:formattable\u2019: area The following object is masked from \u2018package:dplyr\u2019: select Loading required package: lattice Warning message: \u201cpackage \u2018lattice\u2019 was built under R version 4.1.3\u201d Loading required package: ggplot2 Warning message: \u201cpackage \u2018ggplot2\u2019 was built under R version 4.1.3\u201d Loaded mixOmics 6.17.26 Thank you for using mixOmics! Tutorials: http://mixomics.org Bookdown vignette: https://mixomicsteam.github.io/Bookdown Questions, issues: Follow the prompts at http://mixomics.org/contact-us Cite us: citation('mixOmics') Warning message: \u201cpackage \u2018pheatmap\u2019 was built under R version 4.1.3\u201d Warning message: \u201cpackage \u2018edgeR\u2019 was built under R version 4.1.3\u201d Loading required package: limma Warning message: \u201cpackage \u2018limma\u2019 was built under R version 4.1.3\u201d EdgeR - Data filtering and Normalization \u00b6 We will use the edgeR package to test for differentially expressed genes between our Control and Treatment Samples. You can read more about the edgeR package and its functionalities here . This exercise largely follows their user manual. File processing \u00b6 The data for this exercise comes from the 12 tabular files with Reads per Gene counts generated by STAR Mapping in the raw-data alignment part of this course. We want to create a table where each column is a sample, and the content of the table are the read counts from STAR. We must merge the 12 files with Reads per Gene information into a single file. If you aligned datasets in the first notebook with jupyterlab, then you will find the files using the following command: In [2]: Copied! samples <- sort ( system ( \"find results/STAR_output/*_align_contigs_1_2 -name \\\"*ReadsPerGene.out.tab\\\"\" , intern = TRUE )) print ( samples ) Read_counts <- do.call ( cbind , lapply ( samples , function ( x ) read.delim ( file = x , header = FALSE ))) samples < - sort(system(\"find results/STAR_output/*_align_contigs_1_2 -name \\\"*ReadsPerGene.out.tab\\\"\", intern=TRUE)) print(samples) Read_counts < - do.call(cbind, lapply(samples, function(x) read.delim(file=x, header = FALSE))) [1] \"results/STAR_output/S10_align_contigs_1_2/S10_1_1ReadsPerGene.out.tab\" [2] \"results/STAR_output/S10_align_contigs_1_2/S10_1_2ReadsPerGene.out.tab\" [3] \"results/STAR_output/S10_align_contigs_1_2/S10_1_3ReadsPerGene.out.tab\" [4] \"results/STAR_output/S10_align_contigs_1_2/S10_2_1ReadsPerGene.out.tab\" [5] \"results/STAR_output/S10_align_contigs_1_2/S10_2_2ReadsPerGene.out.tab\" [6] \"results/STAR_output/S10_align_contigs_1_2/S10_2_3ReadsPerGene.out.tab\" [7] \"results/STAR_output/TI_align_contigs_1_2/TI_1_1ReadsPerGene.out.tab\" [8] \"results/STAR_output/TI_align_contigs_1_2/TI_1_2ReadsPerGene.out.tab\" [9] \"results/STAR_output/TI_align_contigs_1_2/TI_1_3ReadsPerGene.out.tab\" [10] \"results/STAR_output/TI_align_contigs_1_2/TI_2_1ReadsPerGene.out.tab\" [11] \"results/STAR_output/TI_align_contigs_1_2/TI_2_2ReadsPerGene.out.tab\" [12] \"results/STAR_output/TI_align_contigs_1_2/TI_2_3ReadsPerGene.out.tab\" If you aligned datasets interactively with Galaxy , then you will need to create the folder tabular_files into the results folder copy the tabular files from STAR into the created folder. Each file must have the sample name and end by ReadsPerGene.out.tab . For example S10_1_1ReadsPerGene.out.tab run the following commands removing the # symbol In [ ]: Copied! #samples <- sort(system(\"find results/tabular_files/ -name \\\"*ReadsPerGene.out.tab\\\"\", intern=TRUE)) #print(samples) #Read_counts <- do.call(cbind, lapply(samples, function(x) read.delim(file=x, header = FALSE))) #samples < - sort(system(\"find results/tabular_files/ -name \\\"*ReadsPerGene.out.tab\\\"\", intern=TRUE)) #print(samples) #Read_counts < - do.call(cbind, lapply(samples, function(x) read.delim(file=x, header = FALSE))) The data frame has genes as rows and samples as columns and stores the gene expression counts (value representing the total number of sequence reads that originated from a particular gene in a sample) for each of the 12 samples. This data frame should have 12 columns and 366 rows. In [3]: Copied! rownames ( Read_counts ) <- Read_counts [, 1 ] Read_counts <- Read_counts [ c ( 5 : nrow ( Read_counts )), c ( seq ( 2 , 46 , by = 4 ))] colnames ( Read_counts ) <- c ( \"S10_1_1\" , \"S10_1_2\" , \"S10_1_3\" , \"S10_2_1\" , \"S10_2_2\" , \"S10_2_3\" , \"TI_1_1\" , \"TI_1_2\" , \"TI_1_3\" , \"TI_2_1\" , \"TI_2_2\" , \"TI_2_3\" ) head ( Read_counts , n = 10 ) dim ( Read_counts ) # dimensions of the data frame rownames(Read_counts) < - Read_counts[,1] Read_counts < - Read_counts[c(5:nrow(Read_counts)), c(seq(2, 46, by=4))] colnames(Read_counts) < - c(\"S10_1_1\", \"S10_1_2\", \"S10_1_3\", \"S10_2_1\", \"S10_2_2\", \"S10_2_3\", \"TI_1_1\", \"TI_1_2\", \"TI_1_3\", \"TI_2_1\", \"TI_2_2\", \"TI_2_3\") head(Read_counts, n=10) dim(Read_counts) # dimensions of the data frame A data.frame: 10 \u00d7 12 S10_1_1 S10_1_2 S10_1_3 S10_2_1 S10_2_2 S10_2_3 TI_1_1 TI_1_2 TI_1_3 TI_2_1 TI_2_2 TI_2_3 g175 143 226 227 217 206 193 234 205 198 221 206 165 g176 17 12 15 8 14 18 29 19 30 6 11 23 g177 0 0 0 0 0 0 0 0 0 0 0 0 g178 0 0 0 0 0 0 0 0 2 2 1 2 g179 0 0 0 0 0 0 0 0 0 0 0 0 g180 2773 5223 4350 4139 3209 4644 1015 1313 889 2675 1023 2565 g181 473 679 583 437 390 450 642 700 697 650 459 410 g182 19 15 20 9 8 4 13 7 8 6 5 4 g183 0 0 0 0 0 0 0 0 0 0 0 0 g184 30 22 50 57 103 83 36 29 18 107 69 89 .list-inline {list-style: none; margin:0; padding: 0} .list-inline>li {display: inline-block} .list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex} 366 12 Import the Metadata table. This file, as its name suggests, contains information about each of the 12 RNA-seq samples, such as the treatment (Condition), genotype and replicate. Note that the order of the rows in the Metadata table should be the same as the columns in the Read_counts file generated above. In [4]: Copied! metadata <- read.csv ( \"../Data/Clover_Data/metadata.csv\" , sep = \";\" , row.names = 1 , stringsAsFactors = TRUE ) metadata metadata < - read.csv(\"../Data/Clover_Data/metadata.csv\", sep =\";\", row.names=1, stringsAsFactors=TRUE) metadata A data.frame: 12 \u00d7 3 Condition Genotype Replicate S10_1_1 Control S10 1 S10_1_2 Control S10 2 S10_1_3 Control S10 3 S10_2_1 Treatment S10 1 S10_2_2 Treatment S10 2 S10_2_3 Treatment S10 3 TI_1_1 Control Tienshan 1 TI_1_2 Control Tienshan 2 TI_1_3 Control Tienshan 3 TI_2_1 Treatment Tienshan 1 TI_2_2 Treatment Tienshan 2 TI_2_3 Treatment Tienshan 3 In order to aid the following steps, we will create a Group for each sample (a new column in the metadata) based on the Genotype&Condition of each sample and assign the three replicates to this group. In [5]: Copied! Group <- factor ( paste ( metadata $ Genotype , metadata $ Condition , sep = \"_\" )) metadata <- cbind ( metadata , Group = Group ) metadata Group < - factor(paste(metadata$Genotype, metadata$Condition, sep=\"_\")) metadata < - cbind(metadata,Group=Group) metadata A data.frame: 12 \u00d7 4 Condition Genotype Replicate Group S10_1_1 Control S10 1 S10_Control S10_1_2 Control S10 2 S10_Control S10_1_3 Control S10 3 S10_Control S10_2_1 Treatment S10 1 S10_Treatment S10_2_2 Treatment S10 2 S10_Treatment S10_2_3 Treatment S10 3 S10_Treatment TI_1_1 Control Tienshan 1 Tienshan_Control TI_1_2 Control Tienshan 2 Tienshan_Control TI_1_3 Control Tienshan 3 Tienshan_Control TI_2_1 Treatment Tienshan 1 Tienshan_Treatment TI_2_2 Treatment Tienshan 2 Tienshan_Treatment TI_2_3 Treatment Tienshan 3 Tienshan_Treatment Create the DGEList object \u00b6 We will merge the read counts and the metadata into a list-based data object named DGEList, which can be manipulated as any list object in R. The main components of the DGEList object are the matrix \"counts\" containing our read per gene counts and a data.frame \"samples\" containing the metadata. Note that all the genes with zero counts across all samples were eliminated. In [6]: Copied! DGEList <- DGEList ( Read_counts , remove.zeros = TRUE ) DGEList $ samples $ Condition <- relevel ( metadata $ Condition , ref = \"Control\" ) DGEList $ samples $ Genotype <- metadata $ Genotype DGEList $ samples $ group <- metadata $ Group DGEList DGEList < - DGEList(Read_counts, remove.zeros = TRUE) DGEList$samples$Condition < - relevel(metadata$Condition, ref = \"Control\") DGEList$samples$Genotype < - metadata$Genotype DGEList$samples$group < - metadata$Group DGEList Removing 99 rows with all zero counts $counts A matrix: 267 \u00d7 12 of type int S10_1_1 S10_1_2 S10_1_3 S10_2_1 S10_2_2 S10_2_3 TI_1_1 TI_1_2 TI_1_3 TI_2_1 TI_2_2 TI_2_3 g175 143 226 227 217 206 193 234 205 198 221 206 165 g176 17 12 15 8 14 18 29 19 30 6 11 23 g178 0 0 0 0 0 0 0 0 2 2 1 2 g180 2773 5223 4350 4139 3209 4644 1015 1313 889 2675 1023 2565 g181 473 679 583 437 390 450 642 700 697 650 459 410 g182 19 15 20 9 8 4 13 7 8 6 5 4 g184 30 22 50 57 103 83 36 29 18 107 69 89 g185 0 2 0 0 0 0 0 1 0 0 0 1 g186 1 0 0 0 0 0 0 0 0 0 0 0 g187 1 1 2 0 1 1 58 49 57 28 32 29 g188 316 285 417 200 184 322 1276 855 1341 402 809 547 g190 14 18 29 25 17 31 7 6 12 20 7 6 g191 2 2 1 1 0 0 0 0 0 0 0 0 g192 1 1 1 1 1 0 6 10 2 3 8 2 g193 208 231 301 289 161 279 70 61 60 128 160 91 g194 40 41 37 44 17 43 8 10 7 8 105 25 g195 54 85 85 71 54 43 56 54 42 67 68 56 g196 77 120 118 186 152 177 5 9 5 42 20 34 g197 1 6 5 18 14 21 15 44 12 32 16 17 g198 14 27 10 11 2 2 6 6 1 2 2 0 g199 0 0 0 0 0 0 0 0 0 0 1 0 g200 57 80 94 11 8 23 89 47 67 5 47 5 g203 815 1188 1412 1139 1034 1127 911 852 662 892 781 784 g204 250 312 348 277 275 264 125 104 133 119 91 130 g205 109 132 181 140 114 151 89 73 66 78 46 50 g206 0 1 2 7 4 9 4 0 7 0 1 2 g207 0 1 0 0 4 3 1 3 4 4 3 3 g208 0 1 0 0 0 0 0 1 0 1 0 0 g209 0 0 0 0 0 0 0 0 1 0 0 0 g210 52 76 60 12 12 13 61 73 94 54 45 21 \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee g135 0 0 0 1 0 0 5 1 0 2 0 0 g139 0 1 1 0 0 0 12 13 11 4 3 3 g140 0 5 1 0 0 2 5 4 0 0 2 0 g141 177 217 224 131 117 166 117 85 67 80 79 77 g142 488 713 557 241 154 228 983 1057 1023 1075 794 933 g144 3319 3987 4763 2249 1996 2260 4405 3880 4585 5072 3618 3590 g146 293 330 350 913 775 731 108 92 115 431 151 226 g147 6 3 3 0 8 10 1 1 1 0 1 0 g148 19 30 24 15 4 12 23 19 25 10 19 8 g149 35 62 65 57 58 53 114 103 91 92 79 93 g150 263 411 278 752 1378 1300 106 112 70 516 200 508 g151 44 44 50 92 92 84 23 26 25 56 43 31 g152 242 258 294 425 381 521 15 8 8 16 21 15 g153 142 144 181 233 177 233 31 49 50 50 45 57 g155 0 4 2 1 0 0 1 0 3 0 0 1 g156 0 0 0 0 0 0 0 3 2 0 0 1 g157 6 1 3 223 52 152 4 7 4 153 47 155 g158 0 0 0 7 1 3 0 0 1 1 0 0 g161 25 38 18 1 9 2 63 23 43 0 24 6 g162 31 43 38 43 25 28 0 0 0 0 0 0 g163 1 0 12 37 8 18 9 4 8 16 13 15 g164 69 58 97 294 123 168 56 58 60 146 101 135 g165 203 376 594 1343 2062 1610 265 229 214 488 270 490 g167 2 0 0 2 0 0 0 0 0 0 0 0 g168 2 14 6 0 0 5 31 26 38 3 27 10 g169 0 0 1 0 1 1 0 0 0 0 0 0 g170 0 0 0 0 0 0 0 1 0 0 0 0 g171 0 5 0 0 0 5 0 0 0 1 0 0 g172 1 2 2 6 4 3 3 1 2 3 3 0 g173 80 107 120 78 138 121 67 86 69 96 105 105 $samples A data.frame: 12 \u00d7 5 group lib.size norm.factors Condition Genotype S10_1_1 S10_Control 43614 1 Control S10 S10_1_2 S10_Control 58803 1 Control S10 S10_1_3 S10_Control 62654 1 Control S10 S10_2_1 S10_Treatment 59909 1 Treatment S10 S10_2_2 S10_Treatment 56761 1 Treatment S10 S10_2_3 S10_Treatment 63152 1 Treatment S10 TI_1_1 Tienshan_Control 43387 1 Control Tienshan TI_1_2 Tienshan_Control 38355 1 Control Tienshan TI_1_3 Tienshan_Control 40304 1 Control Tienshan TI_2_1 Tienshan_Treatment 55509 1 Treatment Tienshan TI_2_2 Tienshan_Treatment 39909 1 Treatment Tienshan TI_2_3 Tienshan_Treatment 45008 1 Treatment Tienshan Preliminary data analysis \u00b6 First, we will calculate the \"pseudoCounts\" as log2 of the reads per gene counts. This is not part of the actual differential gene expression analysis but is helpful for data exploration and quality assessment. We will look at a histogram of one of the samples and a boxplot representation of the log2 counts for all the 12 samples. Note that there are many genes with a low number of mapped reads and that there are differences between the average read counts for each library. In [7]: Copied! pseudoCounts <- log2 ( DGEList $ counts + 1 ) head ( pseudoCounts ) hist ( pseudoCounts [ , \"S10_1_1\" ], main = \"\" , xlab = \"Read counts\" ) boxplot ( pseudoCounts , col = \"gray\" , las = 3 , cex.names = 1 ) pseudoCounts < - log2(DGEList$counts + 1) head(pseudoCounts) hist(pseudoCounts[ ,\"S10_1_1\"], main = \"\", xlab = \"Read counts\") boxplot(pseudoCounts, col = \"gray\", las = 3, cex.names = 1) A matrix: 6 \u00d7 12 of type dbl S10_1_1 S10_1_2 S10_1_3 S10_2_1 S10_2_2 S10_2_3 TI_1_1 TI_1_2 TI_1_3 TI_2_1 TI_2_2 TI_2_3 g175 7.169925 7.826548 7.832890 7.768184 7.693487 7.599913 7.876517 7.686501 7.636625 7.794416 7.693487 7.375039 g176 4.169925 3.700440 4.000000 3.169925 3.906891 4.247928 4.906891 4.321928 4.954196 2.807355 3.584963 4.584963 g178 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.584963 1.584963 1.000000 1.584963 g180 11.437752 12.350939 12.087131 12.015415 11.648358 12.181463 9.988685 10.359750 9.797662 11.385862 10.000000 11.325305 g181 8.888743 9.409391 9.189825 8.774787 8.611025 8.816984 9.328675 9.453271 9.447083 9.346514 8.845490 8.682995 g182 4.321928 4.000000 4.392317 3.321928 3.169925 2.321928 3.807355 3.000000 3.169925 2.807355 2.584963 2.321928 We can also create a PCA plot of the samples in order to assess the differences between the Genotypes and Conditions, but also between the replicates. In this plot the samples that are similar cluster together, while samples that are different are further apart. In this type of plot, we would expect samples from the same group (the three replicates for each sample) to exhibit a similar gene expression profile thus clustering together while being separated from the other samples. In [8]: Copied! resPCA <- pca ( t ( pseudoCounts ), ncomp = 6 ) plotIndiv ( resPCA , group = metadata $ Genotype , pch = metadata $ Condition , legend = T , legend.title = 'Genotype' , legend.title.pch = 'Condition' , title = 'PCA plot raw counts' , style = 'ggplot2' , size.xlabel = 10 , size.ylabel = 10 ) resPCA < - pca(t(pseudoCounts), ncomp = 6) plotIndiv(resPCA, group = metadata$Genotype, pch=metadata$Condition, legend = T, legend.title = 'Genotype', legend.title.pch = 'Condition', title = 'PCA plot raw counts', style = 'ggplot2', size.xlabel = 10, size.ylabel = 10) Filtering the lowly expressed genes \u00b6 As seen previously, many genes have a low number of read counts in our samples. The genes with very low counts across all libraries provide little evidence for differential expression, thus we should eliminate these genes before the analysis. One of the filtering methods we can use is the \"filterByExpr\" function provided by the edgeR package. By default, this function keeps only the genes that have at least 10 reads per group, but other cutoffs can also be applied. In [9]: Copied! keep <- filterByExpr ( DGEList , group = metadata $ Group ) #create the filter DGEList <- DGEList [ keep , , keep.lib.sizes = FALSE ] #apply the filter to on the DGEList object table ( keep ) #Check the number of genes that passed the filter keep < - filterByExpr(DGEList, group=metadata$Group) #create the filter DGEList < - DGEList[keep, , keep.lib.sizes=FALSE] #apply the filter to on the DGEList object table(keep) #Check the number of genes that passed the filter keep FALSE TRUE 104 163 Normalization \u00b6 As we are working with multiple samples we need to normalize the read counts per gene in order to account for compositional and technical differences between the 12 RNA-seq libraries. For this, we will calculate normalization factors using the trimmed mean of M-values (TMM) method. You can read more about different normalization methods in the user manual. Note that running \"calcNormFactors\" does not change the actual reads per gene counts, it just fills the \"norm.factors\" column in DGEList$samples . These factors will be used to scale the read counts for each library. From the user guide: \"A normalization factor below one indicates that a small number of high count genes are monopolizing the sequencing, causing the counts for other genes to be lower than would be usual given the library size.\" In [10]: Copied! DGEList <- calcNormFactors ( DGEList , method = \"RLE\" ) DGEList $ samples DGEList < - calcNormFactors(DGEList, method=\"RLE\") DGEList$samples A data.frame: 12 \u00d7 5 group lib.size norm.factors Condition Genotype S10_1_1 S10_Control 43506 1.0897129 Control S10 S10_1_2 S10_Control 58660 1.0385093 Control S10 S10_1_3 S10_Control 62512 1.0362962 Control S10 S10_2_1 S10_Treatment 59741 0.9802860 Treatment S10 S10_2_2 S10_Treatment 56653 0.8418644 Treatment S10 S10_2_3 S10_Treatment 63008 0.8949144 Treatment S10 TI_1_1 Tienshan_Control 43174 1.0618440 Control Tienshan TI_1_2 Tienshan_Control 38203 1.0431678 Control Tienshan TI_1_3 Tienshan_Control 40178 1.0676351 Control Tienshan TI_2_1 Tienshan_Treatment 55391 0.9048196 Treatment Tienshan TI_2_2 Tienshan_Treatment 39810 1.1235077 Treatment Tienshan TI_2_3 Tienshan_Treatment 44910 0.9603761 Treatment Tienshan Normalized counts - Exploratory Data analysis \u00b6 For data analysis purposes normalized log2 counts can be extracted from the DGEList object using the function CPM (counts per million). We will generate the same plots as for the raw counts in order to compare the data before and after normalization. Do the plots for normalized counts look different compared with the plots computed before data filtering and normalization? In [11]: Copied! pseudoNormCounts <- cpm ( DGEList , log = TRUE , prior.count = 1 ) head ( pseudoNormCounts ) hist ( pseudoNormCounts [ , \"S10_1_1\" ], main = \"\" , xlab = \"counts\" ) boxplot ( pseudoNormCounts , col = \"gray\" , las = 3 , cex.names = 1 ) resPCA <- pca ( t ( pseudoNormCounts ), ncomp = 6 ) plotIndiv ( resPCA , group = metadata $ Genotype , pch = metadata $ Condition , legend = T , legend.title = 'Genotype' , legend.title.pch = 'Condition' , title = 'PCA plot normalized counts' , style = 'ggplot2' , size.xlabel = 10 , size.ylabel = 10 ) pseudoNormCounts < - cpm(DGEList, log = TRUE, prior.count = 1) head(pseudoNormCounts) hist(pseudoNormCounts[ ,\"S10_1_1\"], main = \"\", xlab = \"counts\") boxplot(pseudoNormCounts, col = \"gray\", las = 3, cex.names = 1) resPCA < - pca(t(pseudoNormCounts), ncomp = 6) plotIndiv(resPCA, group = metadata$Genotype, pch=metadata$Condition, legend = T, legend.title = 'Genotype', legend.title.pch = 'Condition', title = 'PCA plot normalized counts', style = 'ggplot2', size.xlabel = 10, size.ylabel = 10) A matrix: 6 \u00d7 12 of type dbl S10_1_1 S10_1_2 S10_1_3 S10_2_1 S10_2_2 S10_2_3 TI_1_1 TI_1_2 TI_1_3 TI_2_1 TI_2_2 TI_2_3 g175 11.568005 11.864813 11.782957 11.863090 12.083127 11.749272 12.323049 12.334198 12.178544 12.112851 12.175386 11.908906 g176 8.564108 7.760868 7.974199 7.290213 8.292080 8.405708 9.349782 8.956131 9.490388 7.125494 8.054467 9.111569 g180 15.836359 16.387906 16.035457 16.109276 16.038322 16.329943 14.435626 15.008665 14.340400 15.704307 14.482504 15.860317 g181 13.287211 13.446752 13.138771 12.869139 13.000828 12.965820 13.775545 14.101988 13.989757 13.664955 13.327806 13.217591 g182 8.716557 8.056048 8.360376 7.439590 7.551908 6.505541 8.245462 7.611500 7.689402 7.125494 7.041192 6.815835 g184 9.350249 8.573811 9.628852 9.955925 11.089735 10.542877 9.653135 9.546090 8.779819 11.073313 10.609695 11.024686 EdgeR - Testing for Differentially expressed genes (DEGs) \u00b6 We use edgeR for Differential Gene Expression using the GLM method (Generalized linear model) with treatment and genotype effects After we concluded the exploratory data analysis and the filtering and normalization steps we can now start testing for differentially expressed genes between our samples. For this, we first need to define a \"design matrix\" which describes our experimental design. We construct a matrix containing samples as rows and our previously defined groups (S10_Control, S10_Treatment, Tienshan_Control, Tienshan_Treatment) as columns. The samples belonging to each group are assigned a \"1\" in this matrix. In [12]: Copied! design.matrix <- model.matrix ( ~ 0 + Group ) rownames ( design.matrix ) <- colnames ( DGEList ) colnames ( design.matrix ) <- levels ( metadata $ Group ) design.matrix design.matrix < - model.matrix(~0+Group) rownames(design.matrix) < - colnames(DGEList) colnames(design.matrix) < - levels(metadata$Group) design.matrix A matrix: 12 \u00d7 4 of type dbl S10_Control S10_Treatment Tienshan_Control Tienshan_Treatment S10_1_1 1 0 0 0 S10_1_2 1 0 0 0 S10_1_3 1 0 0 0 S10_2_1 0 1 0 0 S10_2_2 0 1 0 0 S10_2_3 0 1 0 0 TI_1_1 0 0 1 0 TI_1_2 0 0 1 0 TI_1_3 0 0 1 0 TI_2_1 0 0 0 1 TI_2_2 0 0 0 1 TI_2_3 0 0 0 1 For easier pairwise comparisons between the groups we can create some \"contrasts\" using the \"makeContrasts\" function. This will tell the program which samples we will like to consider as our \"Control\" and which as our \"Treatment\" groups. The Control groups will be assigned a \"-1\" and the Treatment groups a \"1\". When using multiple Control and Treatment samples in the same contrast we need to devide by the number of samples used as for example in the contrast S10_Tienshan, where we use both S10 and Ti samples. For example, the contrast S10 = S10_Treatment - S10_Control will test for differentially expressed genes between the S10 treatment samples vs the S10 Control samples. In [13]: Copied! contrasts <- makeContrasts ( S10 = S10_Treatment - S10_Control , Tienshan = Tienshan_Treatment - Tienshan_Control , S10_Tienshan = ( S10_Treatment + Tienshan_Treatment ) / 2 - ( S10_Control + Tienshan_Control ) / 2 , levels = design.matrix ) contrasts contrasts < - makeContrasts( S10 = S10_Treatment-S10_Control, Tienshan = Tienshan_Treatment-Tienshan_Control, S10_Tienshan= (S10_Treatment+Tienshan_Treatment)/2 - (S10_Control+Tienshan_Control)/2, levels=design.matrix) contrasts A matrix: 4 \u00d7 3 of type dbl S10 Tienshan S10_Tienshan S10_Control -1 0 -0.5 S10_Treatment 1 0 0.5 Tienshan_Control 0 -1 -0.5 Tienshan_Treatment 0 1 0.5 Any ideas for other contrasts that migth be interesting to explore? The following cell will run two mandatory steps in order to fit a model in edgeR. First, the dispersion needs to be estimated, this is a measure of the degree of inter-library variation for each gene. Afterwards, a QL ( quasi-likelihood) model representing the sample design is fitted using the \"glmQLFit\" function. You can read more about these steps in the edgeR user guide. In [14]: Copied! DGEList <- estimateDisp ( DGEList , design.matrix ) fit <- glmQLFit ( DGEList , design.matrix ) DGEList < - estimateDisp(DGEList, design.matrix) fit < - glmQLFit(DGEList, design.matrix) DEGs for White clover S10 plants Treatment vs Control \u00b6 Find DEGs for White clover S10 plants in Treatment condition compared with the Control condition We will test for differentially expressed genes using the quasi-likelihood F-tests method. This is easily done just by running the \"glmQFTest\" function on the fit model and selecting one of the contrasts we created above (in this case the \"S10\" contrast). Next, we will use the topTags function to extract the information about all the genes. In [15]: Copied! glmqlf_S10 <- glmQLFTest ( fit , contrast = contrasts [, \"S10\" ]) DEG_S10 <- topTags ( glmqlf_S10 , n = nrow ( DGEList $ counts )) DEG_S10 glmqlf_S10 < - glmQLFTest(fit, contrast=contrasts[,\"S10\"]) DEG_S10 < - topTags(glmqlf_S10, n = nrow(DGEList$counts)) DEG_S10 $table A data.frame: 163 \u00d7 5 logFC logCPM F PValue FDR g39 3.5861702 14.124630 336.66158 5.227331e-10 8.520550e-08 g232 4.0494125 11.950441 157.50997 3.685988e-08 2.591779e-06 g6 2.3225347 12.999541 150.27854 4.770146e-08 2.591779e-06 g350 2.0530029 13.324566 97.56453 4.890245e-07 1.992775e-05 g99 -1.5387874 11.681004 85.17478 9.976659e-07 3.195090e-05 g142 -1.4235276 13.830692 82.52308 1.176107e-06 3.195090e-05 g240 1.3603712 14.708794 79.98114 1.383201e-06 3.220882e-05 g269 -1.4191681 11.834217 75.66563 1.841279e-06 3.751606e-05 g26 2.1254241 11.366827 68.55898 3.047273e-06 5.518949e-05 g129 -5.3324794 8.679594 60.45459 5.738115e-06 9.353127e-05 g272 3.1405978 13.860652 59.08187 6.432977e-06 9.532503e-05 g157 5.3813801 10.414972 57.03712 7.659515e-06 1.040417e-04 g42 -1.9856547 9.962762 53.97164 1.005146e-05 1.260298e-04 g165 2.2666761 13.690016 51.66777 1.243606e-05 1.447913e-04 g101 3.1488142 13.181625 48.21727 1.736838e-05 1.887363e-04 g15 2.7410696 10.684840 47.29143 1.906062e-05 1.941800e-04 g210 -2.2430064 9.993002 46.52627 2.060621e-05 1.975772e-04 g299 -2.3509276 10.984491 45.75893 2.230566e-05 2.019901e-04 g103 2.6810410 10.579777 44.26963 2.609599e-05 2.238762e-04 g144 -0.7963477 16.186987 43.17707 2.936057e-05 2.392886e-04 g77 1.0984806 14.118231 41.46740 3.548119e-05 2.754016e-04 g125 -1.3099534 10.195970 39.85537 4.266319e-05 3.160955e-04 g298 -2.0471647 9.837072 33.49832 9.395967e-05 6.658881e-04 g104 2.4081173 9.219160 38.54240 1.121281e-04 7.615370e-04 g122 -0.6485441 12.457152 30.90261 1.341148e-04 8.744287e-04 g164 1.4415064 11.156457 30.50383 1.419308e-04 8.897970e-04 g146 1.3983889 12.824184 29.92911 1.541544e-04 9.306356e-04 g313 2.2492040 13.614815 28.41728 1.926822e-04 1.121686e-03 g150 1.9650641 13.229706 27.90020 2.083770e-04 1.171222e-03 g13 -0.6522187 13.101579 26.45593 2.608176e-04 1.417109e-03 \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee g96 -1.873792302 8.939397 0.4844512655 0.4999546 0.6041584 g10 0.233134670 14.382992 0.4834790913 0.5003766 0.6041584 g253 0.052426914 13.741219 0.3075042687 0.5896191 0.7066759 g289 -0.212573283 9.390864 0.2887857862 0.6010328 0.7150974 g312 0.093543041 10.849110 0.2666731965 0.6151559 0.7265972 g301 -0.102000599 10.135184 0.2572520652 0.6214023 0.7274503 g221 -0.277095720 8.469909 0.2522121463 0.6248039 0.7274503 g162 -0.145155616 8.517263 0.2278112475 0.6463283 0.7413085 g50 -0.170907352 8.749274 0.2158314533 0.6507284 0.7413085 g203 0.062836598 14.227601 0.2124612164 0.6532634 0.7413085 g88 0.045949497 14.235850 0.2103049178 0.6548983 0.7413085 g355 -0.287897714 8.890754 0.1803234432 0.6787703 0.7630314 g204 -0.055975779 11.947887 0.1408988543 0.7140799 0.7972262 g306 0.054269738 11.294732 0.0923937800 0.7664733 0.8498990 g193 0.049946343 11.682386 0.0642557849 0.8042743 0.8857886 g205 0.037877227 10.986961 0.0473457745 0.8314821 0.9029713 g194 -0.142990391 9.403497 0.0447552162 0.8360811 0.9029713 g362 0.025629967 11.336529 0.0415198735 0.8420254 0.9029713 g315 0.027958374 11.878331 0.0409766489 0.8430470 0.9029713 g180 0.059680256 15.711409 0.0386140448 0.8475743 0.9029713 g282 -0.026492114 11.756078 0.0247991469 0.8775434 0.9288284 g176 -0.061055115 8.587203 0.0144510429 0.9063467 0.9531258 g126 0.061707217 8.311212 0.0024786868 0.9648334 1.0000000 g128 0.063825269 7.671043 0.0019414812 0.9655950 1.0000000 g227 -0.025740630 7.939955 0.0011908008 0.9730516 1.0000000 g121 0.002660852 12.896620 0.0005233398 0.9821327 1.0000000 g284 0.000000000 8.538720 0.0000000000 1.0000000 1.0000000 g116 0.000000000 7.180297 0.0000000000 1.0000000 1.0000000 g117 0.000000000 7.033307 0.0000000000 1.0000000 1.0000000 g118 0.000000000 7.515646 0.0000000000 1.0000000 1.0000000 $adjust.method 'BH' $comparison '-1*S10_Control 1*S10_Treatment' $test 'glm' We have now created a table with certain parameters calculated for each of the genes analysed. logFC represents the base 2 logarithm of the fold change and it shows us how much the expression of the gene has changed between the two conditions. A logFC of 1 means a doubling in the read per gene count between the control and treatment samples. The genes with a logFC higher than 0 are upregulated while the genes with a logFC lower than 0 are downregulated between the control and treatment samples. logCPM represents the average log2-counts-per-million, the abundance of the gene. F - F-statistic. PValue is the raw p-value. FDR (The false discovery rate) represents the adjusted p-value and is calculated using Benjamini and Hochberg's algorithm. It controls the rate of false positive values under multiple testing. Usually, a threshold of under 5% is set for the FDR. The important information for us in this table is stored in the \"logFC\" and the \"FDR\" columns. The top DE genes have small FDR values and large fold changes Many of the genes in the samples are uninteresting for us, as they have a high FDR and/or low logFC values so we cannot consider them as differentially expressed. We will apply a filtering step in order to keep only the statistically significant genes. We will filter out the genes with an FDR higher than 0.05 and an absolute logFC lower than 1. In [16]: Copied! DEG_S10_filtered <- DEG_S10 $ table [ DEG_S10 $ table $ FDR < 0.05 & abs ( DEG_S10 $ table $ logFC ) > 1 ,] #Filtering DEG_S10_filtered <- rownames_to_column ( DEG_S10_filtered ) %>% rename ( gene_ID = rowname ) #Adding the gene_ID column head ( DEG_S10_filtered ) nrow ( DEG_S10_filtered ) # finding the number of genes that passed the filter DEG_S10_filtered < - DEG_S10$table[DEG_S10$table$FDR < 0.05 & abs(DEG_S10$table$logFC) > 1,] #Filtering DEG_S10_filtered < - rownames_to_column(DEG_S10_filtered) %>% rename(gene_ID = rowname) #Adding the gene_ID column head(DEG_S10_filtered) nrow(DEG_S10_filtered) # finding the number of genes that passed the filter A data.frame: 6 \u00d7 6 gene_ID logFC logCPM F PValue FDR 1 g39 3.586170 14.12463 336.66158 5.227331e-10 8.520550e-08 2 g232 4.049413 11.95044 157.50997 3.685988e-08 2.591779e-06 3 g6 2.322535 12.99954 150.27854 4.770146e-08 2.591779e-06 4 g350 2.053003 13.32457 97.56453 4.890245e-07 1.992775e-05 5 g99 -1.538787 11.68100 85.17478 9.976659e-07 3.195090e-05 6 g142 -1.423528 13.83069 82.52308 1.176107e-06 3.195090e-05 52 We can also visualize the selected genes by plotting a Smear plot or a Volcano plot. The Genes that passed the filter are coloured in red, and the top 10 genes with the lowest FDR value are labelled with their gene ID. We can see that the majority of the genes analysed are either not statistically significant or have a very small logFC. In [17]: Copied! plotSmear ( glmqlf_S10 , de.tags = rownames ( DEG_S10 $ table )[ which ( DEG_S10 $ table $ FDR < 0.05 & abs ( DEG_S10 $ table $ logFC ) > 1 )]) text ( x = DEG_S10_filtered $ logCPM [ 1 : 10 ], y = DEG_S10_filtered $ logFC [ 1 : 10 ], labels = DEG_S10_filtered $ gene_ID [ 1 : 10 ], cex = 0.7 , pos = 1 ) abline ( h = c ( -1 , 1 ), col = \"blue\" ) plotSmear(glmqlf_S10, de.tags = rownames(DEG_S10$table)[which(DEG_S10$table$FDR < 0.05 & abs(DEG_S10$table$logFC) > 1)]) text(x=DEG_S10_filtered$logCPM[1:10], y=DEG_S10_filtered$logFC[1:10], labels=DEG_S10_filtered$gene_ID[1:10], cex=0.7, pos=1) abline(h = c(-1, 1), col = \"blue\") We can also create a heatmap with the log2 read counts of the selected differentially expressed genes so that we can visualise the differences in normalized counts between the Control and the Treatment samples. The genes are ordered by the FDR value. In [18]: Copied! annot_col <- data.frame ( row.names = colnames ( pseudoNormCounts )[ 1 : 6 ], Condition = c ( rep ( \"Control\" , 3 ), rep ( \"Treatment\" , 3 ))) pheatmap ( as.matrix ( pseudoNormCounts [ DEG_S10_filtered $ gene_ID , c ( 1 : 6 )]), cluster_rows = F , cluster_col = F , annotation_col = annot_col ) annot_col < - data.frame(row.names = colnames(pseudoNormCounts)[1:6], Condition = c(rep(\"Control\", 3),rep( \"Treatment\", 3))) pheatmap(as.matrix(pseudoNormCounts[DEG_S10_filtered$gene_ID,c(1:6)]), cluster_rows = F, cluster_col = F, annotation_col = annot_col) DEGs for White clover Tienshan Treatment vs Control \u00b6 We can do this using the same functions as above and changing the contrast. This time we will directly filter the differentially expressed genes using the same parameters as for the S10 samples. In [19]: Copied! glmqlf_Ti <- glmQLFTest ( fit , contrast = contrasts [, \"Tienshan\" ]) DEG_Ti <- topTags ( glmqlf_Ti , n = nrow ( DGEList $ counts )) DEG_Ti_filtered <- DEG_Ti $ table [ DEG_Ti $ table $ FDR < 0.05 & abs ( DEG_Ti $ table $ logFC ) > 1 ,] DEG_Ti_filtered <- rownames_to_column ( DEG_Ti_filtered ) %>% rename ( gene_ID = rowname ) print ( head ( DEG_Ti_filtered )) print ( \"Nr of differentially expressed genes:\" ) print ( nrow ( DEG_Ti_filtered )) glmqlf_Ti < - glmQLFTest(fit, contrast=contrasts[,\"Tienshan\"]) DEG_Ti < - topTags(glmqlf_Ti, n = nrow(DGEList$counts)) DEG_Ti_filtered < - DEG_Ti$table[DEG_Ti$table$FDR < 0.05 & abs(DEG_Ti$table$logFC) > 1,] DEG_Ti_filtered < - rownames_to_column(DEG_Ti_filtered) %>% rename(gene_ID = rowname) print(head(DEG_Ti_filtered)) print(\"Nr of differentially expressed genes:\") print(nrow(DEG_Ti_filtered)) gene_ID logFC logCPM F PValue FDR 1 g234 -3.348667 13.00417 278.01679 1.547626e-09 2.522630e-07 2 g269 -1.885843 11.83422 127.39949 1.172628e-07 9.556922e-06 3 g26 2.423725 11.36683 74.33983 2.016212e-06 8.910761e-05 4 g101 4.303290 13.18162 73.17140 2.186690e-06 8.910761e-05 5 g272 3.391225 13.86065 66.80131 3.475790e-06 9.840357e-05 6 g99 -1.430395 11.68100 66.25814 3.622217e-06 9.840357e-05 [1] \"Nr of differentially expressed genes:\" [1] 42 We can now plot a Venn diagram with the DEGs for the two genotypes in order to observe the number of common and specific differentially expressed genes between the two genotypes as response to the cold exposure. You can see that a high percentage of the identified genes are common for the two genotypes, while each genotype has also specific genes. In [20]: Copied! vd <- venn.diagram ( x = list ( DEG_S10_filtered $ gene_ID , DEG_Ti_filtered $ gene_ID ), category.names = c ( \"S10\" , \"Tienshan\" ), lwd = 4 , fill = c ( \"cornflowerblue\" , \"yellowgreen\" ), filename = NULL , cat.cex = 1 , cat.fontface = \"bold\" , output = TRUE ) grid.draw ( vd ) vd < - venn.diagram( x = list(DEG_S10_filtered$gene_ID, DEG_Ti_filtered$gene_ID), category.names = c(\"S10\" , \"Tienshan\"), lwd = 4, fill = c(\"cornflowerblue\", \"yellowgreen\"), filename = NULL, cat.cex = 1, cat.fontface = \"bold\", output=TRUE ) grid.draw(vd) DEGs for S10+Tienshan Treatment vs Control w/o genotype effects \u00b6 Until now we tested for DEGs specific for each of the two genotypes under cold treatment. We can also run a test where we ignore the genotype and just test for the differences in the cold response. Consider the counts for both genotypes as a single dataset using the previously created contrast \"S10_Tienshan\". Do the results look different compared with the previous tests? In [21]: Copied! glmqlf_S10_Ti <- glmQLFTest ( fit , contrast = contrasts [, \"S10_Tienshan\" ]) DEG_S10_Ti <- topTags ( glmqlf_S10_Ti , n = nrow ( DGEList $ counts )) DEG_S10_Ti_filtered <- DEG_S10_Ti $ table [ DEG_S10_Ti $ table $ FDR < 0.05 & abs ( DEG_S10_Ti $ table $ logFC ) > 1 ,] DEG_S10_Ti_filtered <- rownames_to_column ( DEG_S10_Ti_filtered ) %>% rename ( gene_ID = rowname ) print ( head ( DEG_S10_Ti_filtered )) print ( \"Nr of differentially expressed genes:\" ) print ( nrow ( DEG_S10_Ti_filtered )) glmqlf_S10_Ti < - glmQLFTest(fit, contrast=contrasts[,\"S10_Tienshan\"]) DEG_S10_Ti < - topTags(glmqlf_S10_Ti, n = nrow(DGEList$counts)) DEG_S10_Ti_filtered < - DEG_S10_Ti$table[DEG_S10_Ti$table$FDR < 0.05 & abs(DEG_S10_Ti$table$logFC) > 1,] DEG_S10_Ti_filtered < - rownames_to_column(DEG_S10_Ti_filtered) %>% rename(gene_ID = rowname) print(head(DEG_S10_Ti_filtered)) print(\"Nr of differentially expressed genes:\") print(nrow(DEG_S10_Ti_filtered)) gene_ID logFC logCPM F PValue FDR 1 g39 2.057128 14.12463 246.6519 3.039491e-09 4.954370e-07 2 g232 3.261008 11.95044 203.4580 8.934889e-09 5.288546e-07 3 g269 -1.652505 11.83422 200.3564 9.733520e-09 5.288546e-07 4 g6 1.714849 12.99954 166.2297 2.740066e-08 1.116577e-06 5 g99 -1.484591 11.68100 150.3246 4.762148e-08 1.552460e-06 6 g26 2.274575 11.36683 142.8625 6.290957e-08 1.623160e-06 [1] \"Nr of differentially expressed genes:\" [1] 52 Plot the results from the 3 tests in a Venn diagram to visualize the number of common and unique genes In [22]: Copied! vd <- venn.diagram ( x = list ( DEG_S10_filtered $ gene_ID , DEG_Ti_filtered $ gene_ID , DEG_S10_Ti_filtered $ gene_ID ), category.names = c ( \"S10\" , \"Tienshan\" , \"S10_Tienshan\" ), lwd = 3 , fill = c ( \"cornflowerblue\" , \"yellowgreen\" , \"thistle3\" ), filename = NULL , cat.cex = 1 , cat.fontface = \"bold\" , output = TRUE ) grid.draw ( vd ) vd < - venn.diagram( x = list(DEG_S10_filtered$gene_ID, DEG_Ti_filtered$gene_ID, DEG_S10_Ti_filtered$gene_ID), category.names = c(\"S10\" , \"Tienshan\", \"S10_Tienshan\"), lwd = 3, fill = c(\"cornflowerblue\", \"yellowgreen\", \"thistle3\"), filename = NULL, cat.cex = 1, cat.fontface = \"bold\", output=TRUE ) grid.draw(vd) Explore DGE results \u00b6 Select the genes which appear only in the analysis using both genotypes for further examination. \u00b6 We can use the \"anti_join\" function from the dplyr package to keep only the unique genes that appear only when using both genotypes. In [23]: Copied! S10_Ti_unique <- anti_join ( DEG_S10_Ti_filtered , DEG_S10_filtered , by = \"gene_ID\" ) %>% anti_join ( DEG_Ti_filtered , by = \"gene_ID\" ) S10_Ti_unique S10_Ti_unique < - anti_join(DEG_S10_Ti_filtered, DEG_S10_filtered, by=\"gene_ID\") %>% anti_join(DEG_Ti_filtered, by=\"gene_ID\") S10_Ti_unique A data.frame: 2 \u00d7 6 gene_ID logFC logCPM F PValue FDR g247 -1.412652 8.424523 10.877350 0.006535994 0.01500517 g360 1.180849 7.900076 9.804067 0.013809376 0.02813660 Linking the genes selected as differentially expressed back to the raw read counts \u00b6 How do the counts look for these genes, does it make sense that they are differentially expressed only when using the two genotypes? In [24]: Copied! Read_counts <- rownames_to_column ( Read_counts ) %>% rename ( gene_ID = rowname ) S10_Ti_unique_counts <- inner_join ( S10_Ti_unique [, c ( 1 , 2 , 6 )], Read_counts , by = \"gene_ID\" ) S10_Ti_unique_counts Read_counts < - rownames_to_column(Read_counts) %>% rename(gene_ID = rowname) S10_Ti_unique_counts < - inner_join(S10_Ti_unique[,c(1,2,6)], Read_counts, by=\"gene_ID\") S10_Ti_unique_counts A data.frame: 2 \u00d7 15 gene_ID logFC FDR S10_1_1 S10_1_2 S10_1_3 S10_2_1 S10_2_2 S10_2_3 TI_1_1 TI_1_2 TI_1_3 TI_2_1 TI_2_2 TI_2_3 g247 -1.412652 0.01500517 4 9 3 1 2 1 42 27 32 8 22 22 g360 1.180849 0.02813660 1 0 1 3 2 3 16 10 16 22 19 22 Adding functional annotation to DEGs \u00b6 Until now we looked only at gene IDs, but we can also add functional annotations to the DEGs. The functional annotations were generated using protein sequences and the EggNOG software. Identifying the molecular function of the differentially expressed genes can help us do a literature survey in order to check if any of the genes discovered have been previously identified as being involved in the cold response. In [25]: Copied! Functional_annotations <- read.delim ( \"../Data/Clover_Data/Functional_Annotations.txt\" ) S10_Ti_unique_FA <- inner_join ( S10_Ti_unique [, c ( 1 , 2 , 6 )], Functional_annotations , by = \"gene_ID\" ) S10_Ti_unique_FA Functional_annotations < - read.delim(\"../Data/Clover_Data/Functional_Annotations.txt\") S10_Ti_unique_FA < - inner_join(S10_Ti_unique[,c(1,2,6)], Functional_annotations, by=\"gene_ID\") S10_Ti_unique_FA A data.frame: 2 \u00d7 4 gene_ID logFC FDR Human.Readable.Description g247 -1.412652 0.01500517 Nitrogen regulatory protein P-II homolog g360 1.180849 0.02813660 Unknown protein Tasks and Questions Based on the results obtained in the analysis so far, would you change the cut-off for the FDR and logFC to be more strict or more permissive? Look back at the raw counts for different FDR and logFC values and set the thresholds as you find appropriate. You can also plot histograms with the FDR and logFC values. In [ ]: Copied! hist ( DEG_S10 $ table $ FDR , main = \"\" , xlab = \"FDR\" , breaks = 200 , xlim = range ( c ( 0 , 0.1 ))) hist(DEG_S10$table$FDR , main = \"\", xlab = \"FDR\", breaks= 200, xlim = range(c(0, 0.1))) In [ ]: Copied! hist ( DEG_S10 $ table $ logFC , main = \"\" , xlab = \"logFC\" , breaks = 50 , xlim = range ( c ( -6 , 6 ))) hist(DEG_S10$table$logFC , main = \"\", xlab = \"logFC\", breaks= 50, xlim = range(c(-6, 6))) Separate the upregulated and downregulated genes for each genotype and append functional annotations to them. Identify the genes that are commonly upregulated in S10 and Tienshan samples and the uniquely upregulated genes for each genotype. Why do you think some of the proteins appear in duplicates? To answer these questions, it may be convenient to save summary tables from R and open them in excel. See the code below for examples of how to do this. Files can be downloaded by right-clicking on the file name. If you are familiar with R functions, you are welcome to use those for counting. In [ ]: Copied! dir.create ( \"DEG_Output_tables\" , showWarnings = FALSE ) dir.create(\"DEG_Output_tables\", showWarnings = FALSE) In [ ]: Copied! #Create the table with the DEGs, Raw counts(just for the Ti samples in this case, change to columns (2:7) for the S10 samples) and Functional annotations DEG_Ti_counts_FA <- inner_join ( DEG_Ti_filtered [, c ( 1 , 2 , 6 )], Read_counts [, c ( 1 , 8 : 13 )], by = \"gene_ID\" ) %>% inner_join ( Functional_annotations , by = \"gene_ID\" ) #Write the table to file write.table ( DEG_Ti_counts_FA , file = \"DEG_Output_tables/Ti_Treatment_Control_DGE.txt\" , quote = FALSE , row.names = FALSE , sep = \"\\t\" ) #Display the first 10 rows of the table head ( DEG_Ti_counts_FA , n = 10 ) #Create the table with the DEGs, Raw counts(just for the Ti samples in this case, change to columns (2:7) for the S10 samples) and Functional annotations DEG_Ti_counts_FA < - inner_join(DEG_Ti_filtered[,c(1, 2, 6)], Read_counts[, c(1, 8:13)], by=\"gene_ID\") %>% inner_join(Functional_annotations, by=\"gene_ID\") #Write the table to file write.table(DEG_Ti_counts_FA, file = \"DEG_Output_tables/Ti_Treatment_Control_DGE.txt\", quote = FALSE, row.names = FALSE, sep = \"\\t\") #Display the first 10 rows of the table head(DEG_Ti_counts_FA, n=10) Example for filtering and counting the Up/Down genes. You can easily filter using the \"filter()\" function just by specifying the dataframe and a logical argument. In [ ]: Copied! DEG_Ti_up <- filter ( DEG_Ti_counts_FA , logFC > 0 ) print ( \"Nr of upregulated genes:\" ) print ( nrow ( DEG_Ti_up )) DEG_Ti_down <- filter ( DEG_Ti_counts_FA , logFC < 0 ) print ( \"Nr of downregulated genes:\" ) print ( nrow ( DEG_Ti_down )) DEG_Ti_up < - filter(DEG_Ti_counts_FA, logFC > 0) print(\"Nr of upregulated genes:\") print(nrow(DEG_Ti_up)) DEG_Ti_down < - filter(DEG_Ti_counts_FA, logFC < 0) print(\"Nr of downregulated genes:\") print(nrow(DEG_Ti_down)) You can use the \"inner_join\" and the \"anti_join\" functions from the dplyr package to select the common and unique genes for each genotype: example_file_joined <- inner_join(file1, file2, by=\"gene_ID\") Wrapping up \ud83c\udf89 \ud83c\udf89 \ud83c\udf89 \u00b6 In this notebook, you have worked with RNA-seq results for two white clover genotypes exposed to one night of cold treatment, aiming to identify genes that change their expression in response to the cold treatment. You have learned to perform exploratory data analysis of raw and normalized RNA-seq read counts. You have also performed differential gene expression using edgeR .","title":"3.3.Bulk RNA data analysis"},{"location":"nb/bulk.html#edger-data-filtering-and-normalization","text":"We will use the edgeR package to test for differentially expressed genes between our Control and Treatment Samples. You can read more about the edgeR package and its functionalities here . This exercise largely follows their user manual.","title":"EdgeR - Data filtering and Normalization"},{"location":"nb/bulk.html#file-processing","text":"The data for this exercise comes from the 12 tabular files with Reads per Gene counts generated by STAR Mapping in the raw-data alignment part of this course. We want to create a table where each column is a sample, and the content of the table are the read counts from STAR. We must merge the 12 files with Reads per Gene information into a single file. If you aligned datasets in the first notebook with jupyterlab, then you will find the files using the following command: In [2]: Copied! samples <- sort ( system ( \"find results/STAR_output/*_align_contigs_1_2 -name \\\"*ReadsPerGene.out.tab\\\"\" , intern = TRUE )) print ( samples ) Read_counts <- do.call ( cbind , lapply ( samples , function ( x ) read.delim ( file = x , header = FALSE ))) samples < - sort(system(\"find results/STAR_output/*_align_contigs_1_2 -name \\\"*ReadsPerGene.out.tab\\\"\", intern=TRUE)) print(samples) Read_counts < - do.call(cbind, lapply(samples, function(x) read.delim(file=x, header = FALSE))) [1] \"results/STAR_output/S10_align_contigs_1_2/S10_1_1ReadsPerGene.out.tab\" [2] \"results/STAR_output/S10_align_contigs_1_2/S10_1_2ReadsPerGene.out.tab\" [3] \"results/STAR_output/S10_align_contigs_1_2/S10_1_3ReadsPerGene.out.tab\" [4] \"results/STAR_output/S10_align_contigs_1_2/S10_2_1ReadsPerGene.out.tab\" [5] \"results/STAR_output/S10_align_contigs_1_2/S10_2_2ReadsPerGene.out.tab\" [6] \"results/STAR_output/S10_align_contigs_1_2/S10_2_3ReadsPerGene.out.tab\" [7] \"results/STAR_output/TI_align_contigs_1_2/TI_1_1ReadsPerGene.out.tab\" [8] \"results/STAR_output/TI_align_contigs_1_2/TI_1_2ReadsPerGene.out.tab\" [9] \"results/STAR_output/TI_align_contigs_1_2/TI_1_3ReadsPerGene.out.tab\" [10] \"results/STAR_output/TI_align_contigs_1_2/TI_2_1ReadsPerGene.out.tab\" [11] \"results/STAR_output/TI_align_contigs_1_2/TI_2_2ReadsPerGene.out.tab\" [12] \"results/STAR_output/TI_align_contigs_1_2/TI_2_3ReadsPerGene.out.tab\" If you aligned datasets interactively with Galaxy , then you will need to create the folder tabular_files into the results folder copy the tabular files from STAR into the created folder. Each file must have the sample name and end by ReadsPerGene.out.tab . For example S10_1_1ReadsPerGene.out.tab run the following commands removing the # symbol In [ ]: Copied! #samples <- sort(system(\"find results/tabular_files/ -name \\\"*ReadsPerGene.out.tab\\\"\", intern=TRUE)) #print(samples) #Read_counts <- do.call(cbind, lapply(samples, function(x) read.delim(file=x, header = FALSE))) #samples < - sort(system(\"find results/tabular_files/ -name \\\"*ReadsPerGene.out.tab\\\"\", intern=TRUE)) #print(samples) #Read_counts < - do.call(cbind, lapply(samples, function(x) read.delim(file=x, header = FALSE))) The data frame has genes as rows and samples as columns and stores the gene expression counts (value representing the total number of sequence reads that originated from a particular gene in a sample) for each of the 12 samples. This data frame should have 12 columns and 366 rows. In [3]: Copied! rownames ( Read_counts ) <- Read_counts [, 1 ] Read_counts <- Read_counts [ c ( 5 : nrow ( Read_counts )), c ( seq ( 2 , 46 , by = 4 ))] colnames ( Read_counts ) <- c ( \"S10_1_1\" , \"S10_1_2\" , \"S10_1_3\" , \"S10_2_1\" , \"S10_2_2\" , \"S10_2_3\" , \"TI_1_1\" , \"TI_1_2\" , \"TI_1_3\" , \"TI_2_1\" , \"TI_2_2\" , \"TI_2_3\" ) head ( Read_counts , n = 10 ) dim ( Read_counts ) # dimensions of the data frame rownames(Read_counts) < - Read_counts[,1] Read_counts < - Read_counts[c(5:nrow(Read_counts)), c(seq(2, 46, by=4))] colnames(Read_counts) < - c(\"S10_1_1\", \"S10_1_2\", \"S10_1_3\", \"S10_2_1\", \"S10_2_2\", \"S10_2_3\", \"TI_1_1\", \"TI_1_2\", \"TI_1_3\", \"TI_2_1\", \"TI_2_2\", \"TI_2_3\") head(Read_counts, n=10) dim(Read_counts) # dimensions of the data frame A data.frame: 10 \u00d7 12 S10_1_1 S10_1_2 S10_1_3 S10_2_1 S10_2_2 S10_2_3 TI_1_1 TI_1_2 TI_1_3 TI_2_1 TI_2_2 TI_2_3 g175 143 226 227 217 206 193 234 205 198 221 206 165 g176 17 12 15 8 14 18 29 19 30 6 11 23 g177 0 0 0 0 0 0 0 0 0 0 0 0 g178 0 0 0 0 0 0 0 0 2 2 1 2 g179 0 0 0 0 0 0 0 0 0 0 0 0 g180 2773 5223 4350 4139 3209 4644 1015 1313 889 2675 1023 2565 g181 473 679 583 437 390 450 642 700 697 650 459 410 g182 19 15 20 9 8 4 13 7 8 6 5 4 g183 0 0 0 0 0 0 0 0 0 0 0 0 g184 30 22 50 57 103 83 36 29 18 107 69 89 .list-inline {list-style: none; margin:0; padding: 0} .list-inline>li {display: inline-block} .list-inline>li:not(:last-child)::after {content: \"\\00b7\"; padding: 0 .5ex} 366 12 Import the Metadata table. This file, as its name suggests, contains information about each of the 12 RNA-seq samples, such as the treatment (Condition), genotype and replicate. Note that the order of the rows in the Metadata table should be the same as the columns in the Read_counts file generated above. In [4]: Copied! metadata <- read.csv ( \"../Data/Clover_Data/metadata.csv\" , sep = \";\" , row.names = 1 , stringsAsFactors = TRUE ) metadata metadata < - read.csv(\"../Data/Clover_Data/metadata.csv\", sep =\";\", row.names=1, stringsAsFactors=TRUE) metadata A data.frame: 12 \u00d7 3 Condition Genotype Replicate S10_1_1 Control S10 1 S10_1_2 Control S10 2 S10_1_3 Control S10 3 S10_2_1 Treatment S10 1 S10_2_2 Treatment S10 2 S10_2_3 Treatment S10 3 TI_1_1 Control Tienshan 1 TI_1_2 Control Tienshan 2 TI_1_3 Control Tienshan 3 TI_2_1 Treatment Tienshan 1 TI_2_2 Treatment Tienshan 2 TI_2_3 Treatment Tienshan 3 In order to aid the following steps, we will create a Group for each sample (a new column in the metadata) based on the Genotype&Condition of each sample and assign the three replicates to this group. In [5]: Copied! Group <- factor ( paste ( metadata $ Genotype , metadata $ Condition , sep = \"_\" )) metadata <- cbind ( metadata , Group = Group ) metadata Group < - factor(paste(metadata$Genotype, metadata$Condition, sep=\"_\")) metadata < - cbind(metadata,Group=Group) metadata A data.frame: 12 \u00d7 4 Condition Genotype Replicate Group S10_1_1 Control S10 1 S10_Control S10_1_2 Control S10 2 S10_Control S10_1_3 Control S10 3 S10_Control S10_2_1 Treatment S10 1 S10_Treatment S10_2_2 Treatment S10 2 S10_Treatment S10_2_3 Treatment S10 3 S10_Treatment TI_1_1 Control Tienshan 1 Tienshan_Control TI_1_2 Control Tienshan 2 Tienshan_Control TI_1_3 Control Tienshan 3 Tienshan_Control TI_2_1 Treatment Tienshan 1 Tienshan_Treatment TI_2_2 Treatment Tienshan 2 Tienshan_Treatment TI_2_3 Treatment Tienshan 3 Tienshan_Treatment","title":"File processing"},{"location":"nb/bulk.html#create-the-dgelist-object","text":"We will merge the read counts and the metadata into a list-based data object named DGEList, which can be manipulated as any list object in R. The main components of the DGEList object are the matrix \"counts\" containing our read per gene counts and a data.frame \"samples\" containing the metadata. Note that all the genes with zero counts across all samples were eliminated. In [6]: Copied! DGEList <- DGEList ( Read_counts , remove.zeros = TRUE ) DGEList $ samples $ Condition <- relevel ( metadata $ Condition , ref = \"Control\" ) DGEList $ samples $ Genotype <- metadata $ Genotype DGEList $ samples $ group <- metadata $ Group DGEList DGEList < - DGEList(Read_counts, remove.zeros = TRUE) DGEList$samples$Condition < - relevel(metadata$Condition, ref = \"Control\") DGEList$samples$Genotype < - metadata$Genotype DGEList$samples$group < - metadata$Group DGEList Removing 99 rows with all zero counts $counts A matrix: 267 \u00d7 12 of type int S10_1_1 S10_1_2 S10_1_3 S10_2_1 S10_2_2 S10_2_3 TI_1_1 TI_1_2 TI_1_3 TI_2_1 TI_2_2 TI_2_3 g175 143 226 227 217 206 193 234 205 198 221 206 165 g176 17 12 15 8 14 18 29 19 30 6 11 23 g178 0 0 0 0 0 0 0 0 2 2 1 2 g180 2773 5223 4350 4139 3209 4644 1015 1313 889 2675 1023 2565 g181 473 679 583 437 390 450 642 700 697 650 459 410 g182 19 15 20 9 8 4 13 7 8 6 5 4 g184 30 22 50 57 103 83 36 29 18 107 69 89 g185 0 2 0 0 0 0 0 1 0 0 0 1 g186 1 0 0 0 0 0 0 0 0 0 0 0 g187 1 1 2 0 1 1 58 49 57 28 32 29 g188 316 285 417 200 184 322 1276 855 1341 402 809 547 g190 14 18 29 25 17 31 7 6 12 20 7 6 g191 2 2 1 1 0 0 0 0 0 0 0 0 g192 1 1 1 1 1 0 6 10 2 3 8 2 g193 208 231 301 289 161 279 70 61 60 128 160 91 g194 40 41 37 44 17 43 8 10 7 8 105 25 g195 54 85 85 71 54 43 56 54 42 67 68 56 g196 77 120 118 186 152 177 5 9 5 42 20 34 g197 1 6 5 18 14 21 15 44 12 32 16 17 g198 14 27 10 11 2 2 6 6 1 2 2 0 g199 0 0 0 0 0 0 0 0 0 0 1 0 g200 57 80 94 11 8 23 89 47 67 5 47 5 g203 815 1188 1412 1139 1034 1127 911 852 662 892 781 784 g204 250 312 348 277 275 264 125 104 133 119 91 130 g205 109 132 181 140 114 151 89 73 66 78 46 50 g206 0 1 2 7 4 9 4 0 7 0 1 2 g207 0 1 0 0 4 3 1 3 4 4 3 3 g208 0 1 0 0 0 0 0 1 0 1 0 0 g209 0 0 0 0 0 0 0 0 1 0 0 0 g210 52 76 60 12 12 13 61 73 94 54 45 21 \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee g135 0 0 0 1 0 0 5 1 0 2 0 0 g139 0 1 1 0 0 0 12 13 11 4 3 3 g140 0 5 1 0 0 2 5 4 0 0 2 0 g141 177 217 224 131 117 166 117 85 67 80 79 77 g142 488 713 557 241 154 228 983 1057 1023 1075 794 933 g144 3319 3987 4763 2249 1996 2260 4405 3880 4585 5072 3618 3590 g146 293 330 350 913 775 731 108 92 115 431 151 226 g147 6 3 3 0 8 10 1 1 1 0 1 0 g148 19 30 24 15 4 12 23 19 25 10 19 8 g149 35 62 65 57 58 53 114 103 91 92 79 93 g150 263 411 278 752 1378 1300 106 112 70 516 200 508 g151 44 44 50 92 92 84 23 26 25 56 43 31 g152 242 258 294 425 381 521 15 8 8 16 21 15 g153 142 144 181 233 177 233 31 49 50 50 45 57 g155 0 4 2 1 0 0 1 0 3 0 0 1 g156 0 0 0 0 0 0 0 3 2 0 0 1 g157 6 1 3 223 52 152 4 7 4 153 47 155 g158 0 0 0 7 1 3 0 0 1 1 0 0 g161 25 38 18 1 9 2 63 23 43 0 24 6 g162 31 43 38 43 25 28 0 0 0 0 0 0 g163 1 0 12 37 8 18 9 4 8 16 13 15 g164 69 58 97 294 123 168 56 58 60 146 101 135 g165 203 376 594 1343 2062 1610 265 229 214 488 270 490 g167 2 0 0 2 0 0 0 0 0 0 0 0 g168 2 14 6 0 0 5 31 26 38 3 27 10 g169 0 0 1 0 1 1 0 0 0 0 0 0 g170 0 0 0 0 0 0 0 1 0 0 0 0 g171 0 5 0 0 0 5 0 0 0 1 0 0 g172 1 2 2 6 4 3 3 1 2 3 3 0 g173 80 107 120 78 138 121 67 86 69 96 105 105 $samples A data.frame: 12 \u00d7 5 group lib.size norm.factors Condition Genotype S10_1_1 S10_Control 43614 1 Control S10 S10_1_2 S10_Control 58803 1 Control S10 S10_1_3 S10_Control 62654 1 Control S10 S10_2_1 S10_Treatment 59909 1 Treatment S10 S10_2_2 S10_Treatment 56761 1 Treatment S10 S10_2_3 S10_Treatment 63152 1 Treatment S10 TI_1_1 Tienshan_Control 43387 1 Control Tienshan TI_1_2 Tienshan_Control 38355 1 Control Tienshan TI_1_3 Tienshan_Control 40304 1 Control Tienshan TI_2_1 Tienshan_Treatment 55509 1 Treatment Tienshan TI_2_2 Tienshan_Treatment 39909 1 Treatment Tienshan TI_2_3 Tienshan_Treatment 45008 1 Treatment Tienshan","title":"Create the DGEList object"},{"location":"nb/bulk.html#preliminary-data-analysis","text":"First, we will calculate the \"pseudoCounts\" as log2 of the reads per gene counts. This is not part of the actual differential gene expression analysis but is helpful for data exploration and quality assessment. We will look at a histogram of one of the samples and a boxplot representation of the log2 counts for all the 12 samples. Note that there are many genes with a low number of mapped reads and that there are differences between the average read counts for each library. In [7]: Copied! pseudoCounts <- log2 ( DGEList $ counts + 1 ) head ( pseudoCounts ) hist ( pseudoCounts [ , \"S10_1_1\" ], main = \"\" , xlab = \"Read counts\" ) boxplot ( pseudoCounts , col = \"gray\" , las = 3 , cex.names = 1 ) pseudoCounts < - log2(DGEList$counts + 1) head(pseudoCounts) hist(pseudoCounts[ ,\"S10_1_1\"], main = \"\", xlab = \"Read counts\") boxplot(pseudoCounts, col = \"gray\", las = 3, cex.names = 1) A matrix: 6 \u00d7 12 of type dbl S10_1_1 S10_1_2 S10_1_3 S10_2_1 S10_2_2 S10_2_3 TI_1_1 TI_1_2 TI_1_3 TI_2_1 TI_2_2 TI_2_3 g175 7.169925 7.826548 7.832890 7.768184 7.693487 7.599913 7.876517 7.686501 7.636625 7.794416 7.693487 7.375039 g176 4.169925 3.700440 4.000000 3.169925 3.906891 4.247928 4.906891 4.321928 4.954196 2.807355 3.584963 4.584963 g178 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.584963 1.584963 1.000000 1.584963 g180 11.437752 12.350939 12.087131 12.015415 11.648358 12.181463 9.988685 10.359750 9.797662 11.385862 10.000000 11.325305 g181 8.888743 9.409391 9.189825 8.774787 8.611025 8.816984 9.328675 9.453271 9.447083 9.346514 8.845490 8.682995 g182 4.321928 4.000000 4.392317 3.321928 3.169925 2.321928 3.807355 3.000000 3.169925 2.807355 2.584963 2.321928 We can also create a PCA plot of the samples in order to assess the differences between the Genotypes and Conditions, but also between the replicates. In this plot the samples that are similar cluster together, while samples that are different are further apart. In this type of plot, we would expect samples from the same group (the three replicates for each sample) to exhibit a similar gene expression profile thus clustering together while being separated from the other samples. In [8]: Copied! resPCA <- pca ( t ( pseudoCounts ), ncomp = 6 ) plotIndiv ( resPCA , group = metadata $ Genotype , pch = metadata $ Condition , legend = T , legend.title = 'Genotype' , legend.title.pch = 'Condition' , title = 'PCA plot raw counts' , style = 'ggplot2' , size.xlabel = 10 , size.ylabel = 10 ) resPCA < - pca(t(pseudoCounts), ncomp = 6) plotIndiv(resPCA, group = metadata$Genotype, pch=metadata$Condition, legend = T, legend.title = 'Genotype', legend.title.pch = 'Condition', title = 'PCA plot raw counts', style = 'ggplot2', size.xlabel = 10, size.ylabel = 10)","title":"Preliminary data analysis"},{"location":"nb/bulk.html#filtering-the-lowly-expressed-genes","text":"As seen previously, many genes have a low number of read counts in our samples. The genes with very low counts across all libraries provide little evidence for differential expression, thus we should eliminate these genes before the analysis. One of the filtering methods we can use is the \"filterByExpr\" function provided by the edgeR package. By default, this function keeps only the genes that have at least 10 reads per group, but other cutoffs can also be applied. In [9]: Copied! keep <- filterByExpr ( DGEList , group = metadata $ Group ) #create the filter DGEList <- DGEList [ keep , , keep.lib.sizes = FALSE ] #apply the filter to on the DGEList object table ( keep ) #Check the number of genes that passed the filter keep < - filterByExpr(DGEList, group=metadata$Group) #create the filter DGEList < - DGEList[keep, , keep.lib.sizes=FALSE] #apply the filter to on the DGEList object table(keep) #Check the number of genes that passed the filter keep FALSE TRUE 104 163","title":"Filtering the lowly expressed genes"},{"location":"nb/bulk.html#normalization","text":"As we are working with multiple samples we need to normalize the read counts per gene in order to account for compositional and technical differences between the 12 RNA-seq libraries. For this, we will calculate normalization factors using the trimmed mean of M-values (TMM) method. You can read more about different normalization methods in the user manual. Note that running \"calcNormFactors\" does not change the actual reads per gene counts, it just fills the \"norm.factors\" column in DGEList$samples . These factors will be used to scale the read counts for each library. From the user guide: \"A normalization factor below one indicates that a small number of high count genes are monopolizing the sequencing, causing the counts for other genes to be lower than would be usual given the library size.\" In [10]: Copied! DGEList <- calcNormFactors ( DGEList , method = \"RLE\" ) DGEList $ samples DGEList < - calcNormFactors(DGEList, method=\"RLE\") DGEList$samples A data.frame: 12 \u00d7 5 group lib.size norm.factors Condition Genotype S10_1_1 S10_Control 43506 1.0897129 Control S10 S10_1_2 S10_Control 58660 1.0385093 Control S10 S10_1_3 S10_Control 62512 1.0362962 Control S10 S10_2_1 S10_Treatment 59741 0.9802860 Treatment S10 S10_2_2 S10_Treatment 56653 0.8418644 Treatment S10 S10_2_3 S10_Treatment 63008 0.8949144 Treatment S10 TI_1_1 Tienshan_Control 43174 1.0618440 Control Tienshan TI_1_2 Tienshan_Control 38203 1.0431678 Control Tienshan TI_1_3 Tienshan_Control 40178 1.0676351 Control Tienshan TI_2_1 Tienshan_Treatment 55391 0.9048196 Treatment Tienshan TI_2_2 Tienshan_Treatment 39810 1.1235077 Treatment Tienshan TI_2_3 Tienshan_Treatment 44910 0.9603761 Treatment Tienshan","title":"Normalization"},{"location":"nb/bulk.html#normalized-counts-exploratory-data-analysis","text":"For data analysis purposes normalized log2 counts can be extracted from the DGEList object using the function CPM (counts per million). We will generate the same plots as for the raw counts in order to compare the data before and after normalization. Do the plots for normalized counts look different compared with the plots computed before data filtering and normalization? In [11]: Copied! pseudoNormCounts <- cpm ( DGEList , log = TRUE , prior.count = 1 ) head ( pseudoNormCounts ) hist ( pseudoNormCounts [ , \"S10_1_1\" ], main = \"\" , xlab = \"counts\" ) boxplot ( pseudoNormCounts , col = \"gray\" , las = 3 , cex.names = 1 ) resPCA <- pca ( t ( pseudoNormCounts ), ncomp = 6 ) plotIndiv ( resPCA , group = metadata $ Genotype , pch = metadata $ Condition , legend = T , legend.title = 'Genotype' , legend.title.pch = 'Condition' , title = 'PCA plot normalized counts' , style = 'ggplot2' , size.xlabel = 10 , size.ylabel = 10 ) pseudoNormCounts < - cpm(DGEList, log = TRUE, prior.count = 1) head(pseudoNormCounts) hist(pseudoNormCounts[ ,\"S10_1_1\"], main = \"\", xlab = \"counts\") boxplot(pseudoNormCounts, col = \"gray\", las = 3, cex.names = 1) resPCA < - pca(t(pseudoNormCounts), ncomp = 6) plotIndiv(resPCA, group = metadata$Genotype, pch=metadata$Condition, legend = T, legend.title = 'Genotype', legend.title.pch = 'Condition', title = 'PCA plot normalized counts', style = 'ggplot2', size.xlabel = 10, size.ylabel = 10) A matrix: 6 \u00d7 12 of type dbl S10_1_1 S10_1_2 S10_1_3 S10_2_1 S10_2_2 S10_2_3 TI_1_1 TI_1_2 TI_1_3 TI_2_1 TI_2_2 TI_2_3 g175 11.568005 11.864813 11.782957 11.863090 12.083127 11.749272 12.323049 12.334198 12.178544 12.112851 12.175386 11.908906 g176 8.564108 7.760868 7.974199 7.290213 8.292080 8.405708 9.349782 8.956131 9.490388 7.125494 8.054467 9.111569 g180 15.836359 16.387906 16.035457 16.109276 16.038322 16.329943 14.435626 15.008665 14.340400 15.704307 14.482504 15.860317 g181 13.287211 13.446752 13.138771 12.869139 13.000828 12.965820 13.775545 14.101988 13.989757 13.664955 13.327806 13.217591 g182 8.716557 8.056048 8.360376 7.439590 7.551908 6.505541 8.245462 7.611500 7.689402 7.125494 7.041192 6.815835 g184 9.350249 8.573811 9.628852 9.955925 11.089735 10.542877 9.653135 9.546090 8.779819 11.073313 10.609695 11.024686","title":"Normalized counts - Exploratory Data analysis"},{"location":"nb/bulk.html#edger-testing-for-differentially-expressed-genes-degs","text":"We use edgeR for Differential Gene Expression using the GLM method (Generalized linear model) with treatment and genotype effects After we concluded the exploratory data analysis and the filtering and normalization steps we can now start testing for differentially expressed genes between our samples. For this, we first need to define a \"design matrix\" which describes our experimental design. We construct a matrix containing samples as rows and our previously defined groups (S10_Control, S10_Treatment, Tienshan_Control, Tienshan_Treatment) as columns. The samples belonging to each group are assigned a \"1\" in this matrix. In [12]: Copied! design.matrix <- model.matrix ( ~ 0 + Group ) rownames ( design.matrix ) <- colnames ( DGEList ) colnames ( design.matrix ) <- levels ( metadata $ Group ) design.matrix design.matrix < - model.matrix(~0+Group) rownames(design.matrix) < - colnames(DGEList) colnames(design.matrix) < - levels(metadata$Group) design.matrix A matrix: 12 \u00d7 4 of type dbl S10_Control S10_Treatment Tienshan_Control Tienshan_Treatment S10_1_1 1 0 0 0 S10_1_2 1 0 0 0 S10_1_3 1 0 0 0 S10_2_1 0 1 0 0 S10_2_2 0 1 0 0 S10_2_3 0 1 0 0 TI_1_1 0 0 1 0 TI_1_2 0 0 1 0 TI_1_3 0 0 1 0 TI_2_1 0 0 0 1 TI_2_2 0 0 0 1 TI_2_3 0 0 0 1 For easier pairwise comparisons between the groups we can create some \"contrasts\" using the \"makeContrasts\" function. This will tell the program which samples we will like to consider as our \"Control\" and which as our \"Treatment\" groups. The Control groups will be assigned a \"-1\" and the Treatment groups a \"1\". When using multiple Control and Treatment samples in the same contrast we need to devide by the number of samples used as for example in the contrast S10_Tienshan, where we use both S10 and Ti samples. For example, the contrast S10 = S10_Treatment - S10_Control will test for differentially expressed genes between the S10 treatment samples vs the S10 Control samples. In [13]: Copied! contrasts <- makeContrasts ( S10 = S10_Treatment - S10_Control , Tienshan = Tienshan_Treatment - Tienshan_Control , S10_Tienshan = ( S10_Treatment + Tienshan_Treatment ) / 2 - ( S10_Control + Tienshan_Control ) / 2 , levels = design.matrix ) contrasts contrasts < - makeContrasts( S10 = S10_Treatment-S10_Control, Tienshan = Tienshan_Treatment-Tienshan_Control, S10_Tienshan= (S10_Treatment+Tienshan_Treatment)/2 - (S10_Control+Tienshan_Control)/2, levels=design.matrix) contrasts A matrix: 4 \u00d7 3 of type dbl S10 Tienshan S10_Tienshan S10_Control -1 0 -0.5 S10_Treatment 1 0 0.5 Tienshan_Control 0 -1 -0.5 Tienshan_Treatment 0 1 0.5 Any ideas for other contrasts that migth be interesting to explore? The following cell will run two mandatory steps in order to fit a model in edgeR. First, the dispersion needs to be estimated, this is a measure of the degree of inter-library variation for each gene. Afterwards, a QL ( quasi-likelihood) model representing the sample design is fitted using the \"glmQLFit\" function. You can read more about these steps in the edgeR user guide. In [14]: Copied! DGEList <- estimateDisp ( DGEList , design.matrix ) fit <- glmQLFit ( DGEList , design.matrix ) DGEList < - estimateDisp(DGEList, design.matrix) fit < - glmQLFit(DGEList, design.matrix)","title":"EdgeR - Testing for Differentially expressed genes (DEGs)"},{"location":"nb/bulk.html#degs-for-white-clover-s10-plants-treatment-vs-control","text":"Find DEGs for White clover S10 plants in Treatment condition compared with the Control condition We will test for differentially expressed genes using the quasi-likelihood F-tests method. This is easily done just by running the \"glmQFTest\" function on the fit model and selecting one of the contrasts we created above (in this case the \"S10\" contrast). Next, we will use the topTags function to extract the information about all the genes. In [15]: Copied! glmqlf_S10 <- glmQLFTest ( fit , contrast = contrasts [, \"S10\" ]) DEG_S10 <- topTags ( glmqlf_S10 , n = nrow ( DGEList $ counts )) DEG_S10 glmqlf_S10 < - glmQLFTest(fit, contrast=contrasts[,\"S10\"]) DEG_S10 < - topTags(glmqlf_S10, n = nrow(DGEList$counts)) DEG_S10 $table A data.frame: 163 \u00d7 5 logFC logCPM F PValue FDR g39 3.5861702 14.124630 336.66158 5.227331e-10 8.520550e-08 g232 4.0494125 11.950441 157.50997 3.685988e-08 2.591779e-06 g6 2.3225347 12.999541 150.27854 4.770146e-08 2.591779e-06 g350 2.0530029 13.324566 97.56453 4.890245e-07 1.992775e-05 g99 -1.5387874 11.681004 85.17478 9.976659e-07 3.195090e-05 g142 -1.4235276 13.830692 82.52308 1.176107e-06 3.195090e-05 g240 1.3603712 14.708794 79.98114 1.383201e-06 3.220882e-05 g269 -1.4191681 11.834217 75.66563 1.841279e-06 3.751606e-05 g26 2.1254241 11.366827 68.55898 3.047273e-06 5.518949e-05 g129 -5.3324794 8.679594 60.45459 5.738115e-06 9.353127e-05 g272 3.1405978 13.860652 59.08187 6.432977e-06 9.532503e-05 g157 5.3813801 10.414972 57.03712 7.659515e-06 1.040417e-04 g42 -1.9856547 9.962762 53.97164 1.005146e-05 1.260298e-04 g165 2.2666761 13.690016 51.66777 1.243606e-05 1.447913e-04 g101 3.1488142 13.181625 48.21727 1.736838e-05 1.887363e-04 g15 2.7410696 10.684840 47.29143 1.906062e-05 1.941800e-04 g210 -2.2430064 9.993002 46.52627 2.060621e-05 1.975772e-04 g299 -2.3509276 10.984491 45.75893 2.230566e-05 2.019901e-04 g103 2.6810410 10.579777 44.26963 2.609599e-05 2.238762e-04 g144 -0.7963477 16.186987 43.17707 2.936057e-05 2.392886e-04 g77 1.0984806 14.118231 41.46740 3.548119e-05 2.754016e-04 g125 -1.3099534 10.195970 39.85537 4.266319e-05 3.160955e-04 g298 -2.0471647 9.837072 33.49832 9.395967e-05 6.658881e-04 g104 2.4081173 9.219160 38.54240 1.121281e-04 7.615370e-04 g122 -0.6485441 12.457152 30.90261 1.341148e-04 8.744287e-04 g164 1.4415064 11.156457 30.50383 1.419308e-04 8.897970e-04 g146 1.3983889 12.824184 29.92911 1.541544e-04 9.306356e-04 g313 2.2492040 13.614815 28.41728 1.926822e-04 1.121686e-03 g150 1.9650641 13.229706 27.90020 2.083770e-04 1.171222e-03 g13 -0.6522187 13.101579 26.45593 2.608176e-04 1.417109e-03 \u22ee \u22ee \u22ee \u22ee \u22ee \u22ee g96 -1.873792302 8.939397 0.4844512655 0.4999546 0.6041584 g10 0.233134670 14.382992 0.4834790913 0.5003766 0.6041584 g253 0.052426914 13.741219 0.3075042687 0.5896191 0.7066759 g289 -0.212573283 9.390864 0.2887857862 0.6010328 0.7150974 g312 0.093543041 10.849110 0.2666731965 0.6151559 0.7265972 g301 -0.102000599 10.135184 0.2572520652 0.6214023 0.7274503 g221 -0.277095720 8.469909 0.2522121463 0.6248039 0.7274503 g162 -0.145155616 8.517263 0.2278112475 0.6463283 0.7413085 g50 -0.170907352 8.749274 0.2158314533 0.6507284 0.7413085 g203 0.062836598 14.227601 0.2124612164 0.6532634 0.7413085 g88 0.045949497 14.235850 0.2103049178 0.6548983 0.7413085 g355 -0.287897714 8.890754 0.1803234432 0.6787703 0.7630314 g204 -0.055975779 11.947887 0.1408988543 0.7140799 0.7972262 g306 0.054269738 11.294732 0.0923937800 0.7664733 0.8498990 g193 0.049946343 11.682386 0.0642557849 0.8042743 0.8857886 g205 0.037877227 10.986961 0.0473457745 0.8314821 0.9029713 g194 -0.142990391 9.403497 0.0447552162 0.8360811 0.9029713 g362 0.025629967 11.336529 0.0415198735 0.8420254 0.9029713 g315 0.027958374 11.878331 0.0409766489 0.8430470 0.9029713 g180 0.059680256 15.711409 0.0386140448 0.8475743 0.9029713 g282 -0.026492114 11.756078 0.0247991469 0.8775434 0.9288284 g176 -0.061055115 8.587203 0.0144510429 0.9063467 0.9531258 g126 0.061707217 8.311212 0.0024786868 0.9648334 1.0000000 g128 0.063825269 7.671043 0.0019414812 0.9655950 1.0000000 g227 -0.025740630 7.939955 0.0011908008 0.9730516 1.0000000 g121 0.002660852 12.896620 0.0005233398 0.9821327 1.0000000 g284 0.000000000 8.538720 0.0000000000 1.0000000 1.0000000 g116 0.000000000 7.180297 0.0000000000 1.0000000 1.0000000 g117 0.000000000 7.033307 0.0000000000 1.0000000 1.0000000 g118 0.000000000 7.515646 0.0000000000 1.0000000 1.0000000 $adjust.method 'BH' $comparison '-1*S10_Control 1*S10_Treatment' $test 'glm' We have now created a table with certain parameters calculated for each of the genes analysed. logFC represents the base 2 logarithm of the fold change and it shows us how much the expression of the gene has changed between the two conditions. A logFC of 1 means a doubling in the read per gene count between the control and treatment samples. The genes with a logFC higher than 0 are upregulated while the genes with a logFC lower than 0 are downregulated between the control and treatment samples. logCPM represents the average log2-counts-per-million, the abundance of the gene. F - F-statistic. PValue is the raw p-value. FDR (The false discovery rate) represents the adjusted p-value and is calculated using Benjamini and Hochberg's algorithm. It controls the rate of false positive values under multiple testing. Usually, a threshold of under 5% is set for the FDR. The important information for us in this table is stored in the \"logFC\" and the \"FDR\" columns. The top DE genes have small FDR values and large fold changes Many of the genes in the samples are uninteresting for us, as they have a high FDR and/or low logFC values so we cannot consider them as differentially expressed. We will apply a filtering step in order to keep only the statistically significant genes. We will filter out the genes with an FDR higher than 0.05 and an absolute logFC lower than 1. In [16]: Copied! DEG_S10_filtered <- DEG_S10 $ table [ DEG_S10 $ table $ FDR < 0.05 & abs ( DEG_S10 $ table $ logFC ) > 1 ,] #Filtering DEG_S10_filtered <- rownames_to_column ( DEG_S10_filtered ) %>% rename ( gene_ID = rowname ) #Adding the gene_ID column head ( DEG_S10_filtered ) nrow ( DEG_S10_filtered ) # finding the number of genes that passed the filter DEG_S10_filtered < - DEG_S10$table[DEG_S10$table$FDR < 0.05 & abs(DEG_S10$table$logFC) > 1,] #Filtering DEG_S10_filtered < - rownames_to_column(DEG_S10_filtered) %>% rename(gene_ID = rowname) #Adding the gene_ID column head(DEG_S10_filtered) nrow(DEG_S10_filtered) # finding the number of genes that passed the filter A data.frame: 6 \u00d7 6 gene_ID logFC logCPM F PValue FDR 1 g39 3.586170 14.12463 336.66158 5.227331e-10 8.520550e-08 2 g232 4.049413 11.95044 157.50997 3.685988e-08 2.591779e-06 3 g6 2.322535 12.99954 150.27854 4.770146e-08 2.591779e-06 4 g350 2.053003 13.32457 97.56453 4.890245e-07 1.992775e-05 5 g99 -1.538787 11.68100 85.17478 9.976659e-07 3.195090e-05 6 g142 -1.423528 13.83069 82.52308 1.176107e-06 3.195090e-05 52 We can also visualize the selected genes by plotting a Smear plot or a Volcano plot. The Genes that passed the filter are coloured in red, and the top 10 genes with the lowest FDR value are labelled with their gene ID. We can see that the majority of the genes analysed are either not statistically significant or have a very small logFC. In [17]: Copied! plotSmear ( glmqlf_S10 , de.tags = rownames ( DEG_S10 $ table )[ which ( DEG_S10 $ table $ FDR < 0.05 & abs ( DEG_S10 $ table $ logFC ) > 1 )]) text ( x = DEG_S10_filtered $ logCPM [ 1 : 10 ], y = DEG_S10_filtered $ logFC [ 1 : 10 ], labels = DEG_S10_filtered $ gene_ID [ 1 : 10 ], cex = 0.7 , pos = 1 ) abline ( h = c ( -1 , 1 ), col = \"blue\" ) plotSmear(glmqlf_S10, de.tags = rownames(DEG_S10$table)[which(DEG_S10$table$FDR < 0.05 & abs(DEG_S10$table$logFC) > 1)]) text(x=DEG_S10_filtered$logCPM[1:10], y=DEG_S10_filtered$logFC[1:10], labels=DEG_S10_filtered$gene_ID[1:10], cex=0.7, pos=1) abline(h = c(-1, 1), col = \"blue\") We can also create a heatmap with the log2 read counts of the selected differentially expressed genes so that we can visualise the differences in normalized counts between the Control and the Treatment samples. The genes are ordered by the FDR value. In [18]: Copied! annot_col <- data.frame ( row.names = colnames ( pseudoNormCounts )[ 1 : 6 ], Condition = c ( rep ( \"Control\" , 3 ), rep ( \"Treatment\" , 3 ))) pheatmap ( as.matrix ( pseudoNormCounts [ DEG_S10_filtered $ gene_ID , c ( 1 : 6 )]), cluster_rows = F , cluster_col = F , annotation_col = annot_col ) annot_col < - data.frame(row.names = colnames(pseudoNormCounts)[1:6], Condition = c(rep(\"Control\", 3),rep( \"Treatment\", 3))) pheatmap(as.matrix(pseudoNormCounts[DEG_S10_filtered$gene_ID,c(1:6)]), cluster_rows = F, cluster_col = F, annotation_col = annot_col)","title":"DEGs for White clover S10 plants Treatment vs Control"},{"location":"nb/bulk.html#degs-for-white-clover-tienshan-treatment-vs-control","text":"We can do this using the same functions as above and changing the contrast. This time we will directly filter the differentially expressed genes using the same parameters as for the S10 samples. In [19]: Copied! glmqlf_Ti <- glmQLFTest ( fit , contrast = contrasts [, \"Tienshan\" ]) DEG_Ti <- topTags ( glmqlf_Ti , n = nrow ( DGEList $ counts )) DEG_Ti_filtered <- DEG_Ti $ table [ DEG_Ti $ table $ FDR < 0.05 & abs ( DEG_Ti $ table $ logFC ) > 1 ,] DEG_Ti_filtered <- rownames_to_column ( DEG_Ti_filtered ) %>% rename ( gene_ID = rowname ) print ( head ( DEG_Ti_filtered )) print ( \"Nr of differentially expressed genes:\" ) print ( nrow ( DEG_Ti_filtered )) glmqlf_Ti < - glmQLFTest(fit, contrast=contrasts[,\"Tienshan\"]) DEG_Ti < - topTags(glmqlf_Ti, n = nrow(DGEList$counts)) DEG_Ti_filtered < - DEG_Ti$table[DEG_Ti$table$FDR < 0.05 & abs(DEG_Ti$table$logFC) > 1,] DEG_Ti_filtered < - rownames_to_column(DEG_Ti_filtered) %>% rename(gene_ID = rowname) print(head(DEG_Ti_filtered)) print(\"Nr of differentially expressed genes:\") print(nrow(DEG_Ti_filtered)) gene_ID logFC logCPM F PValue FDR 1 g234 -3.348667 13.00417 278.01679 1.547626e-09 2.522630e-07 2 g269 -1.885843 11.83422 127.39949 1.172628e-07 9.556922e-06 3 g26 2.423725 11.36683 74.33983 2.016212e-06 8.910761e-05 4 g101 4.303290 13.18162 73.17140 2.186690e-06 8.910761e-05 5 g272 3.391225 13.86065 66.80131 3.475790e-06 9.840357e-05 6 g99 -1.430395 11.68100 66.25814 3.622217e-06 9.840357e-05 [1] \"Nr of differentially expressed genes:\" [1] 42 We can now plot a Venn diagram with the DEGs for the two genotypes in order to observe the number of common and specific differentially expressed genes between the two genotypes as response to the cold exposure. You can see that a high percentage of the identified genes are common for the two genotypes, while each genotype has also specific genes. In [20]: Copied! vd <- venn.diagram ( x = list ( DEG_S10_filtered $ gene_ID , DEG_Ti_filtered $ gene_ID ), category.names = c ( \"S10\" , \"Tienshan\" ), lwd = 4 , fill = c ( \"cornflowerblue\" , \"yellowgreen\" ), filename = NULL , cat.cex = 1 , cat.fontface = \"bold\" , output = TRUE ) grid.draw ( vd ) vd < - venn.diagram( x = list(DEG_S10_filtered$gene_ID, DEG_Ti_filtered$gene_ID), category.names = c(\"S10\" , \"Tienshan\"), lwd = 4, fill = c(\"cornflowerblue\", \"yellowgreen\"), filename = NULL, cat.cex = 1, cat.fontface = \"bold\", output=TRUE ) grid.draw(vd)","title":"DEGs for White clover Tienshan Treatment vs Control"},{"location":"nb/bulk.html#degs-for-s10tienshan-treatment-vs-control-wo-genotype-effects","text":"Until now we tested for DEGs specific for each of the two genotypes under cold treatment. We can also run a test where we ignore the genotype and just test for the differences in the cold response. Consider the counts for both genotypes as a single dataset using the previously created contrast \"S10_Tienshan\". Do the results look different compared with the previous tests? In [21]: Copied! glmqlf_S10_Ti <- glmQLFTest ( fit , contrast = contrasts [, \"S10_Tienshan\" ]) DEG_S10_Ti <- topTags ( glmqlf_S10_Ti , n = nrow ( DGEList $ counts )) DEG_S10_Ti_filtered <- DEG_S10_Ti $ table [ DEG_S10_Ti $ table $ FDR < 0.05 & abs ( DEG_S10_Ti $ table $ logFC ) > 1 ,] DEG_S10_Ti_filtered <- rownames_to_column ( DEG_S10_Ti_filtered ) %>% rename ( gene_ID = rowname ) print ( head ( DEG_S10_Ti_filtered )) print ( \"Nr of differentially expressed genes:\" ) print ( nrow ( DEG_S10_Ti_filtered )) glmqlf_S10_Ti < - glmQLFTest(fit, contrast=contrasts[,\"S10_Tienshan\"]) DEG_S10_Ti < - topTags(glmqlf_S10_Ti, n = nrow(DGEList$counts)) DEG_S10_Ti_filtered < - DEG_S10_Ti$table[DEG_S10_Ti$table$FDR < 0.05 & abs(DEG_S10_Ti$table$logFC) > 1,] DEG_S10_Ti_filtered < - rownames_to_column(DEG_S10_Ti_filtered) %>% rename(gene_ID = rowname) print(head(DEG_S10_Ti_filtered)) print(\"Nr of differentially expressed genes:\") print(nrow(DEG_S10_Ti_filtered)) gene_ID logFC logCPM F PValue FDR 1 g39 2.057128 14.12463 246.6519 3.039491e-09 4.954370e-07 2 g232 3.261008 11.95044 203.4580 8.934889e-09 5.288546e-07 3 g269 -1.652505 11.83422 200.3564 9.733520e-09 5.288546e-07 4 g6 1.714849 12.99954 166.2297 2.740066e-08 1.116577e-06 5 g99 -1.484591 11.68100 150.3246 4.762148e-08 1.552460e-06 6 g26 2.274575 11.36683 142.8625 6.290957e-08 1.623160e-06 [1] \"Nr of differentially expressed genes:\" [1] 52 Plot the results from the 3 tests in a Venn diagram to visualize the number of common and unique genes In [22]: Copied! vd <- venn.diagram ( x = list ( DEG_S10_filtered $ gene_ID , DEG_Ti_filtered $ gene_ID , DEG_S10_Ti_filtered $ gene_ID ), category.names = c ( \"S10\" , \"Tienshan\" , \"S10_Tienshan\" ), lwd = 3 , fill = c ( \"cornflowerblue\" , \"yellowgreen\" , \"thistle3\" ), filename = NULL , cat.cex = 1 , cat.fontface = \"bold\" , output = TRUE ) grid.draw ( vd ) vd < - venn.diagram( x = list(DEG_S10_filtered$gene_ID, DEG_Ti_filtered$gene_ID, DEG_S10_Ti_filtered$gene_ID), category.names = c(\"S10\" , \"Tienshan\", \"S10_Tienshan\"), lwd = 3, fill = c(\"cornflowerblue\", \"yellowgreen\", \"thistle3\"), filename = NULL, cat.cex = 1, cat.fontface = \"bold\", output=TRUE ) grid.draw(vd)","title":"DEGs for S10+Tienshan Treatment vs Control w/o genotype effects"},{"location":"nb/bulk.html#explore-dge-results","text":"","title":"Explore DGE results"},{"location":"nb/bulk.html#select-the-genes-which-appear-only-in-the-analysis-using-both-genotypes-for-further-examination","text":"We can use the \"anti_join\" function from the dplyr package to keep only the unique genes that appear only when using both genotypes. In [23]: Copied! S10_Ti_unique <- anti_join ( DEG_S10_Ti_filtered , DEG_S10_filtered , by = \"gene_ID\" ) %>% anti_join ( DEG_Ti_filtered , by = \"gene_ID\" ) S10_Ti_unique S10_Ti_unique < - anti_join(DEG_S10_Ti_filtered, DEG_S10_filtered, by=\"gene_ID\") %>% anti_join(DEG_Ti_filtered, by=\"gene_ID\") S10_Ti_unique A data.frame: 2 \u00d7 6 gene_ID logFC logCPM F PValue FDR g247 -1.412652 8.424523 10.877350 0.006535994 0.01500517 g360 1.180849 7.900076 9.804067 0.013809376 0.02813660","title":"Select the genes which appear only in the analysis using both genotypes for further examination."},{"location":"nb/bulk.html#linking-the-genes-selected-as-differentially-expressed-back-to-the-raw-read-counts","text":"How do the counts look for these genes, does it make sense that they are differentially expressed only when using the two genotypes? In [24]: Copied! Read_counts <- rownames_to_column ( Read_counts ) %>% rename ( gene_ID = rowname ) S10_Ti_unique_counts <- inner_join ( S10_Ti_unique [, c ( 1 , 2 , 6 )], Read_counts , by = \"gene_ID\" ) S10_Ti_unique_counts Read_counts < - rownames_to_column(Read_counts) %>% rename(gene_ID = rowname) S10_Ti_unique_counts < - inner_join(S10_Ti_unique[,c(1,2,6)], Read_counts, by=\"gene_ID\") S10_Ti_unique_counts A data.frame: 2 \u00d7 15 gene_ID logFC FDR S10_1_1 S10_1_2 S10_1_3 S10_2_1 S10_2_2 S10_2_3 TI_1_1 TI_1_2 TI_1_3 TI_2_1 TI_2_2 TI_2_3 g247 -1.412652 0.01500517 4 9 3 1 2 1 42 27 32 8 22 22 g360 1.180849 0.02813660 1 0 1 3 2 3 16 10 16 22 19 22","title":"Linking the genes selected as differentially expressed back to the raw read counts"},{"location":"nb/bulk.html#adding-functional-annotation-to-degs","text":"Until now we looked only at gene IDs, but we can also add functional annotations to the DEGs. The functional annotations were generated using protein sequences and the EggNOG software. Identifying the molecular function of the differentially expressed genes can help us do a literature survey in order to check if any of the genes discovered have been previously identified as being involved in the cold response. In [25]: Copied! Functional_annotations <- read.delim ( \"../Data/Clover_Data/Functional_Annotations.txt\" ) S10_Ti_unique_FA <- inner_join ( S10_Ti_unique [, c ( 1 , 2 , 6 )], Functional_annotations , by = \"gene_ID\" ) S10_Ti_unique_FA Functional_annotations < - read.delim(\"../Data/Clover_Data/Functional_Annotations.txt\") S10_Ti_unique_FA < - inner_join(S10_Ti_unique[,c(1,2,6)], Functional_annotations, by=\"gene_ID\") S10_Ti_unique_FA A data.frame: 2 \u00d7 4 gene_ID logFC FDR Human.Readable.Description g247 -1.412652 0.01500517 Nitrogen regulatory protein P-II homolog g360 1.180849 0.02813660 Unknown protein Tasks and Questions Based on the results obtained in the analysis so far, would you change the cut-off for the FDR and logFC to be more strict or more permissive? Look back at the raw counts for different FDR and logFC values and set the thresholds as you find appropriate. You can also plot histograms with the FDR and logFC values. In [ ]: Copied! hist ( DEG_S10 $ table $ FDR , main = \"\" , xlab = \"FDR\" , breaks = 200 , xlim = range ( c ( 0 , 0.1 ))) hist(DEG_S10$table$FDR , main = \"\", xlab = \"FDR\", breaks= 200, xlim = range(c(0, 0.1))) In [ ]: Copied! hist ( DEG_S10 $ table $ logFC , main = \"\" , xlab = \"logFC\" , breaks = 50 , xlim = range ( c ( -6 , 6 ))) hist(DEG_S10$table$logFC , main = \"\", xlab = \"logFC\", breaks= 50, xlim = range(c(-6, 6))) Separate the upregulated and downregulated genes for each genotype and append functional annotations to them. Identify the genes that are commonly upregulated in S10 and Tienshan samples and the uniquely upregulated genes for each genotype. Why do you think some of the proteins appear in duplicates? To answer these questions, it may be convenient to save summary tables from R and open them in excel. See the code below for examples of how to do this. Files can be downloaded by right-clicking on the file name. If you are familiar with R functions, you are welcome to use those for counting. In [ ]: Copied! dir.create ( \"DEG_Output_tables\" , showWarnings = FALSE ) dir.create(\"DEG_Output_tables\", showWarnings = FALSE) In [ ]: Copied! #Create the table with the DEGs, Raw counts(just for the Ti samples in this case, change to columns (2:7) for the S10 samples) and Functional annotations DEG_Ti_counts_FA <- inner_join ( DEG_Ti_filtered [, c ( 1 , 2 , 6 )], Read_counts [, c ( 1 , 8 : 13 )], by = \"gene_ID\" ) %>% inner_join ( Functional_annotations , by = \"gene_ID\" ) #Write the table to file write.table ( DEG_Ti_counts_FA , file = \"DEG_Output_tables/Ti_Treatment_Control_DGE.txt\" , quote = FALSE , row.names = FALSE , sep = \"\\t\" ) #Display the first 10 rows of the table head ( DEG_Ti_counts_FA , n = 10 ) #Create the table with the DEGs, Raw counts(just for the Ti samples in this case, change to columns (2:7) for the S10 samples) and Functional annotations DEG_Ti_counts_FA < - inner_join(DEG_Ti_filtered[,c(1, 2, 6)], Read_counts[, c(1, 8:13)], by=\"gene_ID\") %>% inner_join(Functional_annotations, by=\"gene_ID\") #Write the table to file write.table(DEG_Ti_counts_FA, file = \"DEG_Output_tables/Ti_Treatment_Control_DGE.txt\", quote = FALSE, row.names = FALSE, sep = \"\\t\") #Display the first 10 rows of the table head(DEG_Ti_counts_FA, n=10) Example for filtering and counting the Up/Down genes. You can easily filter using the \"filter()\" function just by specifying the dataframe and a logical argument. In [ ]: Copied! DEG_Ti_up <- filter ( DEG_Ti_counts_FA , logFC > 0 ) print ( \"Nr of upregulated genes:\" ) print ( nrow ( DEG_Ti_up )) DEG_Ti_down <- filter ( DEG_Ti_counts_FA , logFC < 0 ) print ( \"Nr of downregulated genes:\" ) print ( nrow ( DEG_Ti_down )) DEG_Ti_up < - filter(DEG_Ti_counts_FA, logFC > 0) print(\"Nr of upregulated genes:\") print(nrow(DEG_Ti_up)) DEG_Ti_down < - filter(DEG_Ti_counts_FA, logFC < 0) print(\"Nr of downregulated genes:\") print(nrow(DEG_Ti_down)) You can use the \"inner_join\" and the \"anti_join\" functions from the dplyr package to select the common and unique genes for each genotype: example_file_joined <- inner_join(file1, file2, by=\"gene_ID\")","title":"Adding functional annotation to DEGs"},{"location":"nb/bulk.html#wrapping-up","text":"In this notebook, you have worked with RNA-seq results for two white clover genotypes exposed to one night of cold treatment, aiming to identify genes that change their expression in response to the cold treatment. You have learned to perform exploratory data analysis of raw and normalized RNA-seq read counts. You have also performed differential gene expression using edgeR .","title":"Wrapping up \ud83c\udf89 \ud83c\udf89 \ud83c\udf89"},{"location":"nb/vcf.html","text":"(function (global, factory) { typeof exports === 'object' && typeof module !== 'undefined' ? module.exports = factory() : typeof define === 'function' && define.amd ? define(factory) : (global = global || self, global.ClipboardCopyElement = factory()); }(this, function () { 'use strict'; function createNode(text) { const node = document.createElement('pre'); node.style.width = '1px'; node.style.height = '1px'; node.style.position = 'fixed'; node.style.top = '5px'; node.textContent = text; return node; } function copyNode(node) { if ('clipboard' in navigator) { // eslint-disable-next-line flowtype/no-flow-fix-me-comments // $FlowFixMe Clipboard is not defined in Flow yet. return navigator.clipboard.writeText(node.textContent); } const selection = getSelection(); if (selection == null) { return Promise.reject(new Error()); } selection.removeAllRanges(); 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We also subtract one pixel so that no scrollbar appears if we have just one single-line cell in the notebook. This padding is to enable a 'scroll past end' feature in a notebook. */ --jp-notebook-scroll-padding: calc( 100% - var(--jp-code-font-size) * var(--jp-code-line-height) - var(--jp-code-padding) - var(--jp-cell-padding) - 1px ); /* Rendermime styles */ --jp-rendermime-error-background: #fdd; --jp-rendermime-table-row-background: var(--md-grey-100); --jp-rendermime-table-row-hover-background: var(--md-light-blue-50); /* Dialog specific styles */ --jp-dialog-background: rgba(0, 0, 0, 0.25); /* Console specific styles */ --jp-console-padding: 10px; /* Toolbar specific styles */ --jp-toolbar-border-color: var(--jp-border-color1); --jp-toolbar-micro-height: 8px; --jp-toolbar-background: var(--jp-layout-color1); --jp-toolbar-box-shadow: 0px 0px 2px 0px rgba(0, 0, 0, 0.24); --jp-toolbar-header-margin: 4px 4px 0px 4px; --jp-toolbar-active-background: var(--md-grey-300); /* Statusbar specific styles */ --jp-statusbar-height: 24px; /* Input field styles */ --jp-input-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-input-active-background: var(--jp-layout-color1); --jp-input-hover-background: var(--jp-layout-color1); --jp-input-background: var(--md-grey-100); --jp-input-border-color: var(--jp-border-color1); --jp-input-active-border-color: var(--jp-brand-color1); --jp-input-active-box-shadow-color: rgba(19, 124, 189, 0.3); /* General editor styles */ --jp-editor-selected-background: #d9d9d9; --jp-editor-selected-focused-background: #d7d4f0; --jp-editor-cursor-color: var(--jp-ui-font-color0); /* Code mirror specific styles */ --jp-mirror-editor-keyword-color: #008000; --jp-mirror-editor-atom-color: #88f; --jp-mirror-editor-number-color: #080; --jp-mirror-editor-def-color: #00f; --jp-mirror-editor-variable-color: var(--md-grey-900); --jp-mirror-editor-variable-2-color: #05a; --jp-mirror-editor-variable-3-color: #085; --jp-mirror-editor-punctuation-color: #05a; --jp-mirror-editor-property-color: #05a; --jp-mirror-editor-operator-color: #aa22ff; --jp-mirror-editor-comment-color: #408080; --jp-mirror-editor-string-color: #ba2121; --jp-mirror-editor-string-2-color: #708; --jp-mirror-editor-meta-color: #aa22ff; --jp-mirror-editor-qualifier-color: #555; --jp-mirror-editor-builtin-color: #008000; --jp-mirror-editor-bracket-color: #997; --jp-mirror-editor-tag-color: #170; --jp-mirror-editor-attribute-color: #00c; --jp-mirror-editor-header-color: blue; --jp-mirror-editor-quote-color: #090; --jp-mirror-editor-link-color: #00c; --jp-mirror-editor-error-color: #f00; --jp-mirror-editor-hr-color: #999; /* Vega extension styles */ --jp-vega-background: white; /* Sidebar-related styles */ --jp-sidebar-min-width: 250px; /* Search-related styles */ --jp-search-toggle-off-opacity: 0.5; --jp-search-toggle-hover-opacity: 0.8; --jp-search-toggle-on-opacity: 1; --jp-search-selected-match-background-color: rgb(245, 200, 0); --jp-search-selected-match-color: black; --jp-search-unselected-match-background-color: var( --jp-inverse-layout-color0 ); --jp-search-unselected-match-color: var(--jp-ui-inverse-font-color0); /* Icon colors that work well with light or dark backgrounds */ --jp-icon-contrast-color0: var(--md-purple-600); --jp-icon-contrast-color1: var(--md-green-600); --jp-icon-contrast-color2: var(--md-pink-600); --jp-icon-contrast-color3: var(--md-blue-600); } [data-md-color-scheme=\"slate\"] .jupyter-wrapper { /* Elevation * * We style box-shadows using Material Design's idea of elevation. These particular numbers are taken from here: * * https://github.com/material-components/material-components-web * https://material-components-web.appspot.com/elevation.html */ /* The dark theme shadows need a bit of work, but this will probably also require work on the core layout * colors used in the theme as well. */ --jp-shadow-base-lightness: 32; --jp-shadow-umbra-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.2 ); --jp-shadow-penumbra-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.14 ); --jp-shadow-ambient-color: rgba( var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), var(--jp-shadow-base-lightness), 0.12 ); --jp-elevation-z0: none; --jp-elevation-z1: 0px 2px 1px -1px var(--jp-shadow-umbra-color), 0px 1px 1px 0px var(--jp-shadow-penumbra-color), 0px 1px 3px 0px var(--jp-shadow-ambient-color); --jp-elevation-z2: 0px 3px 1px -2px var(--jp-shadow-umbra-color), 0px 2px 2px 0px var(--jp-shadow-penumbra-color), 0px 1px 5px 0px var(--jp-shadow-ambient-color); --jp-elevation-z4: 0px 2px 4px -1px var(--jp-shadow-umbra-color), 0px 4px 5px 0px var(--jp-shadow-penumbra-color), 0px 1px 10px 0px var(--jp-shadow-ambient-color); --jp-elevation-z6: 0px 3px 5px -1px var(--jp-shadow-umbra-color), 0px 6px 10px 0px var(--jp-shadow-penumbra-color), 0px 1px 18px 0px var(--jp-shadow-ambient-color); --jp-elevation-z8: 0px 5px 5px -3px var(--jp-shadow-umbra-color), 0px 8px 10px 1px var(--jp-shadow-penumbra-color), 0px 3px 14px 2px var(--jp-shadow-ambient-color); --jp-elevation-z12: 0px 7px 8px -4px var(--jp-shadow-umbra-color), 0px 12px 17px 2px var(--jp-shadow-penumbra-color), 0px 5px 22px 4px var(--jp-shadow-ambient-color); --jp-elevation-z16: 0px 8px 10px -5px var(--jp-shadow-umbra-color), 0px 16px 24px 2px var(--jp-shadow-penumbra-color), 0px 6px 30px 5px var(--jp-shadow-ambient-color); --jp-elevation-z20: 0px 10px 13px -6px var(--jp-shadow-umbra-color), 0px 20px 31px 3px var(--jp-shadow-penumbra-color), 0px 8px 38px 7px var(--jp-shadow-ambient-color); --jp-elevation-z24: 0px 11px 15px -7px var(--jp-shadow-umbra-color), 0px 24px 38px 3px var(--jp-shadow-penumbra-color), 0px 9px 46px 8px var(--jp-shadow-ambient-color); /* Borders * * The following variables, specify the visual styling of borders in JupyterLab. */ --jp-border-width: 1px; --jp-border-color0: var(--md-grey-700); --jp-border-color1: var(--md-grey-700); --jp-border-color2: var(--md-grey-800); --jp-border-color3: var(--md-grey-900); --jp-border-radius: 2px; /* UI Fonts * * The UI font CSS variables are used for the typography all of the JupyterLab * user interface elements that are not directly user generated content. * * The font sizing here is done assuming that the body font size of --jp-ui-font-size1 * is applied to a parent element. When children elements, such as headings, are sized * in em all things will be computed relative to that body size. */ --jp-ui-font-scale-factor: 1.2; --jp-ui-font-size0: 0.83333em; --jp-ui-font-size1: 13px; /* Base font size */ --jp-ui-font-size2: 1.2em; --jp-ui-font-size3: 1.44em; --jp-ui-font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\"; /* * Use these font colors against the corresponding main layout colors. * In a light theme, these go from dark to light. */ /* Defaults use Material Design specification */ --jp-ui-font-color0: rgba(255, 255, 255, 1); --jp-ui-font-color1: rgba(255, 255, 255, 0.87); --jp-ui-font-color2: rgba(255, 255, 255, 0.54); --jp-ui-font-color3: rgba(255, 255, 255, 0.38); /* * Use these against the brand/accent/warn/error colors. * These will typically go from light to darker, in both a dark and light theme. */ --jp-ui-inverse-font-color0: rgba(0, 0, 0, 1); --jp-ui-inverse-font-color1: rgba(0, 0, 0, 0.8); --jp-ui-inverse-font-color2: rgba(0, 0, 0, 0.5); --jp-ui-inverse-font-color3: rgba(0, 0, 0, 0.3); /* Content Fonts * * Content font variables are used for typography of user generated content. * * The font sizing here is done assuming that the body font size of --jp-content-font-size1 * is applied to a parent element. When children elements, such as headings, are sized * in em all things will be computed relative to that body size. */ --jp-content-line-height: 1.6; --jp-content-font-scale-factor: 1.2; --jp-content-font-size0: 0.83333em; --jp-content-font-size1: 14px; /* Base font size */ --jp-content-font-size2: 1.2em; --jp-content-font-size3: 1.44em; --jp-content-font-size4: 1.728em; --jp-content-font-size5: 2.0736em; /* This gives a magnification of about 125% in presentation mode over normal. */ --jp-content-presentation-font-size1: 17px; --jp-content-heading-line-height: 1; --jp-content-heading-margin-top: 1.2em; --jp-content-heading-margin-bottom: 0.8em; --jp-content-heading-font-weight: 500; /* Defaults use Material Design specification */ --jp-content-font-color0: rgba(255, 255, 255, 1); --jp-content-font-color1: rgba(255, 255, 255, 1); --jp-content-font-color2: rgba(255, 255, 255, 0.7); --jp-content-font-color3: rgba(255, 255, 255, 0.5); --jp-content-link-color: var(--md-blue-300); --jp-content-font-family: -apple-system, BlinkMacSystemFont, \"Segoe UI\", Helvetica, Arial, sans-serif, \"Apple Color Emoji\", \"Segoe UI Emoji\", \"Segoe UI Symbol\"; /* * Code Fonts * * Code font variables are used for typography of code and other monospaces content. */ --jp-code-font-size: 13px; --jp-code-line-height: 1.3077; /* 17px for 13px base */ --jp-code-padding: 5px; /* 5px for 13px base, codemirror highlighting needs integer px value */ --jp-code-font-family-default: Menlo, Consolas, \"DejaVu Sans Mono\", monospace; --jp-code-font-family: var(--jp-code-font-family-default); /* This gives a magnification of about 125% in presentation mode over normal. */ --jp-code-presentation-font-size: 16px; /* may need to tweak cursor width if you change font size */ --jp-code-cursor-width0: 1.4px; --jp-code-cursor-width1: 2px; --jp-code-cursor-width2: 4px; /* Layout * * The following are the main layout colors use in JupyterLab. In a light * theme these would go from light to dark. */ --jp-layout-color0: #111111; --jp-layout-color1: var(--md-grey-900); --jp-layout-color2: var(--md-grey-800); --jp-layout-color3: var(--md-grey-700); --jp-layout-color4: var(--md-grey-600); /* Inverse Layout * * The following are the inverse layout colors use in JupyterLab. In a light * theme these would go from dark to light. */ --jp-inverse-layout-color0: white; --jp-inverse-layout-color1: white; --jp-inverse-layout-color2: var(--md-grey-200); --jp-inverse-layout-color3: var(--md-grey-400); --jp-inverse-layout-color4: var(--md-grey-600); /* Brand/accent */ --jp-brand-color0: var(--md-blue-700); --jp-brand-color1: var(--md-blue-500); --jp-brand-color2: var(--md-blue-300); --jp-brand-color3: var(--md-blue-100); --jp-brand-color4: var(--md-blue-50); --jp-accent-color0: var(--md-green-700); --jp-accent-color1: var(--md-green-500); --jp-accent-color2: var(--md-green-300); --jp-accent-color3: var(--md-green-100); /* State colors (warn, error, success, info) */ --jp-warn-color0: var(--md-orange-700); --jp-warn-color1: var(--md-orange-500); --jp-warn-color2: var(--md-orange-300); --jp-warn-color3: var(--md-orange-100); --jp-error-color0: var(--md-red-700); --jp-error-color1: var(--md-red-500); --jp-error-color2: var(--md-red-300); --jp-error-color3: var(--md-red-100); --jp-success-color0: var(--md-green-700); --jp-success-color1: var(--md-green-500); --jp-success-color2: var(--md-green-300); --jp-success-color3: var(--md-green-100); --jp-info-color0: var(--md-cyan-700); --jp-info-color1: var(--md-cyan-500); --jp-info-color2: var(--md-cyan-300); --jp-info-color3: var(--md-cyan-100); /* Cell specific styles */ --jp-cell-padding: 5px; --jp-cell-collapser-width: 8px; --jp-cell-collapser-min-height: 20px; --jp-cell-collapser-not-active-hover-opacity: 0.6; --jp-cell-editor-background: var(--jp-layout-color1); --jp-cell-editor-border-color: var(--md-grey-700); --jp-cell-editor-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-cell-editor-active-background: var(--jp-layout-color0); --jp-cell-editor-active-border-color: var(--jp-brand-color1); --jp-cell-prompt-width: 64px; --jp-cell-prompt-font-family: var(--jp-code-font-family-default); --jp-cell-prompt-letter-spacing: 0px; --jp-cell-prompt-opacity: 1; --jp-cell-prompt-not-active-opacity: 1; --jp-cell-prompt-not-active-font-color: var(--md-grey-300); /* A custom blend of MD grey and blue 600 * See https://meyerweb.com/eric/tools/color-blend/#546E7A:1E88E5:5:hex */ --jp-cell-inprompt-font-color: #307fc1; /* A custom blend of MD grey and orange 600 * https://meyerweb.com/eric/tools/color-blend/#546E7A:F4511E:5:hex */ --jp-cell-outprompt-font-color: #bf5b3d; /* Notebook specific styles */ --jp-notebook-padding: 10px; --jp-notebook-select-background: var(--jp-layout-color1); --jp-notebook-multiselected-color: rgba(33, 150, 243, 0.24); /* The scroll padding is calculated to fill enough space at the bottom of the notebook to show one single-line cell (with appropriate padding) at the top when the notebook is scrolled all the way to the bottom. We also subtract one pixel so that no scrollbar appears if we have just one single-line cell in the notebook. This padding is to enable a 'scroll past end' feature in a notebook. */ --jp-notebook-scroll-padding: calc( 100% - var(--jp-code-font-size) * var(--jp-code-line-height) - var(--jp-code-padding) - var(--jp-cell-padding) - 1px ); /* Rendermime styles */ --jp-rendermime-error-background: rgba(244, 67, 54, 0.28); --jp-rendermime-table-row-background: var(--md-grey-900); --jp-rendermime-table-row-hover-background: rgba(3, 169, 244, 0.2); /* Dialog specific styles */ --jp-dialog-background: rgba(0, 0, 0, 0.6); /* Console specific styles */ --jp-console-padding: 10px; /* Toolbar specific styles */ --jp-toolbar-border-color: var(--jp-border-color2); --jp-toolbar-micro-height: 8px; --jp-toolbar-background: var(--jp-layout-color1); --jp-toolbar-box-shadow: 0px 0px 2px 0px rgba(0, 0, 0, 0.8); --jp-toolbar-header-margin: 4px 4px 0px 4px; --jp-toolbar-active-background: var(--jp-layout-color0); /* Statusbar specific styles */ --jp-statusbar-height: 24px; /* Input field styles */ --jp-input-box-shadow: inset 0 0 2px var(--md-blue-300); --jp-input-active-background: var(--jp-layout-color0); --jp-input-hover-background: var(--jp-layout-color2); --jp-input-background: var(--md-grey-800); --jp-input-border-color: var(--jp-border-color1); --jp-input-active-border-color: var(--jp-brand-color1); --jp-input-active-box-shadow-color: rgba(19, 124, 189, 0.3); /* General editor styles */ --jp-editor-selected-background: var(--jp-layout-color2); --jp-editor-selected-focused-background: rgba(33, 150, 243, 0.24); --jp-editor-cursor-color: var(--jp-ui-font-color0); /* Code mirror specific styles */ --jp-mirror-editor-keyword-color: var(--md-green-500); --jp-mirror-editor-atom-color: var(--md-blue-300); --jp-mirror-editor-number-color: var(--md-green-400); --jp-mirror-editor-def-color: var(--md-blue-600); --jp-mirror-editor-variable-color: var(--md-grey-300); --jp-mirror-editor-variable-2-color: var(--md-blue-400); --jp-mirror-editor-variable-3-color: var(--md-green-600); --jp-mirror-editor-punctuation-color: var(--md-blue-400); --jp-mirror-editor-property-color: var(--md-blue-400); --jp-mirror-editor-operator-color: #aa22ff; --jp-mirror-editor-comment-color: #408080; --jp-mirror-editor-string-color: #ff7070; --jp-mirror-editor-string-2-color: var(--md-purple-300); --jp-mirror-editor-meta-color: #aa22ff; --jp-mirror-editor-qualifier-color: #555; --jp-mirror-editor-builtin-color: var(--md-green-600); --jp-mirror-editor-bracket-color: #997; --jp-mirror-editor-tag-color: var(--md-green-700); --jp-mirror-editor-attribute-color: var(--md-blue-700); --jp-mirror-editor-header-color: var(--md-blue-500); --jp-mirror-editor-quote-color: var(--md-green-300); --jp-mirror-editor-link-color: var(--md-blue-700); --jp-mirror-editor-error-color: #f00; --jp-mirror-editor-hr-color: #999; /* Vega extension styles */ --jp-vega-background: var(--md-grey-400); /* Sidebar-related styles */ --jp-sidebar-min-width: 250px; /* Search-related styles */ --jp-search-toggle-off-opacity: 0.6; --jp-search-toggle-hover-opacity: 0.8; --jp-search-toggle-on-opacity: 1; --jp-search-selected-match-background-color: rgb(255, 225, 0); --jp-search-selected-match-color: black; --jp-search-unselected-match-background-color: var( --jp-inverse-layout-color0 ); --jp-search-unselected-match-color: var(--jp-ui-inverse-font-color0); /* scrollbar related styles. Supports every browser except Edge. */ /* colors based on JetBrain's Darcula theme */ --jp-scrollbar-background-color: #3f4244; --jp-scrollbar-thumb-color: 88, 96, 97; /* need to specify thumb color as an RGB triplet */ --jp-scrollbar-endpad: 3px; /* the minimum gap between the thumb and the ends of a scrollbar */ /* hacks for setting the thumb shape. These do nothing in Firefox */ --jp-scrollbar-thumb-margin: 3.5px; /* the space in between the sides of the thumb and the track */ --jp-scrollbar-thumb-radius: 9px; /* set to a large-ish value for rounded endcaps on the thumb */ /* Icon colors that work well with light or dark backgrounds */ --jp-icon-contrast-color0: var(--md-purple-600); --jp-icon-contrast-color1: var(--md-green-600); --jp-icon-contrast-color2: var(--md-pink-600); --jp-icon-contrast-color3: var(--md-blue-600); } :root{--md-red-50: #ffebee;--md-red-100: #ffcdd2;--md-red-200: #ef9a9a;--md-red-300: #e57373;--md-red-400: #ef5350;--md-red-500: #f44336;--md-red-600: #e53935;--md-red-700: #d32f2f;--md-red-800: #c62828;--md-red-900: #b71c1c;--md-red-A100: #ff8a80;--md-red-A200: #ff5252;--md-red-A400: #ff1744;--md-red-A700: #d50000;--md-pink-50: #fce4ec;--md-pink-100: #f8bbd0;--md-pink-200: #f48fb1;--md-pink-300: #f06292;--md-pink-400: #ec407a;--md-pink-500: #e91e63;--md-pink-600: #d81b60;--md-pink-700: #c2185b;--md-pink-800: #ad1457;--md-pink-900: #880e4f;--md-pink-A100: #ff80ab;--md-pink-A200: #ff4081;--md-pink-A400: #f50057;--md-pink-A700: #c51162;--md-purple-50: #f3e5f5;--md-purple-100: #e1bee7;--md-purple-200: #ce93d8;--md-purple-300: #ba68c8;--md-purple-400: #ab47bc;--md-purple-500: #9c27b0;--md-purple-600: #8e24aa;--md-purple-700: #7b1fa2;--md-purple-800: #6a1b9a;--md-purple-900: #4a148c;--md-purple-A100: #ea80fc;--md-purple-A200: #e040fb;--md-purple-A400: #d500f9;--md-purple-A700: #aa00ff;--md-deep-purple-50: #ede7f6;--md-deep-purple-100: #d1c4e9;--md-deep-purple-200: #b39ddb;--md-deep-purple-300: #9575cd;--md-deep-purple-400: #7e57c2;--md-deep-purple-500: #673ab7;--md-deep-purple-600: #5e35b1;--md-deep-purple-700: #512da8;--md-deep-purple-800: #4527a0;--md-deep-purple-900: #311b92;--md-deep-purple-A100: #b388ff;--md-deep-purple-A200: #7c4dff;--md-deep-purple-A400: #651fff;--md-deep-purple-A700: #6200ea;--md-indigo-50: #e8eaf6;--md-indigo-100: #c5cae9;--md-indigo-200: #9fa8da;--md-indigo-300: #7986cb;--md-indigo-400: #5c6bc0;--md-indigo-500: #3f51b5;--md-indigo-600: #3949ab;--md-indigo-700: #303f9f;--md-indigo-800: #283593;--md-indigo-900: #1a237e;--md-indigo-A100: #8c9eff;--md-indigo-A200: #536dfe;--md-indigo-A400: #3d5afe;--md-indigo-A700: #304ffe;--md-blue-50: #e3f2fd;--md-blue-100: #bbdefb;--md-blue-200: #90caf9;--md-blue-300: #64b5f6;--md-blue-400: #42a5f5;--md-blue-500: #2196f3;--md-blue-600: #1e88e5;--md-blue-700: #1976d2;--md-blue-800: #1565c0;--md-blue-900: #0d47a1;--md-blue-A100: #82b1ff;--md-blue-A200: #448aff;--md-blue-A400: #2979ff;--md-blue-A700: #2962ff;--md-light-blue-50: #e1f5fe;--md-light-blue-100: #b3e5fc;--md-light-blue-200: #81d4fa;--md-light-blue-300: #4fc3f7;--md-light-blue-400: #29b6f6;--md-light-blue-500: #03a9f4;--md-light-blue-600: #039be5;--md-light-blue-700: #0288d1;--md-light-blue-800: #0277bd;--md-light-blue-900: #01579b;--md-light-blue-A100: #80d8ff;--md-light-blue-A200: #40c4ff;--md-light-blue-A400: #00b0ff;--md-light-blue-A700: #0091ea;--md-cyan-50: #e0f7fa;--md-cyan-100: #b2ebf2;--md-cyan-200: #80deea;--md-cyan-300: #4dd0e1;--md-cyan-400: #26c6da;--md-cyan-500: #00bcd4;--md-cyan-600: #00acc1;--md-cyan-700: #0097a7;--md-cyan-800: #00838f;--md-cyan-900: #006064;--md-cyan-A100: #84ffff;--md-cyan-A200: #18ffff;--md-cyan-A400: #00e5ff;--md-cyan-A700: #00b8d4;--md-teal-50: #e0f2f1;--md-teal-100: #b2dfdb;--md-teal-200: #80cbc4;--md-teal-300: #4db6ac;--md-teal-400: #26a69a;--md-teal-500: #009688;--md-teal-600: #00897b;--md-teal-700: #00796b;--md-teal-800: #00695c;--md-teal-900: #004d40;--md-teal-A100: #a7ffeb;--md-teal-A200: #64ffda;--md-teal-A400: #1de9b6;--md-teal-A700: #00bfa5;--md-green-50: #e8f5e9;--md-green-100: #c8e6c9;--md-green-200: #a5d6a7;--md-green-300: #81c784;--md-green-400: #66bb6a;--md-green-500: #4caf50;--md-green-600: #43a047;--md-green-700: #388e3c;--md-green-800: #2e7d32;--md-green-900: #1b5e20;--md-green-A100: #b9f6ca;--md-green-A200: #69f0ae;--md-green-A400: #00e676;--md-green-A700: 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sourceMappingURL=mkdocs-jupyter.css.map*/ init_mathjax = function() { if (window.MathJax) { // MathJax loaded MathJax.Hub.Config({ TeX: { equationNumbers: { autoNumber: \"AMS\", useLabelIds: true } }, tex2jax: { inlineMath: [ ['$','$'], [\"\\\\(\",\"\\\\)\"] ], displayMath: [ ['$$','$$'], [\"\\\\[\",\"\\\\]\"] ], processEscapes: true, processEnvironments: true }, displayAlign: 'center', CommonHTML: { linebreaks: { automatic: true } } }); MathJax.Hub.Queue([\"Typeset\", MathJax.Hub]); } } init_mathjax(); Variant calling and VCF processing This tutorial will cover the steps for performing Variant calling and working on the resulting VCF file format. We will be using the Hifi and RNA-seq mapping data obtained from Galaxy. At the end of this tutorial you will be able to: call variants using alignment files extract data from VCF files using Python filter and count variants The present tutorial, like the rest of the course material, is available at our open-source github repository . To use this notebook, use the NGS (python) kernel that contains the packages. Choose it by selecting Kernel -> Change Kernel in the menu on top of the window. A few introductory points to run this notebook (click to show): To use this notebook, use the NGS (python) kernel that contains the packages. Choose it by selecting Kernel -> Change Kernel in the menu on top of the window. In this notebook you will use both bash and python commands On some computers, you might see the result of the commands once they are done running. This means you will wait some time while the computer is crunching, and only afterwards you will see the result of the command you have executed You can run the code in each cell by clicking on the run cell button, or by pressing Shift + Enter . When the code is done running, a small green check sign will appear on the left side You need to run the cells in sequential order, please do not run a cell until the one above finished running and do not skip any cells Each cell contains a short description of the code and the output you should get. Please try not to focus on understanding the code for each command in too much detail, but rather try to focus on the output You can create new code cells by pressing + in the Menu bar above. Import the necessary Python libraries: In [1]: Copied! import pandas import allel import numpy as np import matplotlib as mpl import matplotlib.pyplot as plt import seaborn as sns import pandas import allel import numpy as np import matplotlib as mpl import matplotlib.pyplot as plt import seaborn as sns Some of the commands used in the course are functions we implement to simplify reading the code of this course. Mostly, those are commands requiring lines of code that would not add anything to your learning curve (management of plots, trivial calculations, few management of the notebook layout). However, you are free to look at the code into the file Scripts/pythonScripts.py and to reuse our code in your own work (citing our course). In [2]: Copied! % run ../ Scripts / pythonScripts . py %run ../Scripts/pythonScripts.py Create a folder for the data necessary to VCF data analysis In [3]: Copied! %% bash mkdir - p Data_for_VCF_analysis %%bash mkdir -p Data_for_VCF_analysis Use the bam files generated from the alignment of raw reads \u00b6 We will use the data created during the alignment session of the course. You had two possibilities: using the interactive Galaxy platform as explained in the course webpage . In this case you will need to upload the some of the created data into the folder Data_for_VCF_analysis , renaming the files as follows: Hifi reads mapped to Contig1: HIFI_contig_1.bam Hifi reads mapped to Contig2: HIFI_contig_2.bam Hifi reads mapped to Contig 1 and 2: HIFI_contig_1_2_asm20.bam (you can of course choose the one with the map-pb alignment option from the alignment notebook) S10 RNAseq reads mapped to Contig 1 and 2 (After merging the bam files): RNA_S10_merged.bam Ti RNAseq reads mapped to Contig 1 and 2 (After merging the bam files): RNA_TI_merged.bam using the notebook 01_align.ipynb . In that case, you just need to run the command below, linking the data in the results folder into the folder Data_for_VCF_analysis . In [4]: Copied! %% bash ln - fs ` realpath results / HIFI_alignment / PacBio_clover_alignment_1 . sort . bam ` Data_for_VCF_analysis / HIFI_contig_1 . bam ln - fs ` realpath results / HIFI_alignment / PacBio_clover_alignment_2 . sort . bam ` Data_for_VCF_analysis / HIFI_contig_2 . bam ln - fs ` realpath results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sort . bam ` Data_for_VCF_analysis / HIFI_contig_1_2 . bam ln - fs ` realpath results / STAR_output / S10_align_contigs_1_2_merge / S10 . sorted . bam ` Data_for_VCF_analysis / RNA_S10_merged . bam ln - fs ` realpath results / STAR_output / TI_align_contigs_1_2_merge / TI . sorted . bam ` Data_for_VCF_analysis / RNA_TI_merged . bam %%bash ln -fs `realpath results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam` Data_for_VCF_analysis/HIFI_contig_1.bam ln -fs `realpath results/HIFI_alignment/PacBio_clover_alignment_2.sort.bam` Data_for_VCF_analysis/HIFI_contig_2.bam ln -fs `realpath results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sort.bam` Data_for_VCF_analysis/HIFI_contig_1_2.bam ln -fs `realpath results/STAR_output/S10_align_contigs_1_2_merge/S10.sorted.bam` Data_for_VCF_analysis/RNA_S10_merged.bam ln -fs `realpath results/STAR_output/TI_align_contigs_1_2_merge/TI.sorted.bam` Data_for_VCF_analysis/RNA_TI_merged.bam Variant calling \u00b6 We will use a tool named bcftools to find variants in the alignment files ( .bam ) relative to the reference genome, in this case, the file DNA_Contig1_2.fasta . In this way we can identify positions in the genome where the sequence of the aligned reads differ from the reference genome they were mapped to. There are multiple types of genetic variation , e.g. SNPs (single nucleotide polymorphism), indels (insertions or deletions) and structural variations (such as chromosomal rearrangements). Here we will only be working with SNPs, thus we will use the terms variants and SNPs interchangeably. The called variants will be stored in a specific format file, the Variant Call Format ( VCF ). When looking at an alignment files in IGV you should easily recognize the SNP positions. You can see in the figure below that at the marked positions all the mapped reads have a mismatch compared to the reference. You will be calling two types of SNPs in this notebook. First, we will find subgenome SNPs using the Hifi reads mapped to white clover Contig1 and Contig2. These are positions in the contigs that are different between the two subgenomes of white clover. Secondly, we will find SNPs that differentiate between the sequenced white clover S10 (the reference genome) and Ti genotype, using RNA-seq read mapping. Create a folder that will store all the files generated in this notebook. In [5]: Copied! ! mkdir - p results / VCF_Files !mkdir -p results/VCF_Files Call subgenome SNPs using the Hifi alignments and the reference genome \u00b6 We will use the bcftools software to call SNPs from alignment files. bcftools is a toolkit for variant calling and manipulating VCF files. If you are interested, you can find all the functionalities here http://samtools.github.io/bcftools/bcftools.html#call . We mainly need two commands for this step, first bcftools mpileup which takes as input the alignment and the genome reference files, followed by bcftools call to produce VCF files. The cell below will generate 3 VCF files stored in the folder results/VCF_Files using the Hifi alignment files uploaded from Galaxy. In [6]: Copied! ! bcftools mpileup -- threads 4 - Ou -- skip - indels - f ../ Data / Clover_Data / DNA_Contig1_2 . fasta Data_for_VCF_analysis / HIFI_contig_1 . bam | bcftools call - mv - Ov - o results / VCF_Files / HIFI_Contig_1 . vcf ! bcftools mpileup -- threads 4 - Ou -- skip - indels - f ../ Data / Clover_Data / DNA_Contig1_2 . fasta Data_for_VCF_analysis / HIFI_contig_2 . bam | bcftools call - mv - Ov - o results / VCF_Files / HIFI_Contig_2 . vcf ! bcftools mpileup -- threads 4 - Ou -- skip - indels - f ../ Data / Clover_Data / DNA_Contig1_2 . fasta Data_for_VCF_analysis / HIFI_contig_1_2 . bam | bcftools call - mv - Ov - o results / VCF_Files / HIFI_Contig_1_2 . vcf !bcftools mpileup --threads 4 -Ou --skip-indels -f ../Data/Clover_Data/DNA_Contig1_2.fasta Data_for_VCF_analysis/HIFI_contig_1.bam | bcftools call -mv -Ov -o results/VCF_Files/HIFI_Contig_1.vcf !bcftools mpileup --threads 4 -Ou --skip-indels -f ../Data/Clover_Data/DNA_Contig1_2.fasta Data_for_VCF_analysis/HIFI_contig_2.bam | bcftools call -mv -Ov -o results/VCF_Files/HIFI_Contig_2.vcf !bcftools mpileup --threads 4 -Ou --skip-indels -f ../Data/Clover_Data/DNA_Contig1_2.fasta Data_for_VCF_analysis/HIFI_contig_1_2.bam | bcftools call -mv -Ov -o results/VCF_Files/HIFI_Contig_1_2.vcf Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 TASK Inspect the VCF files using IGV, comparing them to the specific alignment BAM files. (You can download the VCF files to your computer from the results/VCF_Files folder) Are there any problematic positions that may not represent true SNPs? How can you use the HiFi reads aligned to Contigs1+2 identify potential problems? Hint: Try scrolling to the ends of the contigs. Call SNPs using the two RNA-seq genotypes, S10 and Ti \u00b6 We will repeat the same step as above this time using the RNA-seq alignment files for the two white clover genotypes (S10 and Ti). These commands will produce another two VCF files, stored in the same folder. In [7]: Copied! ! bcftools mpileup -- threads 4 - Ou -- skip - indels - f reference_data / DNA_Contig1_2 . fasta Data_for_VCF_analysis / RNA_S10_merged . bam | bcftools call - mv - Ov - o results / VCF_Files / RNA_S10_merged . vcf ! bcftools mpileup -- threads 4 - Ou -- skip - indels - f reference_data / DNA_Contig1_2 . fasta Data_for_VCF_analysis / RNA_TI_merged . bam | bcftools call - mv - Ov - o results / VCF_Files / RNA_TI_merged . vcf !bcftools mpileup --threads 4 -Ou --skip-indels -f reference_data/DNA_Contig1_2.fasta Data_for_VCF_analysis/RNA_S10_merged.bam | bcftools call -mv -Ov -o results/VCF_Files/RNA_S10_merged.vcf !bcftools mpileup --threads 4 -Ou --skip-indels -f reference_data/DNA_Contig1_2.fasta Data_for_VCF_analysis/RNA_TI_merged.bam | bcftools call -mv -Ov -o results/VCF_Files/RNA_TI_merged.vcf [mpileup] 1 samples in 1 input files Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] maximum number of reads per input file set to -d 250 Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 TASK Inspect one of the VCFs and the corresponding alignment files in IGV. Is it relevant to filter for false positives in this case, and what parameters would you look further into? VCF files processing and filtering \u00b6 Take a look at what one of the previously generated VCF files contains by running the cell below. A VCF file begins with the meta-information lines starting with ## followed by one header line, starting with # . Next, there are the data lines, each describing a genetic variant for a certain position in the genome. Each data line contains multiple tab-delimited columns with information about the variant. There are 9 fixed columns, labelled \u201cCHROM\u201d, \u201cPOS\u201d, \u201cID\u201d, \u201cREF\u201d, \u201cALT\u201d, \u201cQUAL\u201d, \u201cFILTER\u201d, \u201cINFO\u201d and \u201cFORMAT\u201d. Find more about the content of those columns in this wikipedia page . In the sample column you can find the most likely genotype of the sample. For diploid organisms, there will be a 0 value for reference allele and 1 for the alternate allele. Figure: possible genotypes in the data. For example, here we read the first 50 rows from the RNAseq_S10_merged.vcf file. You can see that the file format follows the same pattern as explained above. In [8]: Copied! ! cat results / VCF_Files / RNA_S10_merged . vcf | head - 50 !cat results/VCF_Files/RNA_S10_merged.vcf | head -50 ##fileformat=VCFv4.2 ##FILTER= ##bcftoolsVersion=1.16+htslib-1.17 ##bcftoolsCommand=mpileup --threads 4 -Ou --skip-indels -f reference_data/DNA_Contig1_2.fasta Data_for_VCF_analysis/RNA_S10_merged.bam ##reference=file://reference_data/DNA_Contig1_2.fasta ##contig= ##contig= ##ALT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##bcftools_callVersion=1.16+htslib-1.17 ##bcftools_callCommand=call -mv -Ov -o results/VCF_Files/RNA_S10_merged.vcf; Date=Mon Jun 19 10:48:17 2023 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Data_for_VCF_analysis/RNA_S10_merged.bam 1 33218 . G A 65.3262 . DP=88;VDB=0.0923504;SGB=-0.692914;RPBZ=3.99376;MQBZ=-1.86933;MQSBZ=-0.901828;BQBZ=-1.8368;SCBZ=2.6559;FS=0;MQ0F=0;AC=1;AN=2;DP4=15,13,16,9;MQ=19 GT:PL 0/1:98,0,138 1 33222 . C G 69.1967 . DP=56;VDB=4.89382e-06;SGB=-0.692352;RPBZ=3.47069;MQBZ=-1.73535;MQSBZ=-0.222384;BQBZ=-1.36705;SCBZ=2.16882;FS=0;MQ0F=0;AC=1;AN=2;DP4=18,13,12,9;MQ=19 GT:PL 0/1:102,0,138 1 33223 . T G 61.1405 . DP=56;VDB=2.99077e-05;SGB=-0.692067;RPBZ=3.40644;MQBZ=-1.80665;MQSBZ=-0.222384;BQBZ=0.830878;SCBZ=2.63256;FS=0;MQ0F=0;AC=1;AN=2;DP4=18,14,12,8;MQ=19 GT:PL 0/1:94,0,132 1 33224 . T G 65.1016 . DP=58;VDB=4.85907e-06;SGB=-0.692352;RPBZ=3.67489;MQBZ=-1.78978;MQSBZ=-0.159627;BQBZ=-1.43699;SCBZ=2.60016;FS=0;MQ0F=0;AC=1;AN=2;DP4=18,15,12,9;MQ=19 GT:PL 0/1:98,0,144 1 33225 . G T 64.0746 . DP=58;VDB=4.36523e-06;SGB=-0.692352;RPBZ=3.67489;MQBZ=-1.78978;MQSBZ=-0.159627;BQBZ=-2.60059;SCBZ=2.60016;FS=0;MQ0F=0;AC=1;AN=2;DP4=18,15,12,9;MQ=19 GT:PL 0/1:97,0,144 1 33227 . T A 64.067 . DP=59;VDB=4.09235e-06;SGB=-0.692352;RPBZ=4.13393;MQBZ=-1.81637;MQSBZ=-0.18317;BQBZ=-1.48941;SCBZ=2.64866;FS=0;MQ0F=0;AC=1;AN=2;DP4=19,15,12,9;MQ=19 GT:PL 0/1:97,0,144 1 49149 . C T 30.4183 . DP=4;VDB=0.0058656;SGB=-0.556411;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,4;MQ=20 GT:PL 1/1:60,12,0 1 83968 . C G 78.0347 . DP=10;VDB=5.52906e-06;SGB=-0.662043;RPBZ=-3;MQBZ=0;MQSBZ=0;BQBZ=-0.333333;SCBZ=1.77187;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,2,7;MQ=20 GT:PL 1/1:105,10,0 1 83970 . T C 78.0347 . DP=10;VDB=8.25997e-06;SGB=-0.662043;RPBZ=-1.79284;MQBZ=0;MQSBZ=0;BQBZ=0;SCBZ=1.77187;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,2,7;MQ=20 GT:PL 1/1:105,10,0 1 83972 . G T 78.0347 . DP=10;VDB=8.25997e-06;SGB=-0.662043;RPBZ=-1.79284;MQBZ=0;MQSBZ=0;BQBZ=0;SCBZ=1.57628;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,2,7;MQ=20 GT:PL 1/1:105,10,0 1 83975 . G A 78.0347 . DP=10;VDB=1.22485e-05;SGB=-0.662043;RPBZ=-1.79284;MQBZ=0;MQSBZ=0;BQBZ=0;SCBZ=1.57628;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,2,7;MQ=20 GT:PL 1/1:105,10,0 1 174956 . C T 10.7923 . DP=2;VDB=0.14;SGB=-0.453602;MQSBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=20 GT:PL 1/1:40,6,0 1 175456 . A G 7.30814 . DP=2;VDB=0.02;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20 GT:PL 1/1:36,6,0 1 211292 . A T 16.7427 . DP=5;VDB=0.0058656;SGB=-0.556411;RPBZ=-2;MQBZ=0;MQSBZ=0;BQBZ=1.22474;SCBZ=2;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,1,4,0;MQ=20 GT:PL 0/1:47,0,5 1 321659 . G A 13.5525 . DP=7;VDB=0.107235;SGB=-0.511536;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=1.73205;SCBZ=0.942809;FS=0;MQ0F=0;AC=1;AN=2;DP4=1,0,1,2;MQ=20 GT:PL 0/1:45,0,8 1 321661 . A C 13.5525 . DP=7;VDB=0.107235;SGB=-0.511536;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=1.73205;SCBZ=0.942809;FS=0;MQ0F=0;AC=1;AN=2;DP4=1,0,1,2;MQ=20 GT:PL 0/1:45,0,8 1 323166 . G A 7.30814 . DP=4;VDB=0.1;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 1 331785 . A T 7.30814 . DP=2;VDB=0.02;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20 GT:PL 1/1:36,6,0 1 331890 . C T 39.4149 . DP=6;VDB=0.100421;SGB=-0.556411;MQSBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,3,1;MQ=20 GT:PL 1/1:69,12,0 Next, in order to generate plots of the metrics stored in the VCF files, we will first import the VCF files in Python using the scikit-allel package. This package contains a series of function helpful for processing variant calling files. For now, we will import only the VCF files generated using the Hifi data alignments. You can ignore the warning. In [9]: Copied! #Import the VCF files Hifi_Contig_1_vcf = allel . read_vcf ( 'results/VCF_Files/HIFI_Contig_1.vcf' , fields = '*' ) Hifi_Contig_2_vcf = allel . read_vcf ( 'results/VCF_Files/HIFI_Contig_2.vcf' , fields = '*' ) Hifi_Contig_1_2_vcf = allel . read_vcf ( 'results/VCF_Files/HIFI_Contig_1_2.vcf' , fields = '*' ) #Import the VCF files Hifi_Contig_1_vcf = allel.read_vcf('results/VCF_Files/HIFI_Contig_1.vcf', fields='*') Hifi_Contig_2_vcf = allel.read_vcf('results/VCF_Files/HIFI_Contig_2.vcf', fields='*') Hifi_Contig_1_2_vcf = allel.read_vcf('results/VCF_Files/HIFI_Contig_1_2.vcf', fields='*') /work/Course_Env/lib/python3.10/site-packages/allel/io/vcf_read.py:1732: UserWarning: invalid INFO header: '##INFO=\\n' warnings.warn('invalid INFO header: %r' % header) Let's check the number of SNPs in each of the three VCF files. The first two VCF files contain subgenome SNPs. You can see that we identified a have a high number of polymorphisms between the two subgenomes. On the other hand the Hifi_Contig1_2_vcf file contains what we would call false positives, as we called SNPs using the same Hifi reads that were used for assembling the reference genome. As expected the number of SNPs in this file is much smaller. In [10]: Copied! print ( \"Number of SNPs in Hifi Contig 1 vcf file:\" , Hifi_Contig_1_vcf [ 'variants/POS' ] . size ) print ( \"Number of SNPs in Hifi Contig 2 vcf file:\" , Hifi_Contig_2_vcf [ 'variants/POS' ] . size ) print ( \"Number of SNPs in Hifi Contig 1 and 2 vcf file:\" , Hifi_Contig_1_2_vcf [ 'variants/POS' ] . size ) print(\"Number of SNPs in Hifi Contig 1 vcf file:\", Hifi_Contig_1_vcf['variants/POS'].size) print(\"Number of SNPs in Hifi Contig 2 vcf file:\", Hifi_Contig_2_vcf['variants/POS'].size) print(\"Number of SNPs in Hifi Contig 1 and 2 vcf file:\", Hifi_Contig_1_2_vcf['variants/POS'].size) Number of SNPs in Hifi Contig 1 vcf file: 31981 Number of SNPs in Hifi Contig 2 vcf file: 30823 Number of SNPs in Hifi Contig 1 and 2 vcf file: 1309 As an overview of the distribution of SNPs, we can plot the density of SNPs across the contigs. We have defined a function called plot_variant_density in the file ../Scripts/pythonScripts.sh that does exactly that. We use that to plot the SNP density across the contigs in the three VCF files in bins of 5000 bp. We can approximate that a SNP density of 0.1 SNPs/bp repesents one polymorphic site at every ten nucleotides. You can see that for the two contigs there are regions more conserved between the two subgenomes, which show a low density of SNPs and more variable regions, which have a higher SNP density. In the third plot we can mainly observe SNPs at the beging of the contigs, as you have probably also oberved when inspecting the files in IGV. Taking a look at the scale of the y-axis you can oberve that the SNP density for Hifi_Contig1_2_vcf is much smaller compared to the other two files. Note: For easier plotting of the files that contain SNPs from both Contig 1 and 2, the SNP density is plotted as an overlay of both contigs. In [11]: Copied! #Plot SNP density plot_variant_density ( Hifi_Contig_1_vcf , window_size = 5000 , title = 'Contig 1 Raw SNP density' ) plot_variant_density ( Hifi_Contig_2_vcf , window_size = 5000 , title = 'Contig 2 Raw SNP density' ) plot_variant_density ( Hifi_Contig_1_2_vcf , window_size = 5000 , title = 'Contig 1 and 2 Raw SNP density' ) #Plot SNP density plot_variant_density(Hifi_Contig_1_vcf, window_size=5000, title='Contig 1 Raw SNP density') plot_variant_density(Hifi_Contig_2_vcf, window_size=5000, title='Contig 2 Raw SNP density') plot_variant_density(Hifi_Contig_1_2_vcf, window_size=5000, title='Contig 1 and 2 Raw SNP density') We can also plot some of the most relevant parameters from the VCF files, such as the read depth and the quality, to have an overview of the quality of the SNPs in these samples. We defined for that the function plot_variant_hist in the file ../Scripts/pythonScripts.sh . We can plot the metrics \"DP\" (Read depth), \"QUAL\" (Quality score), and \"MQ\" (Mapping quality for Hifi_Contig1_vcf . The x-axis represents the chosen metric, while the y-axis represents the number of SNPs. You can observe that the majority of the SNPs from this file have a high quality. In [12]: Copied! plot_variant_hist ( Hifi_Contig_1_vcf , 'DP' , \"mediumblue\" ) plot_variant_hist ( Hifi_Contig_1_vcf , 'QUAL' , \"forestgreen\" ) plot_variant_hist ( Hifi_Contig_1_vcf , 'MQ' , \"darkred\" ) plot_variant_hist(Hifi_Contig_1_vcf,'DP', \"mediumblue\") plot_variant_hist(Hifi_Contig_1_vcf, 'QUAL', \"forestgreen\") plot_variant_hist(Hifi_Contig_1_vcf, 'MQ', \"darkred\") TASK In the two cells below generate the same three plots as above using the VCF files for Contig 2 and Contig 1+2. You will just need to copy the three command lines from the cell above and replace the name of the VCF files. In [ ]: Copied! #Plot the metrics for Contig 2 #Plot the metrics for Contig 2 In [ ]: Copied! #Plot the metrics for Contig 1 + 2 #Plot the metrics for Contig 1 + 2 As you can observe in the plots above, there are some positions with very low read depth and low quality. Those might represent false-positive variants. Thus, we will filter the VCF files in order to eliminate those positions. For this purpose, we will use another bcftools function bcftools filter . We can pass thresholds for all the info metrics to this function using the \"-i\" flag. Below is just an example of the thresholds, you can change the values to suit your files. Note that this command will generate a new filtered VCF file in the \"VCF_Files\" Folder. In [ ]: Copied! ! bcftools filter - i '(QUAL>150) & (DP > 20) & (MQ > 40)' results / VCF_Files / HIFI_Contig_1 . vcf - O v > results / VCF_Files / HIFI_Contig_1_filtered . vcf !bcftools filter -i '(QUAL>150) & (DP > 20) & (MQ > 40)' results/VCF_Files/HIFI_Contig_1.vcf -O v > results/VCF_Files/HIFI_Contig_1_filtered.vcf In [ ]: Copied! ! bcftools filter - i '(QUAL>150) & (DP > 20) & (MQ > 40)' results / VCF_Files / HIFI_Contig_2 . vcf - O v > results / VCF_Files / HIFI_Contig_2_filtered . vcf !bcftools filter -i '(QUAL>150) & (DP > 20) & (MQ > 40)' results/VCF_Files/HIFI_Contig_2.vcf -O v > results/VCF_Files/HIFI_Contig_2_filtered.vcf In [ ]: Copied! ! bcftools filter - i '(QUAL>150) & (DP > 20) & (MQ > 40)' results / VCF_Files / HIFI_Contig_1_2 . vcf - O v > results / VCF_Files / HIFI_Contig_1_2_filtered . vcf !bcftools filter -i '(QUAL>150) & (DP > 20) & (MQ > 40)' results/VCF_Files/HIFI_Contig_1_2.vcf -O v > results/VCF_Files/HIFI_Contig_1_2_filtered.vcf We read the filtered VCF file for Contig1 in python and generate the same plots as before. We can read the VCF file and generate all the plots in one cell this time. We check how many positions have been eliminated by the filter and compare the plots with the ones for the unfiltered VCFs. If you consider that there are still positions with with low quality you can change the filter and repeat the process. In [ ]: Copied! Hifi_Contig1_filtered = allel . read_vcf ( 'results/VCF_Files/HIFI_Contig_1_filtered.vcf' , fields = '*' ) print ( \"Number of SNPs in Contig 1 VCF filtered file:\" , Hifi_Contig1_filtered [ 'variants/POS' ] . size ) #Plot SNP density plot_variant_density ( Hifi_Contig1_filtered , window_size = 5000 , title = 'Contig 1 Filtered variant density' ) #Plot metrics plot_variant_hist ( Hifi_Contig1_filtered , 'DP' , \"mediumblue\" ) plot_variant_hist ( Hifi_Contig1_filtered , 'QUAL' , \"forestgreen\" ) plot_variant_hist ( Hifi_Contig1_filtered , 'MQ' , \"darkred\" ) Hifi_Contig1_filtered = allel.read_vcf('results/VCF_Files/HIFI_Contig_1_filtered.vcf', fields='*') print(\"Number of SNPs in Contig 1 VCF filtered file:\", Hifi_Contig1_filtered['variants/POS'].size) #Plot SNP density plot_variant_density(Hifi_Contig1_filtered, window_size=5000, title='Contig 1 Filtered variant density') #Plot metrics plot_variant_hist(Hifi_Contig1_filtered,'DP', \"mediumblue\") plot_variant_hist(Hifi_Contig1_filtered, 'QUAL', \"forestgreen\") plot_variant_hist(Hifi_Contig1_filtered, 'MQ', \"darkred\") TASK This exercise covers the rest of the notebook and contains explanations as well . The code will work only if you complete correctly the empty cells. Some cells are filled in to help. Compare the VCF files before and after filtering in IGV. In the two cells below generate the same plots as above using the filtered VCF files for Contig 2 and Contig 1 + 2. You will just need to copy the three command lines from the cell above and replace the name of the VCF files. In [ ]: Copied! #Figures for Contig 2 Filtered VCF #Figures for Contig 2 Filtered VCF In [ ]: Copied! #Figures for Contig 1 + 2 Filtered VCF #Figures for Contig 1 + 2 Filtered VCF Repeat the quality check and filtering as described above for the two RNA-seq VCF files: Read the VCF files in Python: In [ ]: Copied! vcf_S10_RNA = allel . read_vcf ( 'results/VCF_Files/RNA_S10_merged.vcf' , fields = '*' ) vcf_Ti_RNA = allel . read_vcf ( 'results/VCF_Files/RNA_TI_merged.vcf' , fields = '*' ) vcf_S10_RNA = allel.read_vcf('results/VCF_Files/RNA_S10_merged.vcf', fields='*') vcf_Ti_RNA = allel.read_vcf('results/VCF_Files/RNA_TI_merged.vcf', fields='*') Print the number of SNPs in the two RNA-seq VCF files. Note that the number of SNPs is much smaller than for the Hifi VCF files. Also, there is a difference in the number of SNPs for the two genotypes. As S10 RNA-seq data originates from the same genotype as the referece genome, one would expect a small number of SNPs to be identified in this case. In [ ]: Copied! print ( \"Number of SNPs in S10 RNA-seq VCF file:\" , vcf_S10_RNA [ 'variants/POS' ] . size ) print ( \"Number of SNPs in Ti RNA-seq VCF file:\" , vcf_Ti_RNA [ 'variants/POS' ] . size ) print(\"Number of SNPs in S10 RNA-seq VCF file:\", vcf_S10_RNA['variants/POS'].size) print(\"Number of SNPs in Ti RNA-seq VCF file:\", vcf_Ti_RNA['variants/POS'].size) Generate SNP density plots using the plot_variant_density() function: In [ ]: Copied! In [ ]: Copied! Generate info histograms using the plot_variant_hist() function for the same fields. You should observe that the metrics for the RNA-seq vcf files are quite different from the ones using Hifi reads. In [ ]: Copied! In [ ]: Copied! Filter the VCF files using bcftools and your selected tresholds after inspecting the VCF files. Add the filter thresholds before running the command. In [ ]: Copied! ! bcftools filter - i 'add filter thresholds here' results / VCF_Files / RNA_S10_merged . vcf - O v > results / VCF_Files / RNA_S10_merged_filtered . vcf ! bcftools filter - i 'add filter thresholds here' results / VCF_Files / RNA_TI_merged . vcf - O v > results / VCF_Files / RNA_TI_merged_filtered . vcf !bcftools filter -i 'add filter thresholds here' results/VCF_Files/RNA_S10_merged.vcf -O v > results/VCF_Files/RNA_S10_merged_filtered.vcf !bcftools filter -i 'add filter thresholds here' results/VCF_Files/RNA_TI_merged.vcf -O v > results/VCF_Files/RNA_TI_merged_filtered.vcf Read the filtered VCFs in python: In [ ]: Copied! vcf_S10_RNA_filtered = allel . read_vcf ( 'results/VCF_Files/RNA_S10_merged_filtered.vcf' , fields = '*' ) vcf_Ti_RNA_filtered = allel . read_vcf ( 'results/VCF_Files/RNA_TI_merged_filtered.vcf' , fields = '*' ) vcf_S10_RNA_filtered = allel.read_vcf('results/VCF_Files/RNA_S10_merged_filtered.vcf', fields='*') vcf_Ti_RNA_filtered = allel.read_vcf('results/VCF_Files/RNA_TI_merged_filtered.vcf', fields='*') Check the number of SNPs in the filtered VCF files: In [ ]: Copied! print ( \"Number of SNPs in the filtered S10 RNA-seq VCF file:\" , vcf_S10_RNA_filtered [ 'variants/POS' ] . size ) print ( \"Number of SNPs in the filtered Ti RNA-seq VCF file:\" , vcf_Ti_RNA_filtered [ 'variants/POS' ] . size ) print(\"Number of SNPs in the filtered S10 RNA-seq VCF file:\", vcf_S10_RNA_filtered['variants/POS'].size) print(\"Number of SNPs in the filtered Ti RNA-seq VCF file:\", vcf_Ti_RNA_filtered['variants/POS'].size) Plot same histograms for the filtered VCF files. In [ ]: Copied! In [ ]: Copied! Question: Is it relevant to filter for false positives in this case, and what parameters would you look further into? Genotypes counting \u00b6 We want to count the different genotypes in each of the five filtered VCF files generated previously. To make this task easier we can take advantage of the counting functions in the scikit-allel package. We have used those to implement a little function called position_count in the file ../Scripts/pythonScripts.sh . You can then use the function with each of the 5 filtered VCF files to count the number of positions. You need to fill the names of the VCF files imported in Python. In [ ]: Copied! #Contig 1 filtered VCF position_count ( Hifi_Contig1_filtered ) #Contig 1 filtered VCF position_count(Hifi_Contig1_filtered) In [ ]: Copied! #Contig 2 filtered VCF position_count () #Contig 2 filtered VCF position_count() In [ ]: Copied! #Contig 1 and 2 filtered VCF position_count () #Contig 1 and 2 filtered VCF position_count() In [ ]: Copied! #RNAseq S10 filtered VCF position_count () #RNAseq S10 filtered VCF position_count() In [ ]: Copied! #RNAseq Ti filtered VCF position_count () #RNAseq Ti filtered VCF position_count() Comparison of VCF files \u00b6 Compare the VCF files with subgenome variants and the VCF files with S10/Tienshan genotype specific variants obtained from RNA-seq mapping We want now to find overlapping position between the Contig 1 and Contig 2 Hifi VCF files and the Ti RNAseq VCF file. To ease this task we will first create two merged VCF files containing: Hifi Contig 1 VCF + Ti RNAseq VCF Hifi Contig 2 VCF + Ti RNAseq VCF Once again, we will use bcftools for this task, using the merge function. However, the bcftools merge function works only with compressed and indexed VCF files, so first we will do this. In [ ]: Copied! ! bcftools view results / VCF_Files / HIFI_Contig_1_filtered . vcf - Oz - o results / VCF_Files / HIFI_Contig_1_filtered . vcf . gz ! bcftools index results / VCF_Files / HIFI_Contig_1_filtered . vcf . gz - f - o results / VCF_Files / HIFI_Contig_1_filtered . vcf . gz . csi ! bcftools view results / VCF_Files / HIFI_Contig_2_filtered . vcf - Oz - o results / VCF_Files / HIFI_Contig_2_filtered . vcf . gz ! bcftools index results / VCF_Files / HIFI_Contig_2_filtered . vcf . gz - f - o results / VCF_Files / HIFI_Contig_2_filtered . vcf . gz . csi ! bcftools view results / VCF_Files / RNA_TI_merged_filtered . vcf - Oz - o results / VCF_Files / RNA_TI_merged_filtered . vcf . gz ! bcftools index results / VCF_Files / RNA_TI_merged_filtered . vcf . gz - f - o results / VCF_Files / RNA_TI_merged_filtered . vcf . gz . csi !bcftools view results/VCF_Files/HIFI_Contig_1_filtered.vcf -Oz -o results/VCF_Files/HIFI_Contig_1_filtered.vcf.gz !bcftools index results/VCF_Files/HIFI_Contig_1_filtered.vcf.gz -f -o results/VCF_Files/HIFI_Contig_1_filtered.vcf.gz.csi !bcftools view results/VCF_Files/HIFI_Contig_2_filtered.vcf -Oz -o results/VCF_Files/HIFI_Contig_2_filtered.vcf.gz !bcftools index results/VCF_Files/HIFI_Contig_2_filtered.vcf.gz -f -o results/VCF_Files/HIFI_Contig_2_filtered.vcf.gz.csi !bcftools view results/VCF_Files/RNA_TI_merged_filtered.vcf -Oz -o results/VCF_Files/RNA_TI_merged_filtered.vcf.gz !bcftools index results/VCF_Files/RNA_TI_merged_filtered.vcf.gz -f -o results/VCF_Files/RNA_TI_merged_filtered.vcf.gz.csi Now we can merge Contig 1 VCF with the Ti RNA VCF and keep only positions that match between the two files by filtering out any positions with missing genotypes. In [ ]: Copied! ! bcftools merge results / VCF_Files / HIFI_Contig_1_filtered . vcf . gz results / VCF_Files / RNA_TI_merged_filtered . vcf . gz | bcftools filter - e 'GT=\"./.\"' > results / VCF_Files / TI_Contig_1_merged . vcf !bcftools merge results/VCF_Files/HIFI_Contig_1_filtered.vcf.gz results/VCF_Files/RNA_TI_merged_filtered.vcf.gz | bcftools filter -e 'GT=\"./.\"' > results/VCF_Files/TI_Contig_1_merged.vcf Merge Contig 2 VCF with the Ti RNA VCF and keep only positions that match between the two files. In [ ]: Copied! ! bcftools merge results / VCF_Files / HIFI_Contig_2_filtered . vcf . gz results / VCF_Files / RNA_TI_merged_filtered . vcf . gz | bcftools filter - e 'GT=\"./.\"' > results / VCF_Files / TI_Contig_2_merged . vcf !bcftools merge results/VCF_Files/HIFI_Contig_2_filtered.vcf.gz results/VCF_Files/RNA_TI_merged_filtered.vcf.gz | bcftools filter -e 'GT=\"./.\"' > results/VCF_Files/TI_Contig_2_merged.vcf Take a look at the merged VCF file. You can see that compared with the VCF files for just one sample, there is now a new column in the file, with the corresponding genotype for the second sample that we merged. In [ ]: Copied! ! cat results / VCF_Files / TI_Contig_1_merged . vcf | head - 50 !cat results/VCF_Files/TI_Contig_1_merged.vcf | head -50 In order to count the genotypes for the matching positions we can use once again bcftools filter command. Only that this time we will filter based on the genotype columns for the two samples (GT[0] and GT[1]). GT[0] repesents the genotype for the first sample in the merge command and GT[1] is the genotype for the second sample in the merge command. AR - heterozygous AA - homozygous alternate For example, the filter GT[0]=\"AR\" && GT[1]=\"AR\" will keep only position in which both samples have a heterozygous genotype. A quick way to count how many positions are in the VCF file is by suing the simple bash command grep . This will count all the lines in the VCF files that do not start with a # , thus all the data lines. In [ ]: Copied! ! echo \"AR + AR:\" ! bcftools filter - i 'GT[0]=\"AR\" && GT[1]=\"AR\"' results / VCF_Files / TI_Contig_1_merged . vcf | grep - c - v \"^#\" ! echo \"AR + AA:\" ! bcftools filter - i 'GT[0]=\"AR\" && GT[1]=\"AA\"' results / VCF_Files / TI_Contig_1_merged . vcf | grep - c - v \"^#\" ! echo \"AA + AR:\" ! bcftools filter - i 'GT[0]=\"AA\" && GT[1]=\"AR\"' results / VCF_Files / TI_Contig_1_merged . vcf | grep - c - v \"^#\" ! echo \"AA + AA:\" ! bcftools filter - i 'GT[0]=\"AA\" && GT[1]=\"AA\"' results / VCF_Files / TI_Contig_1_merged . vcf | grep - c - v \"^#\" !echo \"AR + AR:\" !bcftools filter -i 'GT[0]=\"AR\" && GT[1]=\"AR\"' results/VCF_Files/TI_Contig_1_merged.vcf | grep -c -v \"^#\" !echo \"AR + AA:\" !bcftools filter -i 'GT[0]=\"AR\" && GT[1]=\"AA\"' results/VCF_Files/TI_Contig_1_merged.vcf | grep -c -v \"^#\" !echo \"AA + AR:\" !bcftools filter -i 'GT[0]=\"AA\" && GT[1]=\"AR\"' results/VCF_Files/TI_Contig_1_merged.vcf | grep -c -v \"^#\" !echo \"AA + AA:\" !bcftools filter -i 'GT[0]=\"AA\" && GT[1]=\"AA\"' results/VCF_Files/TI_Contig_1_merged.vcf | grep -c -v \"^#\" Use the same commands as above to count the positions marching the filters in the Contig2_Ti_merged.vcf. In [ ]: Copied! Wrapping up \ud83c\udf89 \ud83c\udf89 \ud83c\udf89 \u00b6 In this exercise, you identified polymorphisms between the two white clover subgenomes using Hifi reads alignment files and SNPs specific for the white clover Tienshan genotype using RNA-seq alignment files. You learned how to import VCF files in Python to extract data and created plots. You also filtered low-quality variants from the VCF files and counted genotypes.","title":"3.2.Variant calling analysis"},{"location":"nb/vcf.html#use-the-bam-files-generated-from-the-alignment-of-raw-reads","text":"We will use the data created during the alignment session of the course. You had two possibilities: using the interactive Galaxy platform as explained in the course webpage . In this case you will need to upload the some of the created data into the folder Data_for_VCF_analysis , renaming the files as follows: Hifi reads mapped to Contig1: HIFI_contig_1.bam Hifi reads mapped to Contig2: HIFI_contig_2.bam Hifi reads mapped to Contig 1 and 2: HIFI_contig_1_2_asm20.bam (you can of course choose the one with the map-pb alignment option from the alignment notebook) S10 RNAseq reads mapped to Contig 1 and 2 (After merging the bam files): RNA_S10_merged.bam Ti RNAseq reads mapped to Contig 1 and 2 (After merging the bam files): RNA_TI_merged.bam using the notebook 01_align.ipynb . In that case, you just need to run the command below, linking the data in the results folder into the folder Data_for_VCF_analysis . In [4]: Copied! %% bash ln - fs ` realpath results / HIFI_alignment / PacBio_clover_alignment_1 . sort . bam ` Data_for_VCF_analysis / HIFI_contig_1 . bam ln - fs ` realpath results / HIFI_alignment / PacBio_clover_alignment_2 . sort . bam ` Data_for_VCF_analysis / HIFI_contig_2 . bam ln - fs ` realpath results / HIFI_alignment / PacBio_clover_alignment_1_2_asm20 . sort . bam ` Data_for_VCF_analysis / HIFI_contig_1_2 . bam ln - fs ` realpath results / STAR_output / S10_align_contigs_1_2_merge / S10 . sorted . bam ` Data_for_VCF_analysis / RNA_S10_merged . bam ln - fs ` realpath results / STAR_output / TI_align_contigs_1_2_merge / TI . sorted . bam ` Data_for_VCF_analysis / RNA_TI_merged . bam %%bash ln -fs `realpath results/HIFI_alignment/PacBio_clover_alignment_1.sort.bam` Data_for_VCF_analysis/HIFI_contig_1.bam ln -fs `realpath results/HIFI_alignment/PacBio_clover_alignment_2.sort.bam` Data_for_VCF_analysis/HIFI_contig_2.bam ln -fs `realpath results/HIFI_alignment/PacBio_clover_alignment_1_2_asm20.sort.bam` Data_for_VCF_analysis/HIFI_contig_1_2.bam ln -fs `realpath results/STAR_output/S10_align_contigs_1_2_merge/S10.sorted.bam` Data_for_VCF_analysis/RNA_S10_merged.bam ln -fs `realpath results/STAR_output/TI_align_contigs_1_2_merge/TI.sorted.bam` Data_for_VCF_analysis/RNA_TI_merged.bam","title":"Use the bam files generated from the alignment of raw reads"},{"location":"nb/vcf.html#variant-calling","text":"We will use a tool named bcftools to find variants in the alignment files ( .bam ) relative to the reference genome, in this case, the file DNA_Contig1_2.fasta . In this way we can identify positions in the genome where the sequence of the aligned reads differ from the reference genome they were mapped to. There are multiple types of genetic variation , e.g. SNPs (single nucleotide polymorphism), indels (insertions or deletions) and structural variations (such as chromosomal rearrangements). Here we will only be working with SNPs, thus we will use the terms variants and SNPs interchangeably. The called variants will be stored in a specific format file, the Variant Call Format ( VCF ). When looking at an alignment files in IGV you should easily recognize the SNP positions. You can see in the figure below that at the marked positions all the mapped reads have a mismatch compared to the reference. You will be calling two types of SNPs in this notebook. First, we will find subgenome SNPs using the Hifi reads mapped to white clover Contig1 and Contig2. These are positions in the contigs that are different between the two subgenomes of white clover. Secondly, we will find SNPs that differentiate between the sequenced white clover S10 (the reference genome) and Ti genotype, using RNA-seq read mapping. Create a folder that will store all the files generated in this notebook. In [5]: Copied! ! mkdir - p results / VCF_Files !mkdir -p results/VCF_Files","title":"Variant calling"},{"location":"nb/vcf.html#call-subgenome-snps-using-the-hifi-alignments-and-the-reference-genome","text":"We will use the bcftools software to call SNPs from alignment files. bcftools is a toolkit for variant calling and manipulating VCF files. If you are interested, you can find all the functionalities here http://samtools.github.io/bcftools/bcftools.html#call . We mainly need two commands for this step, first bcftools mpileup which takes as input the alignment and the genome reference files, followed by bcftools call to produce VCF files. The cell below will generate 3 VCF files stored in the folder results/VCF_Files using the Hifi alignment files uploaded from Galaxy. In [6]: Copied! ! bcftools mpileup -- threads 4 - Ou -- skip - indels - f ../ Data / Clover_Data / DNA_Contig1_2 . fasta Data_for_VCF_analysis / HIFI_contig_1 . bam | bcftools call - mv - Ov - o results / VCF_Files / HIFI_Contig_1 . vcf ! bcftools mpileup -- threads 4 - Ou -- skip - indels - f ../ Data / Clover_Data / DNA_Contig1_2 . fasta Data_for_VCF_analysis / HIFI_contig_2 . bam | bcftools call - mv - Ov - o results / VCF_Files / HIFI_Contig_2 . vcf ! bcftools mpileup -- threads 4 - Ou -- skip - indels - f ../ Data / Clover_Data / DNA_Contig1_2 . fasta Data_for_VCF_analysis / HIFI_contig_1_2 . bam | bcftools call - mv - Ov - o results / VCF_Files / HIFI_Contig_1_2 . vcf !bcftools mpileup --threads 4 -Ou --skip-indels -f ../Data/Clover_Data/DNA_Contig1_2.fasta Data_for_VCF_analysis/HIFI_contig_1.bam | bcftools call -mv -Ov -o results/VCF_Files/HIFI_Contig_1.vcf !bcftools mpileup --threads 4 -Ou --skip-indels -f ../Data/Clover_Data/DNA_Contig1_2.fasta Data_for_VCF_analysis/HIFI_contig_2.bam | bcftools call -mv -Ov -o results/VCF_Files/HIFI_Contig_2.vcf !bcftools mpileup --threads 4 -Ou --skip-indels -f ../Data/Clover_Data/DNA_Contig1_2.fasta Data_for_VCF_analysis/HIFI_contig_1_2.bam | bcftools call -mv -Ov -o results/VCF_Files/HIFI_Contig_1_2.vcf Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 TASK Inspect the VCF files using IGV, comparing them to the specific alignment BAM files. (You can download the VCF files to your computer from the results/VCF_Files folder) Are there any problematic positions that may not represent true SNPs? How can you use the HiFi reads aligned to Contigs1+2 identify potential problems? Hint: Try scrolling to the ends of the contigs.","title":"Call subgenome SNPs using the Hifi alignments and the reference genome"},{"location":"nb/vcf.html#call-snps-using-the-two-rna-seq-genotypes-s10-and-ti","text":"We will repeat the same step as above this time using the RNA-seq alignment files for the two white clover genotypes (S10 and Ti). These commands will produce another two VCF files, stored in the same folder. In [7]: Copied! ! bcftools mpileup -- threads 4 - Ou -- skip - indels - f reference_data / DNA_Contig1_2 . fasta Data_for_VCF_analysis / RNA_S10_merged . bam | bcftools call - mv - Ov - o results / VCF_Files / RNA_S10_merged . vcf ! bcftools mpileup -- threads 4 - Ou -- skip - indels - f reference_data / DNA_Contig1_2 . fasta Data_for_VCF_analysis / RNA_TI_merged . bam | bcftools call - mv - Ov - o results / VCF_Files / RNA_TI_merged . vcf !bcftools mpileup --threads 4 -Ou --skip-indels -f reference_data/DNA_Contig1_2.fasta Data_for_VCF_analysis/RNA_S10_merged.bam | bcftools call -mv -Ov -o results/VCF_Files/RNA_S10_merged.vcf !bcftools mpileup --threads 4 -Ou --skip-indels -f reference_data/DNA_Contig1_2.fasta Data_for_VCF_analysis/RNA_TI_merged.bam | bcftools call -mv -Ov -o results/VCF_Files/RNA_TI_merged.vcf [mpileup] 1 samples in 1 input files Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] maximum number of reads per input file set to -d 250 Note: none of --samples-file, --ploidy or --ploidy-file given, assuming all sites are diploid [mpileup] 1 samples in 1 input files [mpileup] maximum number of reads per input file set to -d 250 TASK Inspect one of the VCFs and the corresponding alignment files in IGV. Is it relevant to filter for false positives in this case, and what parameters would you look further into?","title":"Call SNPs using the two RNA-seq genotypes, S10 and Ti"},{"location":"nb/vcf.html#vcf-files-processing-and-filtering","text":"Take a look at what one of the previously generated VCF files contains by running the cell below. A VCF file begins with the meta-information lines starting with ## followed by one header line, starting with # . Next, there are the data lines, each describing a genetic variant for a certain position in the genome. Each data line contains multiple tab-delimited columns with information about the variant. There are 9 fixed columns, labelled \u201cCHROM\u201d, \u201cPOS\u201d, \u201cID\u201d, \u201cREF\u201d, \u201cALT\u201d, \u201cQUAL\u201d, \u201cFILTER\u201d, \u201cINFO\u201d and \u201cFORMAT\u201d. Find more about the content of those columns in this wikipedia page . In the sample column you can find the most likely genotype of the sample. For diploid organisms, there will be a 0 value for reference allele and 1 for the alternate allele. Figure: possible genotypes in the data. For example, here we read the first 50 rows from the RNAseq_S10_merged.vcf file. You can see that the file format follows the same pattern as explained above. In [8]: Copied! ! cat results / VCF_Files / RNA_S10_merged . vcf | head - 50 !cat results/VCF_Files/RNA_S10_merged.vcf | head -50 ##fileformat=VCFv4.2 ##FILTER= ##bcftoolsVersion=1.16+htslib-1.17 ##bcftoolsCommand=mpileup --threads 4 -Ou --skip-indels -f reference_data/DNA_Contig1_2.fasta Data_for_VCF_analysis/RNA_S10_merged.bam ##reference=file://reference_data/DNA_Contig1_2.fasta ##contig= ##contig= ##ALT= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##INFO= ##FORMAT= ##FORMAT= ##INFO= ##INFO= ##INFO= ##INFO= ##bcftools_callVersion=1.16+htslib-1.17 ##bcftools_callCommand=call -mv -Ov -o results/VCF_Files/RNA_S10_merged.vcf; Date=Mon Jun 19 10:48:17 2023 #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT Data_for_VCF_analysis/RNA_S10_merged.bam 1 33218 . G A 65.3262 . DP=88;VDB=0.0923504;SGB=-0.692914;RPBZ=3.99376;MQBZ=-1.86933;MQSBZ=-0.901828;BQBZ=-1.8368;SCBZ=2.6559;FS=0;MQ0F=0;AC=1;AN=2;DP4=15,13,16,9;MQ=19 GT:PL 0/1:98,0,138 1 33222 . C G 69.1967 . DP=56;VDB=4.89382e-06;SGB=-0.692352;RPBZ=3.47069;MQBZ=-1.73535;MQSBZ=-0.222384;BQBZ=-1.36705;SCBZ=2.16882;FS=0;MQ0F=0;AC=1;AN=2;DP4=18,13,12,9;MQ=19 GT:PL 0/1:102,0,138 1 33223 . T G 61.1405 . DP=56;VDB=2.99077e-05;SGB=-0.692067;RPBZ=3.40644;MQBZ=-1.80665;MQSBZ=-0.222384;BQBZ=0.830878;SCBZ=2.63256;FS=0;MQ0F=0;AC=1;AN=2;DP4=18,14,12,8;MQ=19 GT:PL 0/1:94,0,132 1 33224 . T G 65.1016 . DP=58;VDB=4.85907e-06;SGB=-0.692352;RPBZ=3.67489;MQBZ=-1.78978;MQSBZ=-0.159627;BQBZ=-1.43699;SCBZ=2.60016;FS=0;MQ0F=0;AC=1;AN=2;DP4=18,15,12,9;MQ=19 GT:PL 0/1:98,0,144 1 33225 . G T 64.0746 . DP=58;VDB=4.36523e-06;SGB=-0.692352;RPBZ=3.67489;MQBZ=-1.78978;MQSBZ=-0.159627;BQBZ=-2.60059;SCBZ=2.60016;FS=0;MQ0F=0;AC=1;AN=2;DP4=18,15,12,9;MQ=19 GT:PL 0/1:97,0,144 1 33227 . T A 64.067 . DP=59;VDB=4.09235e-06;SGB=-0.692352;RPBZ=4.13393;MQBZ=-1.81637;MQSBZ=-0.18317;BQBZ=-1.48941;SCBZ=2.64866;FS=0;MQ0F=0;AC=1;AN=2;DP4=19,15,12,9;MQ=19 GT:PL 0/1:97,0,144 1 49149 . C T 30.4183 . DP=4;VDB=0.0058656;SGB=-0.556411;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,4;MQ=20 GT:PL 1/1:60,12,0 1 83968 . C G 78.0347 . DP=10;VDB=5.52906e-06;SGB=-0.662043;RPBZ=-3;MQBZ=0;MQSBZ=0;BQBZ=-0.333333;SCBZ=1.77187;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,2,7;MQ=20 GT:PL 1/1:105,10,0 1 83970 . T C 78.0347 . DP=10;VDB=8.25997e-06;SGB=-0.662043;RPBZ=-1.79284;MQBZ=0;MQSBZ=0;BQBZ=0;SCBZ=1.77187;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,2,7;MQ=20 GT:PL 1/1:105,10,0 1 83972 . G T 78.0347 . DP=10;VDB=8.25997e-06;SGB=-0.662043;RPBZ=-1.79284;MQBZ=0;MQSBZ=0;BQBZ=0;SCBZ=1.57628;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,2,7;MQ=20 GT:PL 1/1:105,10,0 1 83975 . G A 78.0347 . DP=10;VDB=1.22485e-05;SGB=-0.662043;RPBZ=-1.79284;MQBZ=0;MQSBZ=0;BQBZ=0;SCBZ=1.57628;FS=0;MQ0F=0;AC=2;AN=2;DP4=1,0,2,7;MQ=20 GT:PL 1/1:105,10,0 1 174956 . C T 10.7923 . DP=2;VDB=0.14;SGB=-0.453602;MQSBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,1,1;MQ=20 GT:PL 1/1:40,6,0 1 175456 . A G 7.30814 . DP=2;VDB=0.02;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20 GT:PL 1/1:36,6,0 1 211292 . A T 16.7427 . DP=5;VDB=0.0058656;SGB=-0.556411;RPBZ=-2;MQBZ=0;MQSBZ=0;BQBZ=1.22474;SCBZ=2;FS=0;MQ0F=0;AC=1;AN=2;DP4=0,1,4,0;MQ=20 GT:PL 0/1:47,0,5 1 321659 . G A 13.5525 . DP=7;VDB=0.107235;SGB=-0.511536;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=1.73205;SCBZ=0.942809;FS=0;MQ0F=0;AC=1;AN=2;DP4=1,0,1,2;MQ=20 GT:PL 0/1:45,0,8 1 321661 . A C 13.5525 . DP=7;VDB=0.107235;SGB=-0.511536;RPBZ=1.34164;MQBZ=0;MQSBZ=0;BQBZ=1.73205;SCBZ=0.942809;FS=0;MQ0F=0;AC=1;AN=2;DP4=1,0,1,2;MQ=20 GT:PL 0/1:45,0,8 1 323166 . G A 7.30814 . DP=4;VDB=0.1;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,0,2;MQ=20 GT:PL 1/1:36,6,0 1 331785 . A T 7.30814 . DP=2;VDB=0.02;SGB=-0.453602;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,2,0;MQ=20 GT:PL 1/1:36,6,0 1 331890 . C T 39.4149 . DP=6;VDB=0.100421;SGB=-0.556411;MQSBZ=0;FS=0;MQ0F=0;AC=2;AN=2;DP4=0,0,3,1;MQ=20 GT:PL 1/1:69,12,0 Next, in order to generate plots of the metrics stored in the VCF files, we will first import the VCF files in Python using the scikit-allel package. This package contains a series of function helpful for processing variant calling files. For now, we will import only the VCF files generated using the Hifi data alignments. You can ignore the warning. In [9]: Copied! #Import the VCF files Hifi_Contig_1_vcf = allel . read_vcf ( 'results/VCF_Files/HIFI_Contig_1.vcf' , fields = '*' ) Hifi_Contig_2_vcf = allel . read_vcf ( 'results/VCF_Files/HIFI_Contig_2.vcf' , fields = '*' ) Hifi_Contig_1_2_vcf = allel . read_vcf ( 'results/VCF_Files/HIFI_Contig_1_2.vcf' , fields = '*' ) #Import the VCF files Hifi_Contig_1_vcf = allel.read_vcf('results/VCF_Files/HIFI_Contig_1.vcf', fields='*') Hifi_Contig_2_vcf = allel.read_vcf('results/VCF_Files/HIFI_Contig_2.vcf', fields='*') Hifi_Contig_1_2_vcf = allel.read_vcf('results/VCF_Files/HIFI_Contig_1_2.vcf', fields='*') /work/Course_Env/lib/python3.10/site-packages/allel/io/vcf_read.py:1732: UserWarning: invalid INFO header: '##INFO=\\n' warnings.warn('invalid INFO header: %r' % header) Let's check the number of SNPs in each of the three VCF files. The first two VCF files contain subgenome SNPs. You can see that we identified a have a high number of polymorphisms between the two subgenomes. On the other hand the Hifi_Contig1_2_vcf file contains what we would call false positives, as we called SNPs using the same Hifi reads that were used for assembling the reference genome. As expected the number of SNPs in this file is much smaller. In [10]: Copied! print ( \"Number of SNPs in Hifi Contig 1 vcf file:\" , Hifi_Contig_1_vcf [ 'variants/POS' ] . size ) print ( \"Number of SNPs in Hifi Contig 2 vcf file:\" , Hifi_Contig_2_vcf [ 'variants/POS' ] . size ) print ( \"Number of SNPs in Hifi Contig 1 and 2 vcf file:\" , Hifi_Contig_1_2_vcf [ 'variants/POS' ] . size ) print(\"Number of SNPs in Hifi Contig 1 vcf file:\", Hifi_Contig_1_vcf['variants/POS'].size) print(\"Number of SNPs in Hifi Contig 2 vcf file:\", Hifi_Contig_2_vcf['variants/POS'].size) print(\"Number of SNPs in Hifi Contig 1 and 2 vcf file:\", Hifi_Contig_1_2_vcf['variants/POS'].size) Number of SNPs in Hifi Contig 1 vcf file: 31981 Number of SNPs in Hifi Contig 2 vcf file: 30823 Number of SNPs in Hifi Contig 1 and 2 vcf file: 1309 As an overview of the distribution of SNPs, we can plot the density of SNPs across the contigs. We have defined a function called plot_variant_density in the file ../Scripts/pythonScripts.sh that does exactly that. We use that to plot the SNP density across the contigs in the three VCF files in bins of 5000 bp. We can approximate that a SNP density of 0.1 SNPs/bp repesents one polymorphic site at every ten nucleotides. You can see that for the two contigs there are regions more conserved between the two subgenomes, which show a low density of SNPs and more variable regions, which have a higher SNP density. In the third plot we can mainly observe SNPs at the beging of the contigs, as you have probably also oberved when inspecting the files in IGV. Taking a look at the scale of the y-axis you can oberve that the SNP density for Hifi_Contig1_2_vcf is much smaller compared to the other two files. Note: For easier plotting of the files that contain SNPs from both Contig 1 and 2, the SNP density is plotted as an overlay of both contigs. In [11]: Copied! #Plot SNP density plot_variant_density ( Hifi_Contig_1_vcf , window_size = 5000 , title = 'Contig 1 Raw SNP density' ) plot_variant_density ( Hifi_Contig_2_vcf , window_size = 5000 , title = 'Contig 2 Raw SNP density' ) plot_variant_density ( Hifi_Contig_1_2_vcf , window_size = 5000 , title = 'Contig 1 and 2 Raw SNP density' ) #Plot SNP density plot_variant_density(Hifi_Contig_1_vcf, window_size=5000, title='Contig 1 Raw SNP density') plot_variant_density(Hifi_Contig_2_vcf, window_size=5000, title='Contig 2 Raw SNP density') plot_variant_density(Hifi_Contig_1_2_vcf, window_size=5000, title='Contig 1 and 2 Raw SNP density') We can also plot some of the most relevant parameters from the VCF files, such as the read depth and the quality, to have an overview of the quality of the SNPs in these samples. We defined for that the function plot_variant_hist in the file ../Scripts/pythonScripts.sh . We can plot the metrics \"DP\" (Read depth), \"QUAL\" (Quality score), and \"MQ\" (Mapping quality for Hifi_Contig1_vcf . The x-axis represents the chosen metric, while the y-axis represents the number of SNPs. You can observe that the majority of the SNPs from this file have a high quality. In [12]: Copied! plot_variant_hist ( Hifi_Contig_1_vcf , 'DP' , \"mediumblue\" ) plot_variant_hist ( Hifi_Contig_1_vcf , 'QUAL' , \"forestgreen\" ) plot_variant_hist ( Hifi_Contig_1_vcf , 'MQ' , \"darkred\" ) plot_variant_hist(Hifi_Contig_1_vcf,'DP', \"mediumblue\") plot_variant_hist(Hifi_Contig_1_vcf, 'QUAL', \"forestgreen\") plot_variant_hist(Hifi_Contig_1_vcf, 'MQ', \"darkred\") TASK In the two cells below generate the same three plots as above using the VCF files for Contig 2 and Contig 1+2. You will just need to copy the three command lines from the cell above and replace the name of the VCF files. In [ ]: Copied! #Plot the metrics for Contig 2 #Plot the metrics for Contig 2 In [ ]: Copied! #Plot the metrics for Contig 1 + 2 #Plot the metrics for Contig 1 + 2 As you can observe in the plots above, there are some positions with very low read depth and low quality. Those might represent false-positive variants. Thus, we will filter the VCF files in order to eliminate those positions. For this purpose, we will use another bcftools function bcftools filter . We can pass thresholds for all the info metrics to this function using the \"-i\" flag. Below is just an example of the thresholds, you can change the values to suit your files. Note that this command will generate a new filtered VCF file in the \"VCF_Files\" Folder. In [ ]: Copied! ! bcftools filter - i '(QUAL>150) & (DP > 20) & (MQ > 40)' results / VCF_Files / HIFI_Contig_1 . vcf - O v > results / VCF_Files / HIFI_Contig_1_filtered . vcf !bcftools filter -i '(QUAL>150) & (DP > 20) & (MQ > 40)' results/VCF_Files/HIFI_Contig_1.vcf -O v > results/VCF_Files/HIFI_Contig_1_filtered.vcf In [ ]: Copied! ! bcftools filter - i '(QUAL>150) & (DP > 20) & (MQ > 40)' results / VCF_Files / HIFI_Contig_2 . vcf - O v > results / VCF_Files / HIFI_Contig_2_filtered . vcf !bcftools filter -i '(QUAL>150) & (DP > 20) & (MQ > 40)' results/VCF_Files/HIFI_Contig_2.vcf -O v > results/VCF_Files/HIFI_Contig_2_filtered.vcf In [ ]: Copied! ! bcftools filter - i '(QUAL>150) & (DP > 20) & (MQ > 40)' results / VCF_Files / HIFI_Contig_1_2 . vcf - O v > results / VCF_Files / HIFI_Contig_1_2_filtered . vcf !bcftools filter -i '(QUAL>150) & (DP > 20) & (MQ > 40)' results/VCF_Files/HIFI_Contig_1_2.vcf -O v > results/VCF_Files/HIFI_Contig_1_2_filtered.vcf We read the filtered VCF file for Contig1 in python and generate the same plots as before. We can read the VCF file and generate all the plots in one cell this time. We check how many positions have been eliminated by the filter and compare the plots with the ones for the unfiltered VCFs. If you consider that there are still positions with with low quality you can change the filter and repeat the process. In [ ]: Copied! Hifi_Contig1_filtered = allel . read_vcf ( 'results/VCF_Files/HIFI_Contig_1_filtered.vcf' , fields = '*' ) print ( \"Number of SNPs in Contig 1 VCF filtered file:\" , Hifi_Contig1_filtered [ 'variants/POS' ] . size ) #Plot SNP density plot_variant_density ( Hifi_Contig1_filtered , window_size = 5000 , title = 'Contig 1 Filtered variant density' ) #Plot metrics plot_variant_hist ( Hifi_Contig1_filtered , 'DP' , \"mediumblue\" ) plot_variant_hist ( Hifi_Contig1_filtered , 'QUAL' , \"forestgreen\" ) plot_variant_hist ( Hifi_Contig1_filtered , 'MQ' , \"darkred\" ) Hifi_Contig1_filtered = allel.read_vcf('results/VCF_Files/HIFI_Contig_1_filtered.vcf', fields='*') print(\"Number of SNPs in Contig 1 VCF filtered file:\", Hifi_Contig1_filtered['variants/POS'].size) #Plot SNP density plot_variant_density(Hifi_Contig1_filtered, window_size=5000, title='Contig 1 Filtered variant density') #Plot metrics plot_variant_hist(Hifi_Contig1_filtered,'DP', \"mediumblue\") plot_variant_hist(Hifi_Contig1_filtered, 'QUAL', \"forestgreen\") plot_variant_hist(Hifi_Contig1_filtered, 'MQ', \"darkred\") TASK This exercise covers the rest of the notebook and contains explanations as well . The code will work only if you complete correctly the empty cells. Some cells are filled in to help. Compare the VCF files before and after filtering in IGV. In the two cells below generate the same plots as above using the filtered VCF files for Contig 2 and Contig 1 + 2. You will just need to copy the three command lines from the cell above and replace the name of the VCF files. In [ ]: Copied! #Figures for Contig 2 Filtered VCF #Figures for Contig 2 Filtered VCF In [ ]: Copied! #Figures for Contig 1 + 2 Filtered VCF #Figures for Contig 1 + 2 Filtered VCF Repeat the quality check and filtering as described above for the two RNA-seq VCF files: Read the VCF files in Python: In [ ]: Copied! vcf_S10_RNA = allel . read_vcf ( 'results/VCF_Files/RNA_S10_merged.vcf' , fields = '*' ) vcf_Ti_RNA = allel . read_vcf ( 'results/VCF_Files/RNA_TI_merged.vcf' , fields = '*' ) vcf_S10_RNA = allel.read_vcf('results/VCF_Files/RNA_S10_merged.vcf', fields='*') vcf_Ti_RNA = allel.read_vcf('results/VCF_Files/RNA_TI_merged.vcf', fields='*') Print the number of SNPs in the two RNA-seq VCF files. Note that the number of SNPs is much smaller than for the Hifi VCF files. Also, there is a difference in the number of SNPs for the two genotypes. As S10 RNA-seq data originates from the same genotype as the referece genome, one would expect a small number of SNPs to be identified in this case. In [ ]: Copied! print ( \"Number of SNPs in S10 RNA-seq VCF file:\" , vcf_S10_RNA [ 'variants/POS' ] . size ) print ( \"Number of SNPs in Ti RNA-seq VCF file:\" , vcf_Ti_RNA [ 'variants/POS' ] . size ) print(\"Number of SNPs in S10 RNA-seq VCF file:\", vcf_S10_RNA['variants/POS'].size) print(\"Number of SNPs in Ti RNA-seq VCF file:\", vcf_Ti_RNA['variants/POS'].size) Generate SNP density plots using the plot_variant_density() function: In [ ]: Copied! In [ ]: Copied! Generate info histograms using the plot_variant_hist() function for the same fields. You should observe that the metrics for the RNA-seq vcf files are quite different from the ones using Hifi reads. In [ ]: Copied! In [ ]: Copied! Filter the VCF files using bcftools and your selected tresholds after inspecting the VCF files. Add the filter thresholds before running the command. In [ ]: Copied! ! bcftools filter - i 'add filter thresholds here' results / VCF_Files / RNA_S10_merged . vcf - O v > results / VCF_Files / RNA_S10_merged_filtered . vcf ! bcftools filter - i 'add filter thresholds here' results / VCF_Files / RNA_TI_merged . vcf - O v > results / VCF_Files / RNA_TI_merged_filtered . vcf !bcftools filter -i 'add filter thresholds here' results/VCF_Files/RNA_S10_merged.vcf -O v > results/VCF_Files/RNA_S10_merged_filtered.vcf !bcftools filter -i 'add filter thresholds here' results/VCF_Files/RNA_TI_merged.vcf -O v > results/VCF_Files/RNA_TI_merged_filtered.vcf Read the filtered VCFs in python: In [ ]: Copied! vcf_S10_RNA_filtered = allel . read_vcf ( 'results/VCF_Files/RNA_S10_merged_filtered.vcf' , fields = '*' ) vcf_Ti_RNA_filtered = allel . read_vcf ( 'results/VCF_Files/RNA_TI_merged_filtered.vcf' , fields = '*' ) vcf_S10_RNA_filtered = allel.read_vcf('results/VCF_Files/RNA_S10_merged_filtered.vcf', fields='*') vcf_Ti_RNA_filtered = allel.read_vcf('results/VCF_Files/RNA_TI_merged_filtered.vcf', fields='*') Check the number of SNPs in the filtered VCF files: In [ ]: Copied! print ( \"Number of SNPs in the filtered S10 RNA-seq VCF file:\" , vcf_S10_RNA_filtered [ 'variants/POS' ] . size ) print ( \"Number of SNPs in the filtered Ti RNA-seq VCF file:\" , vcf_Ti_RNA_filtered [ 'variants/POS' ] . size ) print(\"Number of SNPs in the filtered S10 RNA-seq VCF file:\", vcf_S10_RNA_filtered['variants/POS'].size) print(\"Number of SNPs in the filtered Ti RNA-seq VCF file:\", vcf_Ti_RNA_filtered['variants/POS'].size) Plot same histograms for the filtered VCF files. In [ ]: Copied! In [ ]: Copied! Question: Is it relevant to filter for false positives in this case, and what parameters would you look further into?","title":"VCF files processing and filtering"},{"location":"nb/vcf.html#genotypes-counting","text":"We want to count the different genotypes in each of the five filtered VCF files generated previously. To make this task easier we can take advantage of the counting functions in the scikit-allel package. We have used those to implement a little function called position_count in the file ../Scripts/pythonScripts.sh . You can then use the function with each of the 5 filtered VCF files to count the number of positions. You need to fill the names of the VCF files imported in Python. In [ ]: Copied! #Contig 1 filtered VCF position_count ( Hifi_Contig1_filtered ) #Contig 1 filtered VCF position_count(Hifi_Contig1_filtered) In [ ]: Copied! #Contig 2 filtered VCF position_count () #Contig 2 filtered VCF position_count() In [ ]: Copied! #Contig 1 and 2 filtered VCF position_count () #Contig 1 and 2 filtered VCF position_count() In [ ]: Copied! #RNAseq S10 filtered VCF position_count () #RNAseq S10 filtered VCF position_count() In [ ]: Copied! #RNAseq Ti filtered VCF position_count () #RNAseq Ti filtered VCF position_count()","title":"Genotypes counting"},{"location":"nb/vcf.html#comparison-of-vcf-files","text":"Compare the VCF files with subgenome variants and the VCF files with S10/Tienshan genotype specific variants obtained from RNA-seq mapping We want now to find overlapping position between the Contig 1 and Contig 2 Hifi VCF files and the Ti RNAseq VCF file. To ease this task we will first create two merged VCF files containing: Hifi Contig 1 VCF + Ti RNAseq VCF Hifi Contig 2 VCF + Ti RNAseq VCF Once again, we will use bcftools for this task, using the merge function. However, the bcftools merge function works only with compressed and indexed VCF files, so first we will do this. In [ ]: Copied! ! bcftools view results / VCF_Files / HIFI_Contig_1_filtered . vcf - Oz - o results / VCF_Files / HIFI_Contig_1_filtered . vcf . gz ! bcftools index results / VCF_Files / HIFI_Contig_1_filtered . vcf . gz - f - o results / VCF_Files / HIFI_Contig_1_filtered . vcf . gz . csi ! bcftools view results / VCF_Files / HIFI_Contig_2_filtered . vcf - Oz - o results / VCF_Files / HIFI_Contig_2_filtered . vcf . gz ! bcftools index results / VCF_Files / HIFI_Contig_2_filtered . vcf . gz - f - o results / VCF_Files / HIFI_Contig_2_filtered . vcf . gz . csi ! bcftools view results / VCF_Files / RNA_TI_merged_filtered . vcf - Oz - o results / VCF_Files / RNA_TI_merged_filtered . vcf . gz ! bcftools index results / VCF_Files / RNA_TI_merged_filtered . vcf . gz - f - o results / VCF_Files / RNA_TI_merged_filtered . vcf . gz . csi !bcftools view results/VCF_Files/HIFI_Contig_1_filtered.vcf -Oz -o results/VCF_Files/HIFI_Contig_1_filtered.vcf.gz !bcftools index results/VCF_Files/HIFI_Contig_1_filtered.vcf.gz -f -o results/VCF_Files/HIFI_Contig_1_filtered.vcf.gz.csi !bcftools view results/VCF_Files/HIFI_Contig_2_filtered.vcf -Oz -o results/VCF_Files/HIFI_Contig_2_filtered.vcf.gz !bcftools index results/VCF_Files/HIFI_Contig_2_filtered.vcf.gz -f -o results/VCF_Files/HIFI_Contig_2_filtered.vcf.gz.csi !bcftools view results/VCF_Files/RNA_TI_merged_filtered.vcf -Oz -o results/VCF_Files/RNA_TI_merged_filtered.vcf.gz !bcftools index results/VCF_Files/RNA_TI_merged_filtered.vcf.gz -f -o results/VCF_Files/RNA_TI_merged_filtered.vcf.gz.csi Now we can merge Contig 1 VCF with the Ti RNA VCF and keep only positions that match between the two files by filtering out any positions with missing genotypes. In [ ]: Copied! ! bcftools merge results / VCF_Files / HIFI_Contig_1_filtered . vcf . gz results / VCF_Files / RNA_TI_merged_filtered . vcf . gz | bcftools filter - e 'GT=\"./.\"' > results / VCF_Files / TI_Contig_1_merged . vcf !bcftools merge results/VCF_Files/HIFI_Contig_1_filtered.vcf.gz results/VCF_Files/RNA_TI_merged_filtered.vcf.gz | bcftools filter -e 'GT=\"./.\"' > results/VCF_Files/TI_Contig_1_merged.vcf Merge Contig 2 VCF with the Ti RNA VCF and keep only positions that match between the two files. In [ ]: Copied! ! bcftools merge results / VCF_Files / HIFI_Contig_2_filtered . vcf . gz results / VCF_Files / RNA_TI_merged_filtered . vcf . gz | bcftools filter - e 'GT=\"./.\"' > results / VCF_Files / TI_Contig_2_merged . vcf !bcftools merge results/VCF_Files/HIFI_Contig_2_filtered.vcf.gz results/VCF_Files/RNA_TI_merged_filtered.vcf.gz | bcftools filter -e 'GT=\"./.\"' > results/VCF_Files/TI_Contig_2_merged.vcf Take a look at the merged VCF file. You can see that compared with the VCF files for just one sample, there is now a new column in the file, with the corresponding genotype for the second sample that we merged. In [ ]: Copied! ! cat results / VCF_Files / TI_Contig_1_merged . vcf | head - 50 !cat results/VCF_Files/TI_Contig_1_merged.vcf | head -50 In order to count the genotypes for the matching positions we can use once again bcftools filter command. Only that this time we will filter based on the genotype columns for the two samples (GT[0] and GT[1]). GT[0] repesents the genotype for the first sample in the merge command and GT[1] is the genotype for the second sample in the merge command. AR - heterozygous AA - homozygous alternate For example, the filter GT[0]=\"AR\" && GT[1]=\"AR\" will keep only position in which both samples have a heterozygous genotype. A quick way to count how many positions are in the VCF file is by suing the simple bash command grep . This will count all the lines in the VCF files that do not start with a # , thus all the data lines. In [ ]: Copied! ! echo \"AR + AR:\" ! bcftools filter - i 'GT[0]=\"AR\" && GT[1]=\"AR\"' results / VCF_Files / TI_Contig_1_merged . vcf | grep - c - v \"^#\" ! echo \"AR + AA:\" ! bcftools filter - i 'GT[0]=\"AR\" && GT[1]=\"AA\"' results / VCF_Files / TI_Contig_1_merged . vcf | grep - c - v \"^#\" ! echo \"AA + AR:\" ! bcftools filter - i 'GT[0]=\"AA\" && GT[1]=\"AR\"' results / VCF_Files / TI_Contig_1_merged . vcf | grep - c - v \"^#\" ! echo \"AA + AA:\" ! bcftools filter - i 'GT[0]=\"AA\" && GT[1]=\"AA\"' results / VCF_Files / TI_Contig_1_merged . vcf | grep - c - v \"^#\" !echo \"AR + AR:\" !bcftools filter -i 'GT[0]=\"AR\" && GT[1]=\"AR\"' results/VCF_Files/TI_Contig_1_merged.vcf | grep -c -v \"^#\" !echo \"AR + AA:\" !bcftools filter -i 'GT[0]=\"AR\" && GT[1]=\"AA\"' results/VCF_Files/TI_Contig_1_merged.vcf | grep -c -v \"^#\" !echo \"AA + AR:\" !bcftools filter -i 'GT[0]=\"AA\" && GT[1]=\"AR\"' results/VCF_Files/TI_Contig_1_merged.vcf | grep -c -v \"^#\" !echo \"AA + AA:\" !bcftools filter -i 'GT[0]=\"AA\" && GT[1]=\"AA\"' results/VCF_Files/TI_Contig_1_merged.vcf | grep -c -v \"^#\" Use the same commands as above to count the positions marching the filters in the Contig2_Ti_merged.vcf. In [ ]: Copied!","title":"Comparison of VCF files"},{"location":"nb/vcf.html#wrapping-up","text":"In this exercise, you identified polymorphisms between the two white clover subgenomes using Hifi reads alignment files and SNPs specific for the white clover Tienshan genotype using RNA-seq alignment files. You learned how to import VCF files in Python to extract data and created plots. You also filtered low-quality variants from the VCF files and counted genotypes.","title":"Wrapping up \ud83c\udf89 \ud83c\udf89 \ud83c\udf89"}]} \ No newline at end of file diff --git a/site_libs/bootstrap/bootstrap-dark.min.css b/site_libs/bootstrap/bootstrap-dark.min.css new file mode 100644 index 0000000..bcb315e --- /dev/null +++ b/site_libs/bootstrap/bootstrap-dark.min.css @@ -0,0 +1,12 @@ +/*! + * Bootstrap v5.3.1 (https://getbootstrap.com/) + * Copyright 2011-2023 The Bootstrap Authors + * Licensed under MIT (https://github.com/twbs/bootstrap/blob/main/LICENSE) + */@import"https://fonts.googleapis.com/css2?family=Lato:ital,wght@0,400;0,700;1,400&display=swap";:root,[data-bs-theme=light]{--bs-blue: #375a7f;--bs-indigo: #6610f2;--bs-purple: #6f42c1;--bs-pink: #e83e8c;--bs-red: #e74c3c;--bs-orange: #fd7e14;--bs-yellow: #f39c12;--bs-green: #00bc8c;--bs-teal: #20c997;--bs-cyan: #3498db;--bs-black: #000;--bs-white: #fff;--bs-gray: #6c757d;--bs-gray-dark: #343a40;--bs-gray-100: 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2rem;--bs-nav-link-padding-y: 0.5rem;--bs-nav-link-font-weight: ;--bs-nav-link-color: #00bc8c;--bs-nav-link-hover-color: #009670;--bs-nav-link-disabled-color: #6f6f6f;display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding-left:0;margin-bottom:0;list-style:none}.nav-link{display:block;padding:var(--bs-nav-link-padding-y) var(--bs-nav-link-padding-x);font-size:var(--bs-nav-link-font-size);font-weight:var(--bs-nav-link-font-weight);color:var(--bs-nav-link-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background:none;border:0;transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out}@media(prefers-reduced-motion: reduce){.nav-link{transition:none}}.nav-link:hover,.nav-link:focus{color:var(--bs-nav-link-hover-color)}.nav-link:focus-visible{outline:0;box-shadow:0 0 0 .25rem 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var(--bs-accordion-border-color)}.accordion-button:not(.collapsed)::after{background-image:var(--bs-accordion-btn-active-icon);transform:var(--bs-accordion-btn-icon-transform)}.accordion-button::after{flex-shrink:0;-webkit-flex-shrink:0;width:var(--bs-accordion-btn-icon-width);height:var(--bs-accordion-btn-icon-width);margin-left:auto;content:"";background-image:var(--bs-accordion-btn-icon);background-repeat:no-repeat;background-size:var(--bs-accordion-btn-icon-width);transition:var(--bs-accordion-btn-icon-transition)}@media(prefers-reduced-motion: reduce){.accordion-button::after{transition:none}}.accordion-button:hover{z-index:2}.accordion-button:focus{z-index:3;border-color:var(--bs-accordion-btn-focus-border-color);outline:0;box-shadow:var(--bs-accordion-btn-focus-box-shadow)}.accordion-header{margin-bottom:0}.accordion-item{color:var(--bs-accordion-color);background-color:var(--bs-accordion-bg);border:var(--bs-accordion-border-width) solid 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var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme=dark] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23879cb2'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23879cb2'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0.75rem;--bs-breadcrumb-padding-y: 0.375rem;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: #434343;--bs-breadcrumb-border-radius: 0.25rem;--bs-breadcrumb-divider-color: rgba(255, 255, 255, 0.75);--bs-breadcrumb-item-padding-x: 0.5rem;--bs-breadcrumb-item-active-color: rgba(255, 255, 255, 0.75);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, ">") /* rtl: var(--bs-breadcrumb-divider, ">") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: 0.75rem;--bs-pagination-padding-y: 0.375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: #fff;--bs-pagination-bg: #00bc8c;--bs-pagination-border-width: 0;--bs-pagination-border-color: transparent;--bs-pagination-border-radius: 0.25rem;--bs-pagination-hover-color: #fff;--bs-pagination-hover-bg: #00efb2;--bs-pagination-hover-border-color: transparent;--bs-pagination-focus-color: #009670;--bs-pagination-focus-bg: #ebebeb;--bs-pagination-focus-box-shadow: 0 0 0 0.25rem rgba(55, 90, 127, 0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #00efb2;--bs-pagination-active-border-color: transparent;--bs-pagination-disabled-color: #fff;--bs-pagination-disabled-bg: #007053;--bs-pagination-disabled-border-color: transparent;display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out,box-shadow .15s ease-in-out}@media(prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(0*-1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: 0.75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: 0.5rem}.pagination-sm{--bs-pagination-padding-x: 0.5rem;--bs-pagination-padding-y: 0.25rem;--bs-pagination-font-size:0.875rem;--bs-pagination-border-radius: 0.2em}.badge{--bs-badge-padding-x: 0.65em;--bs-badge-padding-y: 0.35em;--bs-badge-font-size:0.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: 0.25rem;display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: 1px solid var(--bs-alert-border-color);--bs-alert-border-radius: 0.25rem;--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:1rem}}.progress,.progress-stacked{--bs-progress-height: 1rem;--bs-progress-font-size:0.75rem;--bs-progress-bg: #434343;--bs-progress-border-radius: 0.25rem;--bs-progress-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.075);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #375a7f;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media(prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media(prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: #fff;--bs-list-group-bg: #2d2d2d;--bs-list-group-border-color: #434343;--bs-list-group-border-width: 1px;--bs-list-group-border-radius: 0.25rem;--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: 0.5rem;--bs-list-group-action-color: rgba(255, 255, 255, 0.75);--bs-list-group-action-hover-color: #fff;--bs-list-group-action-hover-bg: #434343;--bs-list-group-action-active-color: #fff;--bs-list-group-action-active-bg: #222;--bs-list-group-disabled-color: rgba(255, 255, 255, 0.75);--bs-list-group-disabled-bg: #2d2d2d;--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #375a7f;--bs-list-group-active-border-color: 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". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1*var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media(min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #fff;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23fff'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: 0.4;--bs-btn-close-hover-opacity: 1;--bs-btn-close-focus-shadow: 0 0 0 0.25rem rgba(55, 90, 127, 0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: 0.25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:rgba(0,0,0,0) var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.25rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme=dark] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: 0.75rem;--bs-toast-padding-y: 0.5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:0.875rem;--bs-toast-color: ;--bs-toast-bg: #434343;--bs-toast-border-width: 1px;--bs-toast-border-color: rgba(0, 0, 0, 0.175);--bs-toast-border-radius: 0.25rem;--bs-toast-box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.15);--bs-toast-header-color: rgba(255, 255, 255, 0.75);--bs-toast-header-bg: #2d2d2d;--bs-toast-header-border-color: rgba(0, 0, 0, 0.175);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) 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1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: #434343;--bs-modal-header-border-width: 1px;--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: 0.5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: #434343;--bs-modal-footer-border-width: 1px;position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform .3s ease-out;transform:translate(0, -50px)}@media(prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin)*2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable 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auto}.modal-title{margin-bottom:0;line-height:var(--bs-modal-title-line-height)}.modal-body{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-modal-padding)}.modal-footer{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:flex-end;-webkit-justify-content:flex-end;padding:calc(var(--bs-modal-padding) - var(--bs-modal-footer-gap)*.5);background-color:var(--bs-modal-footer-bg);border-top:var(--bs-modal-footer-border-width) solid var(--bs-modal-footer-border-color);border-bottom-right-radius:var(--bs-modal-inner-border-radius);border-bottom-left-radius:var(--bs-modal-inner-border-radius)}.modal-footer>*{margin:calc(var(--bs-modal-footer-gap)*.5)}@media(min-width: 576px){.modal{--bs-modal-margin: 1.75rem;--bs-modal-box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.15)}.modal-dialog{max-width:var(--bs-modal-width);margin-right:auto;margin-left:auto}.modal-sm{--bs-modal-width: 300px}}@media(min-width: 992px){.modal-lg,.modal-xl{--bs-modal-width: 800px}}@media(min-width: 1200px){.modal-xl{--bs-modal-width: 1140px}}.modal-fullscreen{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen .modal-header,.modal-fullscreen .modal-footer{border-radius:0}.modal-fullscreen .modal-body{overflow-y:auto}@media(max-width: 575.98px){.modal-fullscreen-sm-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-sm-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-sm-down .modal-header,.modal-fullscreen-sm-down .modal-footer{border-radius:0}.modal-fullscreen-sm-down .modal-body{overflow-y:auto}}@media(max-width: 767.98px){.modal-fullscreen-md-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-md-down 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.modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xxl-down .modal-header,.modal-fullscreen-xxl-down .modal-footer{border-radius:0}.modal-fullscreen-xxl-down .modal-body{overflow-y:auto}}.tooltip{--bs-tooltip-zindex: 1080;--bs-tooltip-max-width: 200px;--bs-tooltip-padding-x: 0.5rem;--bs-tooltip-padding-y: 0.25rem;--bs-tooltip-margin: ;--bs-tooltip-font-size:0.875rem;--bs-tooltip-color: #222;--bs-tooltip-bg: #000;--bs-tooltip-border-radius: 0.25rem;--bs-tooltip-opacity: 0.9;--bs-tooltip-arrow-width: 0.8rem;--bs-tooltip-arrow-height: 0.4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:Lato,-apple-system,BlinkMacSystemFont,"Segoe UI",Roboto,"Helvetica Neue",Arial,sans-serif,"Apple Color Emoji","Segoe UI Emoji","Segoe UI 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#52585d;--bs-btn-hover-border-color: #484e53;--bs-btn-focus-shadow-rgb: 82, 88, 93;--bs-btn-active-color: #fff;--bs-btn-active-bg: #5d6166;--bs-btn-active-border-color: #484e53;--bs-btn-active-shadow: 2px 2px 4px #999999;--bs-btn-disabled-color: #fff;--bs-btn-disabled-bg: #343a40;--bs-btn-disabled-border-color: #343a40}.btn-outline-default{--bs-btn-color: #fff;--bs-btn-border-color: #fff;--bs-btn-hover-color: #000;--bs-btn-hover-bg: #fff;--bs-btn-hover-border-color: #fff;--bs-btn-focus-shadow-rgb: 255, 255, 255;--bs-btn-active-color: #000;--bs-btn-active-bg: #fff;--bs-btn-active-border-color: #fff;--bs-btn-active-shadow: 2px 2px 4px #999999;--bs-btn-disabled-color: #fff;--bs-btn-disabled-bg: transparent;--bs-btn-disabled-border-color: #fff;--bs-btn-bg: transparent;--bs-gradient: none}.btn-outline-primary{--bs-btn-color: #2196f3;--bs-btn-border-color: #2196f3;--bs-btn-hover-color: #fff;--bs-btn-hover-bg: #2196f3;--bs-btn-hover-border-color: #2196f3;--bs-btn-focus-shadow-rgb: 33, 150, 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0);--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255, 255, 255, 0.7%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}[data-bs-theme=dark] .navbar-toggler-icon{--bs-navbar-toggler-icon-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 30 30'%3e%3cpath stroke='rgba%28255, 255, 255, 0.7%29' stroke-linecap='round' stroke-miterlimit='10' stroke-width='2' d='M4 7h22M4 15h22M4 23h22'/%3e%3c/svg%3e")}.card{--bs-card-spacer-y: 1rem;--bs-card-spacer-x: 1rem;--bs-card-title-spacer-y: 0.5rem;--bs-card-title-color: ;--bs-card-subtitle-color: ;--bs-card-border-width: 0;--bs-card-border-color: transparent;--bs-card-border-radius: 0.25rem;--bs-card-box-shadow: ;--bs-card-inner-border-radius: 0.25rem;--bs-card-cap-padding-y: 0.5rem;--bs-card-cap-padding-x: 1rem;--bs-card-cap-bg: rgba(52, 58, 64, 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var(--bs-accordion-border-color)}.accordion-item:first-of-type{border-top-left-radius:var(--bs-accordion-border-radius);border-top-right-radius:var(--bs-accordion-border-radius)}.accordion-item:first-of-type .accordion-button{border-top-left-radius:var(--bs-accordion-inner-border-radius);border-top-right-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:not(:first-of-type){border-top:0}.accordion-item:last-of-type{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-item:last-of-type .accordion-button.collapsed{border-bottom-right-radius:var(--bs-accordion-inner-border-radius);border-bottom-left-radius:var(--bs-accordion-inner-border-radius)}.accordion-item:last-of-type .accordion-collapse{border-bottom-right-radius:var(--bs-accordion-border-radius);border-bottom-left-radius:var(--bs-accordion-border-radius)}.accordion-body{padding:var(--bs-accordion-body-padding-y) var(--bs-accordion-body-padding-x)}.accordion-flush .accordion-collapse{border-width:0}.accordion-flush .accordion-item{border-right:0;border-left:0;border-radius:0}.accordion-flush .accordion-item:first-child{border-top:0}.accordion-flush .accordion-item:last-child{border-bottom:0}.accordion-flush .accordion-item .accordion-button,.accordion-flush .accordion-item .accordion-button.collapsed{border-radius:0}[data-bs-theme=dark] .accordion-button::after{--bs-accordion-btn-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%237ac0f8'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e");--bs-accordion-btn-active-icon: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%237ac0f8'%3e%3cpath fill-rule='evenodd' d='M1.646 4.646a.5.5 0 0 1 .708 0L8 10.293l5.646-5.647a.5.5 0 0 1 .708.708l-6 6a.5.5 0 0 1-.708 0l-6-6a.5.5 0 0 1 0-.708z'/%3e%3c/svg%3e")}.breadcrumb{--bs-breadcrumb-padding-x: 0;--bs-breadcrumb-padding-y: 0;--bs-breadcrumb-margin-bottom: 1rem;--bs-breadcrumb-bg: ;--bs-breadcrumb-border-radius: ;--bs-breadcrumb-divider-color: rgba(68, 68, 68, 0.75);--bs-breadcrumb-item-padding-x: 0.5rem;--bs-breadcrumb-item-active-color: rgba(68, 68, 68, 0.75);display:flex;display:-webkit-flex;flex-wrap:wrap;-webkit-flex-wrap:wrap;padding:var(--bs-breadcrumb-padding-y) var(--bs-breadcrumb-padding-x);margin-bottom:var(--bs-breadcrumb-margin-bottom);font-size:var(--bs-breadcrumb-font-size);list-style:none;background-color:var(--bs-breadcrumb-bg);border-radius:var(--bs-breadcrumb-border-radius)}.breadcrumb-item+.breadcrumb-item{padding-left:var(--bs-breadcrumb-item-padding-x)}.breadcrumb-item+.breadcrumb-item::before{float:left;padding-right:var(--bs-breadcrumb-item-padding-x);color:var(--bs-breadcrumb-divider-color);content:var(--bs-breadcrumb-divider, ">") /* rtl: var(--bs-breadcrumb-divider, ">") */}.breadcrumb-item.active{color:var(--bs-breadcrumb-item-active-color)}.pagination{--bs-pagination-padding-x: 0.75rem;--bs-pagination-padding-y: 0.375rem;--bs-pagination-font-size:1rem;--bs-pagination-color: #2196f3;--bs-pagination-bg: #fff;--bs-pagination-border-width: 1px;--bs-pagination-border-color: #dee2e6;--bs-pagination-border-radius: 0.25rem;--bs-pagination-hover-color: #1a78c2;--bs-pagination-hover-bg: #f8f9fa;--bs-pagination-hover-border-color: #dee2e6;--bs-pagination-focus-color: #1a78c2;--bs-pagination-focus-bg: #eee;--bs-pagination-focus-box-shadow: 0 0 0 0.25rem rgba(33, 150, 243, 0.25);--bs-pagination-active-color: #fff;--bs-pagination-active-bg: #2196f3;--bs-pagination-active-border-color: #2196f3;--bs-pagination-disabled-color: rgba(68, 68, 68, 0.75);--bs-pagination-disabled-bg: #eee;--bs-pagination-disabled-border-color: #dee2e6;display:flex;display:-webkit-flex;padding-left:0;list-style:none}.page-link{position:relative;display:block;padding:var(--bs-pagination-padding-y) var(--bs-pagination-padding-x);font-size:var(--bs-pagination-font-size);color:var(--bs-pagination-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-pagination-bg);border:var(--bs-pagination-border-width) solid var(--bs-pagination-border-color);transition:color .15s ease-in-out,background-color .15s ease-in-out,border-color .15s ease-in-out,box-shadow .15s ease-in-out}@media(prefers-reduced-motion: reduce){.page-link{transition:none}}.page-link:hover{z-index:2;color:var(--bs-pagination-hover-color);background-color:var(--bs-pagination-hover-bg);border-color:var(--bs-pagination-hover-border-color)}.page-link:focus{z-index:3;color:var(--bs-pagination-focus-color);background-color:var(--bs-pagination-focus-bg);outline:0;box-shadow:var(--bs-pagination-focus-box-shadow)}.page-link.active,.active>.page-link{z-index:3;color:var(--bs-pagination-active-color);background-color:var(--bs-pagination-active-bg);background-image:var(--bs-gradient);border-color:var(--bs-pagination-active-border-color)}.page-link.disabled,.disabled>.page-link{color:var(--bs-pagination-disabled-color);pointer-events:none;background-color:var(--bs-pagination-disabled-bg);border-color:var(--bs-pagination-disabled-border-color)}.page-item:not(:first-child) .page-link{margin-left:calc(1px*-1)}.page-item:first-child .page-link{border-top-left-radius:var(--bs-pagination-border-radius);border-bottom-left-radius:var(--bs-pagination-border-radius)}.page-item:last-child .page-link{border-top-right-radius:var(--bs-pagination-border-radius);border-bottom-right-radius:var(--bs-pagination-border-radius)}.pagination-lg{--bs-pagination-padding-x: 1.5rem;--bs-pagination-padding-y: 0.75rem;--bs-pagination-font-size:1.25rem;--bs-pagination-border-radius: 0.5rem}.pagination-sm{--bs-pagination-padding-x: 0.5rem;--bs-pagination-padding-y: 0.25rem;--bs-pagination-font-size:0.875rem;--bs-pagination-border-radius: 0.2em}.badge{--bs-badge-padding-x: 0.65em;--bs-badge-padding-y: 0.35em;--bs-badge-font-size:0.75em;--bs-badge-font-weight: 700;--bs-badge-color: #fff;--bs-badge-border-radius: 0.25rem;display:inline-block;padding:var(--bs-badge-padding-y) var(--bs-badge-padding-x);font-size:var(--bs-badge-font-size);font-weight:var(--bs-badge-font-weight);line-height:1;color:var(--bs-badge-color);text-align:center;white-space:nowrap;vertical-align:baseline;border-radius:var(--bs-badge-border-radius);background-image:var(--bs-gradient)}.badge:empty{display:none}.btn .badge{position:relative;top:-1px}.alert{--bs-alert-bg: transparent;--bs-alert-padding-x: 1rem;--bs-alert-padding-y: 1rem;--bs-alert-margin-bottom: 1rem;--bs-alert-color: inherit;--bs-alert-border-color: transparent;--bs-alert-border: 1px solid var(--bs-alert-border-color);--bs-alert-border-radius: 0.25rem;--bs-alert-link-color: inherit;position:relative;padding:var(--bs-alert-padding-y) var(--bs-alert-padding-x);margin-bottom:var(--bs-alert-margin-bottom);color:var(--bs-alert-color);background-color:var(--bs-alert-bg);border:var(--bs-alert-border);border-radius:var(--bs-alert-border-radius)}.alert-heading{color:inherit}.alert-link{font-weight:700;color:var(--bs-alert-link-color)}.alert-dismissible{padding-right:3rem}.alert-dismissible .btn-close{position:absolute;top:0;right:0;z-index:2;padding:1.25rem 1rem}.alert-default{--bs-alert-color: var(--bs-default-text-emphasis);--bs-alert-bg: var(--bs-default-bg-subtle);--bs-alert-border-color: var(--bs-default-border-subtle);--bs-alert-link-color: var(--bs-default-text-emphasis)}.alert-primary{--bs-alert-color: var(--bs-primary-text-emphasis);--bs-alert-bg: var(--bs-primary-bg-subtle);--bs-alert-border-color: var(--bs-primary-border-subtle);--bs-alert-link-color: var(--bs-primary-text-emphasis)}.alert-secondary{--bs-alert-color: var(--bs-secondary-text-emphasis);--bs-alert-bg: var(--bs-secondary-bg-subtle);--bs-alert-border-color: var(--bs-secondary-border-subtle);--bs-alert-link-color: var(--bs-secondary-text-emphasis)}.alert-success{--bs-alert-color: var(--bs-success-text-emphasis);--bs-alert-bg: var(--bs-success-bg-subtle);--bs-alert-border-color: var(--bs-success-border-subtle);--bs-alert-link-color: var(--bs-success-text-emphasis)}.alert-info{--bs-alert-color: var(--bs-info-text-emphasis);--bs-alert-bg: var(--bs-info-bg-subtle);--bs-alert-border-color: var(--bs-info-border-subtle);--bs-alert-link-color: var(--bs-info-text-emphasis)}.alert-warning{--bs-alert-color: var(--bs-warning-text-emphasis);--bs-alert-bg: var(--bs-warning-bg-subtle);--bs-alert-border-color: var(--bs-warning-border-subtle);--bs-alert-link-color: var(--bs-warning-text-emphasis)}.alert-danger{--bs-alert-color: var(--bs-danger-text-emphasis);--bs-alert-bg: var(--bs-danger-bg-subtle);--bs-alert-border-color: var(--bs-danger-border-subtle);--bs-alert-link-color: var(--bs-danger-text-emphasis)}.alert-light{--bs-alert-color: var(--bs-light-text-emphasis);--bs-alert-bg: var(--bs-light-bg-subtle);--bs-alert-border-color: var(--bs-light-border-subtle);--bs-alert-link-color: var(--bs-light-text-emphasis)}.alert-dark{--bs-alert-color: var(--bs-dark-text-emphasis);--bs-alert-bg: var(--bs-dark-bg-subtle);--bs-alert-border-color: var(--bs-dark-border-subtle);--bs-alert-link-color: var(--bs-dark-text-emphasis)}@keyframes progress-bar-stripes{0%{background-position-x:.375rem}}.progress,.progress-stacked{--bs-progress-height: 0.375rem;--bs-progress-font-size:0.75rem;--bs-progress-bg: #eee;--bs-progress-border-radius: 0;--bs-progress-box-shadow: inset 0 1px 2px rgba(0, 0, 0, 0.075);--bs-progress-bar-color: #fff;--bs-progress-bar-bg: #2196f3;--bs-progress-bar-transition: width 0.6s ease;display:flex;display:-webkit-flex;height:var(--bs-progress-height);overflow:hidden;font-size:var(--bs-progress-font-size);background-color:var(--bs-progress-bg);border-radius:var(--bs-progress-border-radius);box-shadow:var(--bs-progress-box-shadow)}.progress-bar{display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;justify-content:center;-webkit-justify-content:center;overflow:hidden;color:var(--bs-progress-bar-color);text-align:center;white-space:nowrap;background-color:var(--bs-progress-bar-bg);transition:var(--bs-progress-bar-transition)}@media(prefers-reduced-motion: reduce){.progress-bar{transition:none}}.progress-bar-striped{background-image:linear-gradient(45deg, rgba(255, 255, 255, 0.15) 25%, transparent 25%, transparent 50%, rgba(255, 255, 255, 0.15) 50%, rgba(255, 255, 255, 0.15) 75%, transparent 75%, transparent);background-size:var(--bs-progress-height) var(--bs-progress-height)}.progress-stacked>.progress{overflow:visible}.progress-stacked>.progress>.progress-bar{width:100%}.progress-bar-animated{animation:1s linear infinite progress-bar-stripes}@media(prefers-reduced-motion: reduce){.progress-bar-animated{animation:none}}.list-group{--bs-list-group-color: #444;--bs-list-group-bg: #fff;--bs-list-group-border-color: #dee2e6;--bs-list-group-border-width: 1px;--bs-list-group-border-radius: 0.25rem;--bs-list-group-item-padding-x: 1rem;--bs-list-group-item-padding-y: 0.5rem;--bs-list-group-action-color: rgba(68, 68, 68, 0.75);--bs-list-group-action-hover-color: #000;--bs-list-group-action-hover-bg: #f8f9fa;--bs-list-group-action-active-color: #444;--bs-list-group-action-active-bg: #eee;--bs-list-group-disabled-color: rgba(68, 68, 68, 0.75);--bs-list-group-disabled-bg: #fff;--bs-list-group-active-color: #fff;--bs-list-group-active-bg: #2196f3;--bs-list-group-active-border-color: #2196f3;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;padding-left:0;margin-bottom:0;border-radius:var(--bs-list-group-border-radius)}.list-group-numbered{list-style-type:none;counter-reset:section}.list-group-numbered>.list-group-item::before{content:counters(section, ".") ". ";counter-increment:section}.list-group-item-action{width:100%;color:var(--bs-list-group-action-color);text-align:inherit}.list-group-item-action:hover,.list-group-item-action:focus{z-index:1;color:var(--bs-list-group-action-hover-color);text-decoration:none;background-color:var(--bs-list-group-action-hover-bg)}.list-group-item-action:active{color:var(--bs-list-group-action-active-color);background-color:var(--bs-list-group-action-active-bg)}.list-group-item{position:relative;display:block;padding:var(--bs-list-group-item-padding-y) var(--bs-list-group-item-padding-x);color:var(--bs-list-group-color);text-decoration:none;-webkit-text-decoration:none;-moz-text-decoration:none;-ms-text-decoration:none;-o-text-decoration:none;background-color:var(--bs-list-group-bg);border:var(--bs-list-group-border-width) solid var(--bs-list-group-border-color)}.list-group-item:first-child{border-top-left-radius:inherit;border-top-right-radius:inherit}.list-group-item:last-child{border-bottom-right-radius:inherit;border-bottom-left-radius:inherit}.list-group-item.disabled,.list-group-item:disabled{color:var(--bs-list-group-disabled-color);pointer-events:none;background-color:var(--bs-list-group-disabled-bg)}.list-group-item.active{z-index:2;color:var(--bs-list-group-active-color);background-color:var(--bs-list-group-active-bg);border-color:var(--bs-list-group-active-border-color)}.list-group-item+.list-group-item{border-top-width:0}.list-group-item+.list-group-item.active{margin-top:calc(-1*var(--bs-list-group-border-width));border-top-width:var(--bs-list-group-border-width)}.list-group-horizontal{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal>.list-group-item.active{margin-top:0}.list-group-horizontal>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}@media(min-width: 576px){.list-group-horizontal-sm{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-sm>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-sm>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-sm>.list-group-item.active{margin-top:0}.list-group-horizontal-sm>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-sm>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 768px){.list-group-horizontal-md{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-md>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-md>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-md>.list-group-item.active{margin-top:0}.list-group-horizontal-md>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-md>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 992px){.list-group-horizontal-lg{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-lg>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-lg>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-lg>.list-group-item.active{margin-top:0}.list-group-horizontal-lg>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-lg>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1200px){.list-group-horizontal-xl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xl>.list-group-item.active{margin-top:0}.list-group-horizontal-xl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}@media(min-width: 1400px){.list-group-horizontal-xxl{flex-direction:row;-webkit-flex-direction:row}.list-group-horizontal-xxl>.list-group-item:first-child:not(:last-child){border-bottom-left-radius:var(--bs-list-group-border-radius);border-top-right-radius:0}.list-group-horizontal-xxl>.list-group-item:last-child:not(:first-child){border-top-right-radius:var(--bs-list-group-border-radius);border-bottom-left-radius:0}.list-group-horizontal-xxl>.list-group-item.active{margin-top:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item{border-top-width:var(--bs-list-group-border-width);border-left-width:0}.list-group-horizontal-xxl>.list-group-item+.list-group-item.active{margin-left:calc(-1*var(--bs-list-group-border-width));border-left-width:var(--bs-list-group-border-width)}}.list-group-flush{border-radius:0}.list-group-flush>.list-group-item{border-width:0 0 var(--bs-list-group-border-width)}.list-group-flush>.list-group-item:last-child{border-bottom-width:0}.list-group-item-default{--bs-list-group-color: var(--bs-default-text-emphasis);--bs-list-group-bg: var(--bs-default-bg-subtle);--bs-list-group-border-color: var(--bs-default-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-default-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-default-border-subtle);--bs-list-group-active-color: var(--bs-default-bg-subtle);--bs-list-group-active-bg: var(--bs-default-text-emphasis);--bs-list-group-active-border-color: var(--bs-default-text-emphasis)}.list-group-item-primary{--bs-list-group-color: var(--bs-primary-text-emphasis);--bs-list-group-bg: var(--bs-primary-bg-subtle);--bs-list-group-border-color: var(--bs-primary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-primary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-primary-border-subtle);--bs-list-group-active-color: var(--bs-primary-bg-subtle);--bs-list-group-active-bg: var(--bs-primary-text-emphasis);--bs-list-group-active-border-color: var(--bs-primary-text-emphasis)}.list-group-item-secondary{--bs-list-group-color: var(--bs-secondary-text-emphasis);--bs-list-group-bg: var(--bs-secondary-bg-subtle);--bs-list-group-border-color: var(--bs-secondary-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-secondary-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-secondary-border-subtle);--bs-list-group-active-color: var(--bs-secondary-bg-subtle);--bs-list-group-active-bg: var(--bs-secondary-text-emphasis);--bs-list-group-active-border-color: var(--bs-secondary-text-emphasis)}.list-group-item-success{--bs-list-group-color: var(--bs-success-text-emphasis);--bs-list-group-bg: var(--bs-success-bg-subtle);--bs-list-group-border-color: var(--bs-success-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-success-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-success-border-subtle);--bs-list-group-active-color: var(--bs-success-bg-subtle);--bs-list-group-active-bg: var(--bs-success-text-emphasis);--bs-list-group-active-border-color: var(--bs-success-text-emphasis)}.list-group-item-info{--bs-list-group-color: var(--bs-info-text-emphasis);--bs-list-group-bg: var(--bs-info-bg-subtle);--bs-list-group-border-color: var(--bs-info-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-info-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-info-border-subtle);--bs-list-group-active-color: var(--bs-info-bg-subtle);--bs-list-group-active-bg: var(--bs-info-text-emphasis);--bs-list-group-active-border-color: var(--bs-info-text-emphasis)}.list-group-item-warning{--bs-list-group-color: var(--bs-warning-text-emphasis);--bs-list-group-bg: var(--bs-warning-bg-subtle);--bs-list-group-border-color: var(--bs-warning-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-warning-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-warning-border-subtle);--bs-list-group-active-color: var(--bs-warning-bg-subtle);--bs-list-group-active-bg: var(--bs-warning-text-emphasis);--bs-list-group-active-border-color: var(--bs-warning-text-emphasis)}.list-group-item-danger{--bs-list-group-color: var(--bs-danger-text-emphasis);--bs-list-group-bg: var(--bs-danger-bg-subtle);--bs-list-group-border-color: var(--bs-danger-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-danger-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-danger-border-subtle);--bs-list-group-active-color: var(--bs-danger-bg-subtle);--bs-list-group-active-bg: var(--bs-danger-text-emphasis);--bs-list-group-active-border-color: var(--bs-danger-text-emphasis)}.list-group-item-light{--bs-list-group-color: var(--bs-light-text-emphasis);--bs-list-group-bg: var(--bs-light-bg-subtle);--bs-list-group-border-color: var(--bs-light-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-light-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-light-border-subtle);--bs-list-group-active-color: var(--bs-light-bg-subtle);--bs-list-group-active-bg: var(--bs-light-text-emphasis);--bs-list-group-active-border-color: var(--bs-light-text-emphasis)}.list-group-item-dark{--bs-list-group-color: var(--bs-dark-text-emphasis);--bs-list-group-bg: var(--bs-dark-bg-subtle);--bs-list-group-border-color: var(--bs-dark-border-subtle);--bs-list-group-action-hover-color: var(--bs-emphasis-color);--bs-list-group-action-hover-bg: var(--bs-dark-border-subtle);--bs-list-group-action-active-color: var(--bs-emphasis-color);--bs-list-group-action-active-bg: var(--bs-dark-border-subtle);--bs-list-group-active-color: var(--bs-dark-bg-subtle);--bs-list-group-active-bg: var(--bs-dark-text-emphasis);--bs-list-group-active-border-color: var(--bs-dark-text-emphasis)}.btn-close{--bs-btn-close-color: #fff;--bs-btn-close-bg: url("data:image/svg+xml,%3csvg xmlns='http://www.w3.org/2000/svg' viewBox='0 0 16 16' fill='%23fff'%3e%3cpath d='M.293.293a1 1 0 0 1 1.414 0L8 6.586 14.293.293a1 1 0 1 1 1.414 1.414L9.414 8l6.293 6.293a1 1 0 0 1-1.414 1.414L8 9.414l-6.293 6.293a1 1 0 0 1-1.414-1.414L6.586 8 .293 1.707a1 1 0 0 1 0-1.414z'/%3e%3c/svg%3e");--bs-btn-close-opacity: 0.6;--bs-btn-close-hover-opacity: 1;--bs-btn-close-focus-shadow: 0 0 0 0.25rem rgba(33, 150, 243, 0.25);--bs-btn-close-focus-opacity: 1;--bs-btn-close-disabled-opacity: 0.25;--bs-btn-close-white-filter: invert(1) grayscale(100%) brightness(200%);box-sizing:content-box;width:1em;height:1em;padding:.25em .25em;color:var(--bs-btn-close-color);background:rgba(0,0,0,0) var(--bs-btn-close-bg) center/1em auto no-repeat;border:0;border-radius:.25rem;opacity:var(--bs-btn-close-opacity)}.btn-close:hover{color:var(--bs-btn-close-color);text-decoration:none;opacity:var(--bs-btn-close-hover-opacity)}.btn-close:focus{outline:0;box-shadow:var(--bs-btn-close-focus-shadow);opacity:var(--bs-btn-close-focus-opacity)}.btn-close:disabled,.btn-close.disabled{pointer-events:none;user-select:none;-webkit-user-select:none;-moz-user-select:none;-ms-user-select:none;-o-user-select:none;opacity:var(--bs-btn-close-disabled-opacity)}.btn-close-white{filter:var(--bs-btn-close-white-filter)}[data-bs-theme=dark] .btn-close{filter:var(--bs-btn-close-white-filter)}.toast{--bs-toast-zindex: 1090;--bs-toast-padding-x: 0.75rem;--bs-toast-padding-y: 0.5rem;--bs-toast-spacing: 1.5rem;--bs-toast-max-width: 350px;--bs-toast-font-size:0.875rem;--bs-toast-color: ;--bs-toast-bg: rgba(255, 255, 255, 0.85);--bs-toast-border-width: 1px;--bs-toast-border-color: rgba(0, 0, 0, 0.175);--bs-toast-border-radius: 0.25rem;--bs-toast-box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.15);--bs-toast-header-color: rgba(68, 68, 68, 0.75);--bs-toast-header-bg: rgba(255, 255, 255, 0.85);--bs-toast-header-border-color: rgba(0, 0, 0, 0.175);width:var(--bs-toast-max-width);max-width:100%;font-size:var(--bs-toast-font-size);color:var(--bs-toast-color);pointer-events:auto;background-color:var(--bs-toast-bg);background-clip:padding-box;border:var(--bs-toast-border-width) solid var(--bs-toast-border-color);box-shadow:var(--bs-toast-box-shadow);border-radius:var(--bs-toast-border-radius)}.toast.showing{opacity:0}.toast:not(.show){display:none}.toast-container{--bs-toast-zindex: 1090;position:absolute;z-index:var(--bs-toast-zindex);width:max-content;width:-webkit-max-content;width:-moz-max-content;width:-ms-max-content;width:-o-max-content;max-width:100%;pointer-events:none}.toast-container>:not(:last-child){margin-bottom:var(--bs-toast-spacing)}.toast-header{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;padding:var(--bs-toast-padding-y) var(--bs-toast-padding-x);color:var(--bs-toast-header-color);background-color:var(--bs-toast-header-bg);background-clip:padding-box;border-bottom:var(--bs-toast-border-width) solid var(--bs-toast-header-border-color);border-top-left-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width));border-top-right-radius:calc(var(--bs-toast-border-radius) - var(--bs-toast-border-width))}.toast-header .btn-close{margin-right:calc(-0.5*var(--bs-toast-padding-x));margin-left:var(--bs-toast-padding-x)}.toast-body{padding:var(--bs-toast-padding-x);word-wrap:break-word}.modal{--bs-modal-zindex: 1055;--bs-modal-width: 500px;--bs-modal-padding: 1rem;--bs-modal-margin: 0.5rem;--bs-modal-color: ;--bs-modal-bg: #fff;--bs-modal-border-color: transparent;--bs-modal-border-width: 1px;--bs-modal-border-radius: 0.5rem;--bs-modal-box-shadow: 0 0.125rem 0.25rem rgba(0, 0, 0, 0.075);--bs-modal-inner-border-radius: calc(0.5rem - 1px);--bs-modal-header-padding-x: 1rem;--bs-modal-header-padding-y: 1rem;--bs-modal-header-padding: 1rem 1rem;--bs-modal-header-border-color: #dee2e6;--bs-modal-header-border-width: 1px;--bs-modal-title-line-height: 1.5;--bs-modal-footer-gap: 0.5rem;--bs-modal-footer-bg: ;--bs-modal-footer-border-color: #dee2e6;--bs-modal-footer-border-width: 1px;position:fixed;top:0;left:0;z-index:var(--bs-modal-zindex);display:none;width:100%;height:100%;overflow-x:hidden;overflow-y:auto;outline:0}.modal-dialog{position:relative;width:auto;margin:var(--bs-modal-margin);pointer-events:none}.modal.fade .modal-dialog{transition:transform .3s ease-out;transform:translate(0, -50px)}@media(prefers-reduced-motion: reduce){.modal.fade .modal-dialog{transition:none}}.modal.show .modal-dialog{transform:none}.modal.modal-static .modal-dialog{transform:scale(1.02)}.modal-dialog-scrollable{height:calc(100% - var(--bs-modal-margin)*2)}.modal-dialog-scrollable .modal-content{max-height:100%;overflow:hidden}.modal-dialog-scrollable .modal-body{overflow-y:auto}.modal-dialog-centered{display:flex;display:-webkit-flex;align-items:center;-webkit-align-items:center;min-height:calc(100% - var(--bs-modal-margin)*2)}.modal-content{position:relative;display:flex;display:-webkit-flex;flex-direction:column;-webkit-flex-direction:column;width:100%;color:var(--bs-modal-color);pointer-events:auto;background-color:var(--bs-modal-bg);background-clip:padding-box;border:var(--bs-modal-border-width) solid var(--bs-modal-border-color);border-radius:var(--bs-modal-border-radius);box-shadow:var(--bs-modal-box-shadow);outline:0}.modal-backdrop{--bs-backdrop-zindex: 1050;--bs-backdrop-bg: #000;--bs-backdrop-opacity: 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auto}.modal-title{margin-bottom:0;line-height:var(--bs-modal-title-line-height)}.modal-body{position:relative;flex:1 1 auto;-webkit-flex:1 1 auto;padding:var(--bs-modal-padding)}.modal-footer{display:flex;display:-webkit-flex;flex-shrink:0;-webkit-flex-shrink:0;flex-wrap:wrap;-webkit-flex-wrap:wrap;align-items:center;-webkit-align-items:center;justify-content:flex-end;-webkit-justify-content:flex-end;padding:calc(var(--bs-modal-padding) - var(--bs-modal-footer-gap)*.5);background-color:var(--bs-modal-footer-bg);border-top:var(--bs-modal-footer-border-width) solid var(--bs-modal-footer-border-color);border-bottom-right-radius:var(--bs-modal-inner-border-radius);border-bottom-left-radius:var(--bs-modal-inner-border-radius)}.modal-footer>*{margin:calc(var(--bs-modal-footer-gap)*.5)}@media(min-width: 576px){.modal{--bs-modal-margin: 1.75rem;--bs-modal-box-shadow: 0 0.5rem 1rem rgba(0, 0, 0, 0.15)}.modal-dialog{max-width:var(--bs-modal-width);margin-right:auto;margin-left:auto}.modal-sm{--bs-modal-width: 300px}}@media(min-width: 992px){.modal-lg,.modal-xl{--bs-modal-width: 800px}}@media(min-width: 1200px){.modal-xl{--bs-modal-width: 1140px}}.modal-fullscreen{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen .modal-header,.modal-fullscreen .modal-footer{border-radius:0}.modal-fullscreen .modal-body{overflow-y:auto}@media(max-width: 575.98px){.modal-fullscreen-sm-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-sm-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-sm-down .modal-header,.modal-fullscreen-sm-down .modal-footer{border-radius:0}.modal-fullscreen-sm-down .modal-body{overflow-y:auto}}@media(max-width: 767.98px){.modal-fullscreen-md-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-md-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-md-down .modal-header,.modal-fullscreen-md-down .modal-footer{border-radius:0}.modal-fullscreen-md-down .modal-body{overflow-y:auto}}@media(max-width: 991.98px){.modal-fullscreen-lg-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-lg-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-lg-down .modal-header,.modal-fullscreen-lg-down .modal-footer{border-radius:0}.modal-fullscreen-lg-down .modal-body{overflow-y:auto}}@media(max-width: 1199.98px){.modal-fullscreen-xl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xl-down .modal-header,.modal-fullscreen-xl-down .modal-footer{border-radius:0}.modal-fullscreen-xl-down .modal-body{overflow-y:auto}}@media(max-width: 1399.98px){.modal-fullscreen-xxl-down{width:100vw;max-width:none;height:100%;margin:0}.modal-fullscreen-xxl-down .modal-content{height:100%;border:0;border-radius:0}.modal-fullscreen-xxl-down .modal-header,.modal-fullscreen-xxl-down .modal-footer{border-radius:0}.modal-fullscreen-xxl-down .modal-body{overflow-y:auto}}.tooltip{--bs-tooltip-zindex: 1080;--bs-tooltip-max-width: 200px;--bs-tooltip-padding-x: 0.5rem;--bs-tooltip-padding-y: 0.25rem;--bs-tooltip-margin: ;--bs-tooltip-font-size:0.875rem;--bs-tooltip-color: #fff;--bs-tooltip-bg: #444;--bs-tooltip-border-radius: 0.25rem;--bs-tooltip-opacity: 0.9;--bs-tooltip-arrow-width: 0.8rem;--bs-tooltip-arrow-height: 0.4rem;z-index:var(--bs-tooltip-zindex);display:block;margin:var(--bs-tooltip-margin);font-family:Roboto,-apple-system,BlinkMacSystemFont,"Segoe UI","Helvetica 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H{constructor(t){super(),this._config=this._getConfig(t),this._isAppended=!1,this._element=null}static get Default(){return Xi}static get DefaultType(){return Yi}static get NAME(){return Vi}show(t){if(!this._config.isVisible)return void g(t);this._append();const e=this._getElement();this._config.isAnimated&&d(e),e.classList.add(Ki),this._emulateAnimation((()=>{g(t)}))}hide(t){this._config.isVisible?(this._getElement().classList.remove(Ki),this._emulateAnimation((()=>{this.dispose(),g(t)}))):g(t)}dispose(){this._isAppended&&(N.off(this._element,Qi),this._element.remove(),this._isAppended=!1)}_getElement(){if(!this._element){const t=document.createElement("div");t.className=this._config.className,this._config.isAnimated&&t.classList.add("fade"),this._element=t}return this._element}_configAfterMerge(t){return t.rootElement=r(t.rootElement),t}_append(){if(this._isAppended)return;const t=this._getElement();this._config.rootElement.append(t),N.on(t,Qi,(()=>{g(this._config.clickCallback)})),this._isAppended=!0}_emulateAnimation(t){_(t,this._getElement(),this._config.isAnimated)}}const Gi=".bs.focustrap",Ji=`focusin${Gi}`,Zi=`keydown.tab${Gi}`,tn="backward",en={autofocus:!0,trapElement:null},nn={autofocus:"boolean",trapElement:"element"};class sn extends H{constructor(t){super(),this._config=this._getConfig(t),this._isActive=!1,this._lastTabNavDirection=null}static get Default(){return en}static get DefaultType(){return nn}static get NAME(){return"focustrap"}activate(){this._isActive||(this._config.autofocus&&this._config.trapElement.focus(),N.off(document,Gi),N.on(document,Ji,(t=>this._handleFocusin(t))),N.on(document,Zi,(t=>this._handleKeydown(t))),this._isActive=!0)}deactivate(){this._isActive&&(this._isActive=!1,N.off(document,Gi))}_handleFocusin(t){const{trapElement:e}=this._config;if(t.target===document||t.target===e||e.contains(t.target))return;const i=z.focusableChildren(e);0===i.length?e.focus():this._lastTabNavDirection===tn?i[i.length-1].focus():i[0].focus()}_handleKeydown(t){"Tab"===t.key&&(this._lastTabNavDirection=t.shiftKey?tn:"forward")}}const on=".fixed-top, .fixed-bottom, .is-fixed, .sticky-top",rn=".sticky-top",an="padding-right",ln="margin-right";class cn{constructor(){this._element=document.body}getWidth(){const t=document.documentElement.clientWidth;return Math.abs(window.innerWidth-t)}hide(){const t=this.getWidth();this._disableOverFlow(),this._setElementAttributes(this._element,an,(e=>e+t)),this._setElementAttributes(on,an,(e=>e+t)),this._setElementAttributes(rn,ln,(e=>e-t))}reset(){this._resetElementAttributes(this._element,"overflow"),this._resetElementAttributes(this._element,an),this._resetElementAttributes(on,an),this._resetElementAttributes(rn,ln)}isOverflowing(){return this.getWidth()>0}_disableOverFlow(){this._saveInitialAttribute(this._element,"overflow"),this._element.style.overflow="hidden"}_setElementAttributes(t,e,i){const n=this.getWidth();this._applyManipulationCallback(t,(t=>{if(t!==this._element&&window.innerWidth>t.clientWidth+n)return;this._saveInitialAttribute(t,e);const s=window.getComputedStyle(t).getPropertyValue(e);t.style.setProperty(e,`${i(Number.parseFloat(s))}px`)}))}_saveInitialAttribute(t,e){const i=t.style.getPropertyValue(e);i&&F.setDataAttribute(t,e,i)}_resetElementAttributes(t,e){this._applyManipulationCallback(t,(t=>{const i=F.getDataAttribute(t,e);null!==i?(F.removeDataAttribute(t,e),t.style.setProperty(e,i)):t.style.removeProperty(e)}))}_applyManipulationCallback(t,e){if(o(t))e(t);else for(const i of z.find(t,this._element))e(i)}}const hn=".bs.modal",dn=`hide${hn}`,un=`hidePrevented${hn}`,fn=`hidden${hn}`,pn=`show${hn}`,mn=`shown${hn}`,gn=`resize${hn}`,_n=`click.dismiss${hn}`,bn=`mousedown.dismiss${hn}`,vn=`keydown.dismiss${hn}`,yn=`click${hn}.data-api`,wn="modal-open",An="show",En="modal-static",Tn={backdrop:!0,focus:!0,keyboard:!0},Cn={backdrop:"(boolean|string)",focus:"boolean",keyboard:"boolean"};class On extends W{constructor(t,e){super(t,e),this._dialog=z.findOne(".modal-dialog",this._element),this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._isShown=!1,this._isTransitioning=!1,this._scrollBar=new cn,this._addEventListeners()}static get Default(){return Tn}static get DefaultType(){return Cn}static get NAME(){return"modal"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||this._isTransitioning||N.trigger(this._element,pn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._isTransitioning=!0,this._scrollBar.hide(),document.body.classList.add(wn),this._adjustDialog(),this._backdrop.show((()=>this._showElement(t))))}hide(){this._isShown&&!this._isTransitioning&&(N.trigger(this._element,dn).defaultPrevented||(this._isShown=!1,this._isTransitioning=!0,this._focustrap.deactivate(),this._element.classList.remove(An),this._queueCallback((()=>this._hideModal()),this._element,this._isAnimated())))}dispose(){N.off(window,hn),N.off(this._dialog,hn),this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}handleUpdate(){this._adjustDialog()}_initializeBackDrop(){return new Ui({isVisible:Boolean(this._config.backdrop),isAnimated:this._isAnimated()})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_showElement(t){document.body.contains(this._element)||document.body.append(this._element),this._element.style.display="block",this._element.removeAttribute("aria-hidden"),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.scrollTop=0;const e=z.findOne(".modal-body",this._dialog);e&&(e.scrollTop=0),d(this._element),this._element.classList.add(An),this._queueCallback((()=>{this._config.focus&&this._focustrap.activate(),this._isTransitioning=!1,N.trigger(this._element,mn,{relatedTarget:t})}),this._dialog,this._isAnimated())}_addEventListeners(){N.on(this._element,vn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():this._triggerBackdropTransition())})),N.on(window,gn,(()=>{this._isShown&&!this._isTransitioning&&this._adjustDialog()})),N.on(this._element,bn,(t=>{N.one(this._element,_n,(e=>{this._element===t.target&&this._element===e.target&&("static"!==this._config.backdrop?this._config.backdrop&&this.hide():this._triggerBackdropTransition())}))}))}_hideModal(){this._element.style.display="none",this._element.setAttribute("aria-hidden",!0),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._isTransitioning=!1,this._backdrop.hide((()=>{document.body.classList.remove(wn),this._resetAdjustments(),this._scrollBar.reset(),N.trigger(this._element,fn)}))}_isAnimated(){return this._element.classList.contains("fade")}_triggerBackdropTransition(){if(N.trigger(this._element,un).defaultPrevented)return;const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._element.style.overflowY;"hidden"===e||this._element.classList.contains(En)||(t||(this._element.style.overflowY="hidden"),this._element.classList.add(En),this._queueCallback((()=>{this._element.classList.remove(En),this._queueCallback((()=>{this._element.style.overflowY=e}),this._dialog)}),this._dialog),this._element.focus())}_adjustDialog(){const t=this._element.scrollHeight>document.documentElement.clientHeight,e=this._scrollBar.getWidth(),i=e>0;if(i&&!t){const t=p()?"paddingLeft":"paddingRight";this._element.style[t]=`${e}px`}if(!i&&t){const t=p()?"paddingRight":"paddingLeft";this._element.style[t]=`${e}px`}}_resetAdjustments(){this._element.style.paddingLeft="",this._element.style.paddingRight=""}static jQueryInterface(t,e){return this.each((function(){const i=On.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===i[t])throw new TypeError(`No method named "${t}"`);i[t](e)}}))}}N.on(document,yn,'[data-bs-toggle="modal"]',(function(t){const e=z.getElementFromSelector(this);["A","AREA"].includes(this.tagName)&&t.preventDefault(),N.one(e,pn,(t=>{t.defaultPrevented||N.one(e,fn,(()=>{a(this)&&this.focus()}))}));const i=z.findOne(".modal.show");i&&On.getInstance(i).hide(),On.getOrCreateInstance(e).toggle(this)})),R(On),m(On);const xn=".bs.offcanvas",kn=".data-api",Ln=`load${xn}${kn}`,Sn="show",Dn="showing",$n="hiding",In=".offcanvas.show",Nn=`show${xn}`,Pn=`shown${xn}`,Mn=`hide${xn}`,jn=`hidePrevented${xn}`,Fn=`hidden${xn}`,Hn=`resize${xn}`,Wn=`click${xn}${kn}`,Bn=`keydown.dismiss${xn}`,zn={backdrop:!0,keyboard:!0,scroll:!1},Rn={backdrop:"(boolean|string)",keyboard:"boolean",scroll:"boolean"};class qn extends W{constructor(t,e){super(t,e),this._isShown=!1,this._backdrop=this._initializeBackDrop(),this._focustrap=this._initializeFocusTrap(),this._addEventListeners()}static get Default(){return zn}static get DefaultType(){return Rn}static get NAME(){return"offcanvas"}toggle(t){return this._isShown?this.hide():this.show(t)}show(t){this._isShown||N.trigger(this._element,Nn,{relatedTarget:t}).defaultPrevented||(this._isShown=!0,this._backdrop.show(),this._config.scroll||(new cn).hide(),this._element.setAttribute("aria-modal",!0),this._element.setAttribute("role","dialog"),this._element.classList.add(Dn),this._queueCallback((()=>{this._config.scroll&&!this._config.backdrop||this._focustrap.activate(),this._element.classList.add(Sn),this._element.classList.remove(Dn),N.trigger(this._element,Pn,{relatedTarget:t})}),this._element,!0))}hide(){this._isShown&&(N.trigger(this._element,Mn).defaultPrevented||(this._focustrap.deactivate(),this._element.blur(),this._isShown=!1,this._element.classList.add($n),this._backdrop.hide(),this._queueCallback((()=>{this._element.classList.remove(Sn,$n),this._element.removeAttribute("aria-modal"),this._element.removeAttribute("role"),this._config.scroll||(new cn).reset(),N.trigger(this._element,Fn)}),this._element,!0)))}dispose(){this._backdrop.dispose(),this._focustrap.deactivate(),super.dispose()}_initializeBackDrop(){const t=Boolean(this._config.backdrop);return new Ui({className:"offcanvas-backdrop",isVisible:t,isAnimated:!0,rootElement:this._element.parentNode,clickCallback:t?()=>{"static"!==this._config.backdrop?this.hide():N.trigger(this._element,jn)}:null})}_initializeFocusTrap(){return new sn({trapElement:this._element})}_addEventListeners(){N.on(this._element,Bn,(t=>{"Escape"===t.key&&(this._config.keyboard?this.hide():N.trigger(this._element,jn))}))}static jQueryInterface(t){return this.each((function(){const e=qn.getOrCreateInstance(this,t);if("string"==typeof t){if(void 0===e[t]||t.startsWith("_")||"constructor"===t)throw new TypeError(`No method named "${t}"`);e[t](this)}}))}}N.on(document,Wn,'[data-bs-toggle="offcanvas"]',(function(t){const e=z.getElementFromSelector(this);if(["A","AREA"].includes(this.tagName)&&t.preventDefault(),l(this))return;N.one(e,Fn,(()=>{a(this)&&this.focus()}));const i=z.findOne(In);i&&i!==e&&qn.getInstance(i).hide(),qn.getOrCreateInstance(e).toggle(this)})),N.on(window,Ln,(()=>{for(const t of z.find(In))qn.getOrCreateInstance(t).show()})),N.on(window,Hn,(()=>{for(const t of z.find("[aria-modal][class*=show][class*=offcanvas-]"))"fixed"!==getComputedStyle(t).position&&qn.getOrCreateInstance(t).hide()})),R(qn),m(qn);const Vn={"*":["class","dir","id","lang","role",/^aria-[\w-]*$/i],a:["target","href","title","rel"],area:[],b:[],br:[],col:[],code:[],div:[],em:[],hr:[],h1:[],h2:[],h3:[],h4:[],h5:[],h6:[],i:[],img:["src","srcset","alt","title","width","height"],li:[],ol:[],p:[],pre:[],s:[],small:[],span:[],sub:[],sup:[],strong:[],u:[],ul:[]},Kn=new Set(["background","cite","href","itemtype","longdesc","poster","src","xlink:href"]),Qn=/^(?!javascript:)(?:[a-z0-9+.-]+:|[^&:/?#]*(?:[/?#]|$))/i,Xn=(t,e)=>{const i=t.nodeName.toLowerCase();return e.includes(i)?!Kn.has(i)||Boolean(Qn.test(t.nodeValue)):e.filter((t=>t instanceof RegExp)).some((t=>t.test(i)))},Yn={allowList:Vn,content:{},extraClass:"",html:!1,sanitize:!0,sanitizeFn:null,template:"
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")),e}_typeCheckConfig(t){super._typeCheckConfig(t),this._checkContent(t.content)}_checkContent(t){for(const[e,i]of Object.entries(t))super._typeCheckConfig({selector:e,entry:i},Gn)}_setContent(t,e,i){const n=z.findOne(i,t);n&&((e=this._resolvePossibleFunction(e))?o(e)?this._putElementInTemplate(r(e),n):this._config.html?n.innerHTML=this._maybeSanitize(e):n.textContent=e:n.remove())}_maybeSanitize(t){return this._config.sanitize?function(t,e,i){if(!t.length)return t;if(i&&"function"==typeof i)return i(t);const n=(new window.DOMParser).parseFromString(t,"text/html"),s=[].concat(...n.body.querySelectorAll("*"));for(const t of s){const i=t.nodeName.toLowerCase();if(!Object.keys(e).includes(i)){t.remove();continue}const n=[].concat(...t.attributes),s=[].concat(e["*"]||[],e[i]||[]);for(const e of n)Xn(e,s)||t.removeAttribute(e.nodeName)}return n.body.innerHTML}(t,this._config.allowList,this._config.sanitizeFn):t}_resolvePossibleFunction(t){return g(t,[this])}_putElementInTemplate(t,e){if(this._config.html)return e.innerHTML="",void e.append(t);e.textContent=t.textContent}}const Zn=new Set(["sanitize","allowList","sanitizeFn"]),ts="fade",es="show",is=".modal",ns="hide.bs.modal",ss="hover",os="focus",rs={AUTO:"auto",TOP:"top",RIGHT:p()?"left":"right",BOTTOM:"bottom",LEFT:p()?"right":"left"},as={allowList:Vn,animation:!0,boundary:"clippingParents",container:!1,customClass:"",delay:0,fallbackPlacements:["top","right","bottom","left"],html:!1,offset:[0,6],placement:"top",popperConfig:null,sanitize:!0,sanitizeFn:null,selector:!1,template:'',title:"",trigger:"hover focus"},ls={allowList:"object",animation:"boolean",boundary:"(string|element)",container:"(string|element|boolean)",customClass:"(string|function)",delay:"(number|object)",fallbackPlacements:"array",html:"boolean",offset:"(array|string|function)",placement:"(string|function)",popperConfig:"(null|object|function)",sanitize:"boolean",sanitizeFn:"(null|function)",selector:"(string|boolean)",template:"string",title:"(string|element|function)",trigger:"string"};class cs extends W{constructor(t,e){if(void 0===vi)throw new TypeError("Bootstrap's tooltips require Popper (https://popper.js.org)");super(t,e),this._isEnabled=!0,this._timeout=0,this._isHovered=null,this._activeTrigger={},this._popper=null,this._templateFactory=null,this._newContent=null,this.tip=null,this._setListeners(),this._config.selector||this._fixTitle()}static get Default(){return as}static get DefaultType(){return ls}static get NAME(){return"tooltip"}enable(){this._isEnabled=!0}disable(){this._isEnabled=!1}toggleEnabled(){this._isEnabled=!this._isEnabled}toggle(){this._isEnabled&&(this._activeTrigger.click=!this._activeTrigger.click,this._isShown()?this._leave():this._enter())}dispose(){clearTimeout(this._timeout),N.off(this._element.closest(is),ns,this._hideModalHandler),this._element.getAttribute("data-bs-original-title")&&this._element.setAttribute("title",this._element.getAttribute("data-bs-original-title")),this._disposePopper(),super.dispose()}show(){if("none"===this._element.style.display)throw new Error("Please use show on visible elements");if(!this._isWithContent()||!this._isEnabled)return;const t=N.trigger(this._element,this.constructor.eventName("show")),e=(c(this._element)||this._element.ownerDocument.documentElement).contains(this._element);if(t.defaultPrevented||!e)return;this._disposePopper();const i=this._getTipElement();this._element.setAttribute("aria-describedby",i.getAttribute("id"));const{container:n}=this._config;if(this._element.ownerDocument.documentElement.contains(this.tip)||(n.append(i),N.trigger(this._element,this.constructor.eventName("inserted"))),this._popper=this._createPopper(i),i.classList.add(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.on(t,"mouseover",h);this._queueCallback((()=>{N.trigger(this._element,this.constructor.eventName("shown")),!1===this._isHovered&&this._leave(),this._isHovered=!1}),this.tip,this._isAnimated())}hide(){if(this._isShown()&&!N.trigger(this._element,this.constructor.eventName("hide")).defaultPrevented){if(this._getTipElement().classList.remove(es),"ontouchstart"in document.documentElement)for(const t of[].concat(...document.body.children))N.off(t,"mouseover",h);this._activeTrigger.click=!1,this._activeTrigger[os]=!1,this._activeTrigger[ss]=!1,this._isHovered=null,this._queueCallback((()=>{this._isWithActiveTrigger()||(this._isHovered||this._disposePopper(),this._element.removeAttribute("aria-describedby"),N.trigger(this._element,this.constructor.eventName("hidden")))}),this.tip,this._isAnimated())}}update(){this._popper&&this._popper.update()}_isWithContent(){return Boolean(this._getTitle())}_getTipElement(){return this.tip||(this.tip=this._createTipElement(this._newContent||this._getContentForTemplate())),this.tip}_createTipElement(t){const e=this._getTemplateFactory(t).toHtml();if(!e)return null;e.classList.remove(ts,es),e.classList.add(`bs-${this.constructor.NAME}-auto`);const i=(t=>{do{t+=Math.floor(1e6*Math.random())}while(document.getElementById(t));return t})(this.constructor.NAME).toString();return e.setAttribute("id",i),this._isAnimated()&&e.classList.add(ts),e}setContent(t){this._newContent=t,this._isShown()&&(this._disposePopper(),this.show())}_getTemplateFactory(t){return this._templateFactory?this._templateFactory.changeContent(t):this._templateFactory=new Jn({...this._config,content:t,extraClass:this._resolvePossibleFunction(this._config.customClass)}),this._templateFactory}_getContentForTemplate(){return{".tooltip-inner":this._getTitle()}}_getTitle(){return this._resolvePossibleFunction(this._config.title)||this._element.getAttribute("data-bs-original-title")}_initializeOnDelegatedTarget(t){return this.constructor.getOrCreateInstance(t.delegateTarget,this._getDelegateConfig())}_isAnimated(){return this._config.animation||this.tip&&this.tip.classList.contains(ts)}_isShown(){return this.tip&&this.tip.classList.contains(es)}_createPopper(t){const e=g(this._config.placement,[this,t,this._element]),i=rs[e.toUpperCase()];return bi(this._element,t,this._getPopperConfig(i))}_getOffset(){const{offset:t}=this._config;return"string"==typeof t?t.split(",").map((t=>Number.parseInt(t,10))):"function"==typeof t?e=>t(e,this._element):t}_resolvePossibleFunction(t){return g(t,[this._element])}_getPopperConfig(t){const e={placement:t,modifiers:[{name:"flip",options:{fallbackPlacements:this._config.fallbackPlacements}},{name:"offset",options:{offset:this._getOffset()}},{name:"preventOverflow",options:{boundary:this._config.boundary}},{name:"arrow",options:{element:`.${this.constructor.NAME}-arrow`}},{name:"preSetPlacement",enabled:!0,phase:"beforeMain",fn:t=>{this._getTipElement().setAttribute("data-popper-placement",t.state.placement)}}]};return{...e,...g(this._config.popperConfig,[e])}}_setListeners(){const t=this._config.trigger.split(" ");for(const e of t)if("click"===e)N.on(this._element,this.constructor.eventName("click"),this._config.selector,(t=>{this._initializeOnDelegatedTarget(t).toggle()}));else 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t=this._element.getAttribute("title");t&&(this._element.getAttribute("aria-label")||this._element.textContent.trim()||this._element.setAttribute("aria-label",t),this._element.setAttribute("data-bs-original-title",t),this._element.removeAttribute("title"))}_enter(){this._isShown()||this._isHovered?this._isHovered=!0:(this._isHovered=!0,this._setTimeout((()=>{this._isHovered&&this.show()}),this._config.delay.show))}_leave(){this._isWithActiveTrigger()||(this._isHovered=!1,this._setTimeout((()=>{this._isHovered||this.hide()}),this._config.delay.hide))}_setTimeout(t,e){clearTimeout(this._timeout),this._timeout=setTimeout(t,e)}_isWithActiveTrigger(){return Object.values(this._activeTrigger).includes(!0)}_getConfig(t){const e=F.getDataAttributes(this._element);for(const t of Object.keys(e))Zn.has(t)&&delete e[t];return t={...e,..."object"==typeof t&&t?t:{}},t=this._mergeConfigObj(t),t=this._configAfterMerge(t),this._typeCheckConfig(t),t}_configAfterMerge(t){return 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t=this.preV,i=e.touches.length,n=e.touches[0].pageX,s=e.touches[0].pageY;if(this.isDoubleTap=!1,i>1){var l=e.touches[1].pageX,o=e.touches[1].pageY,r={x:e.touches[1].pageX-n,y:e.touches[1].pageY-s};null!==t.x&&(this.pinchStartLen>0&&(e.zoom=Y(r)/this.pinchStartLen,this.pinch.dispatch(e,this.element)),e.angle=q(r,t),this.rotate.dispatch(e,this.element)),t.x=r.x,t.y=r.y,null!==this.x2&&null!==this.sx2?(e.deltaX=(n-this.x2+l-this.sx2)/2,e.deltaY=(s-this.y2+o-this.sy2)/2):(e.deltaX=0,e.deltaY=0),this.twoFingerPressMove.dispatch(e,this.element),this.sx2=l,this.sy2=o}else{if(null!==this.x2){e.deltaX=n-this.x2,e.deltaY=s-this.y2;var a=Math.abs(this.x1-this.x2),h=Math.abs(this.y1-this.y2);(a>10||h>10)&&(this._preventTap=!0)}else e.deltaX=0,e.deltaY=0;this.pressMove.dispatch(e,this.element)}this.touchMove.dispatch(e,this.element),this._cancelLongTap(),this.x2=n,this.y2=s,i>1&&e.preventDefault()}}},{key:"end",value:function(e){if(e.changedTouches){this._cancelLongTap();var t=this;e.touches.length<2&&(this.multipointEnd.dispatch(e,this.element),this.sx2=this.sy2=null),this.x2&&Math.abs(this.x1-this.x2)>30||this.y2&&Math.abs(this.y1-this.y2)>30?(e.direction=this._swipeDirection(this.x1,this.x2,this.y1,this.y2),this.swipeTimeout=setTimeout((function(){t.swipe.dispatch(e,t.element)}),0)):(this.tapTimeout=setTimeout((function(){t._preventTap||t.tap.dispatch(e,t.element),t.isDoubleTap&&(t.doubleTap.dispatch(e,t.element),t.isDoubleTap=!1)}),0),t.isDoubleTap||(t.singleTapTimeout=setTimeout((function(){t.singleTap.dispatch(e,t.element)}),250))),this.touchEnd.dispatch(e,this.element),this.preV.x=0,this.preV.y=0,this.zoom=1,this.pinchStartLen=null,this.x1=this.x2=this.y1=this.y2=null}}},{key:"cancelAll",value:function(){this._preventTap=!0,clearTimeout(this.singleTapTimeout),clearTimeout(this.tapTimeout),clearTimeout(this.longTapTimeout),clearTimeout(this.swipeTimeout)}},{key:"cancel",value:function(e){this.cancelAll(),this.touchCancel.dispatch(e,this.element)}},{key:"_cancelLongTap",value:function(){clearTimeout(this.longTapTimeout)}},{key:"_cancelSingleTap",value:function(){clearTimeout(this.singleTapTimeout)}},{key:"_swipeDirection",value:function(e,t,i,n){return Math.abs(e-t)>=Math.abs(i-n)?e-t>0?"Left":"Right":i-n>0?"Up":"Down"}},{key:"on",value:function(e,t){this[e]&&this[e].add(t)}},{key:"off",value:function(e,t){this[e]&&this[e].del(t)}},{key:"destroy",value:function(){return this.singleTapTimeout&&clearTimeout(this.singleTapTimeout),this.tapTimeout&&clearTimeout(this.tapTimeout),this.longTapTimeout&&clearTimeout(this.longTapTimeout),this.swipeTimeout&&clearTimeout(this.swipeTimeout),this.element.removeEventListener("touchstart",this.start),this.element.removeEventListener("touchmove",this.move),this.element.removeEventListener("touchend",this.end),this.element.removeEventListener("touchcancel",this.cancel),this.rotate.del(),this.touchStart.del(),this.multipointStart.del(),this.multipointEnd.del(),this.pinch.del(),this.swipe.del(),this.tap.del(),this.doubleTap.del(),this.longTap.del(),this.singleTap.del(),this.pressMove.del(),this.twoFingerPressMove.del(),this.touchMove.del(),this.touchEnd.del(),this.touchCancel.del(),this.preV=this.pinchStartLen=this.zoom=this.isDoubleTap=this.delta=this.last=this.now=this.tapTimeout=this.singleTapTimeout=this.longTapTimeout=this.swipeTimeout=this.x1=this.x2=this.y1=this.y2=this.preTapPosition=this.rotate=this.touchStart=this.multipointStart=this.multipointEnd=this.pinch=this.swipe=this.tap=this.doubleTap=this.longTap=this.singleTap=this.pressMove=this.touchMove=this.touchEnd=this.touchCancel=this.twoFingerPressMove=null,window.removeEventListener("scroll",this._cancelAllHandler),null}}]),e}();function W(e){var t=function(){var e,t=document.createElement("fakeelement"),i={transition:"transitionend",OTransition:"oTransitionEnd",MozTransition:"transitionend",WebkitTransition:"webkitTransitionEnd"};for(e in i)if(void 0!==t.style[e])return i[e]}(),i=window.innerWidth||document.documentElement.clientWidth||document.body.clientWidth,n=c(e,"gslide-media")?e:e.querySelector(".gslide-media"),s=u(n,".ginner-container"),l=e.querySelector(".gslide-description");i>769&&(n=s),h(n,"greset"),v(n,"translate3d(0, 0, 0)"),a(t,{onElement:n,once:!0,withCallback:function(e,t){d(n,"greset")}}),n.style.opacity="",l&&(l.style.opacity="")}function B(e){if(e.events.hasOwnProperty("touch"))return!1;var t,i,n,s=y(),l=s.width,o=s.height,r=!1,a=null,g=null,f=null,p=!1,m=1,x=1,b=!1,S=!1,w=null,T=null,C=null,k=null,E=0,A=0,L=!1,I=!1,O={},P={},M=0,z=0,X=document.getElementById("glightbox-slider"),Y=document.querySelector(".goverlay"),q=new _(X,{touchStart:function(t){if(r=!0,(c(t.targetTouches[0].target,"ginner-container")||u(t.targetTouches[0].target,".gslide-desc")||"a"==t.targetTouches[0].target.nodeName.toLowerCase())&&(r=!1),u(t.targetTouches[0].target,".gslide-inline")&&!c(t.targetTouches[0].target.parentNode,"gslide-inline")&&(r=!1),r){if(P=t.targetTouches[0],O.pageX=t.targetTouches[0].pageX,O.pageY=t.targetTouches[0].pageY,M=t.targetTouches[0].clientX,z=t.targetTouches[0].clientY,a=e.activeSlide,g=a.querySelector(".gslide-media"),n=a.querySelector(".gslide-inline"),f=null,c(g,"gslide-image")&&(f=g.querySelector("img")),(window.innerWidth||document.documentElement.clientWidth||document.body.clientWidth)>769&&(g=a.querySelector(".ginner-container")),d(Y,"greset"),t.pageX>20&&t.pageXo){var a=O.pageX-P.pageX;if(Math.abs(a)<=13)return!1}p=!0;var h,d=s.targetTouches[0].clientX,c=s.targetTouches[0].clientY,u=M-d,m=z-c;if(Math.abs(u)>Math.abs(m)?(L=!1,I=!0):(I=!1,L=!0),t=P.pageX-O.pageX,E=100*t/l,i=P.pageY-O.pageY,A=100*i/o,L&&f&&(h=1-Math.abs(i)/o,Y.style.opacity=h,e.settings.touchFollowAxis&&(E=0)),I&&(h=1-Math.abs(t)/l,g.style.opacity=h,e.settings.touchFollowAxis&&(A=0)),!f)return v(g,"translate3d(".concat(E,"%, 0, 0)"));v(g,"translate3d(".concat(E,"%, ").concat(A,"%, 0)"))}},touchEnd:function(){if(r){if(p=!1,S||b)return C=w,void(k=T);var t=Math.abs(parseInt(A)),i=Math.abs(parseInt(E));if(!(t>29&&f))return t<29&&i<25?(h(Y,"greset"),Y.style.opacity=1,W(g)):void 0;e.close()}},multipointEnd:function(){setTimeout((function(){b=!1}),50)},multipointStart:function(){b=!0,m=x||1},pinch:function(e){if(!f||p)return!1;b=!0,f.scaleX=f.scaleY=m*e.zoom;var t=m*e.zoom;if(S=!0,t<=1)return S=!1,t=1,k=null,C=null,w=null,T=null,void f.setAttribute("style","");t>4.5&&(t=4.5),f.style.transform="scale3d(".concat(t,", ").concat(t,", 1)"),x=t},pressMove:function(e){if(S&&!b){var t=P.pageX-O.pageX,i=P.pageY-O.pageY;C&&(t+=C),k&&(i+=k),w=t,T=i;var n="translate3d(".concat(t,"px, ").concat(i,"px, 0)");x&&(n+=" scale3d(".concat(x,", ").concat(x,", 1)")),v(f,n)}},swipe:function(t){if(!S)if(b)b=!1;else{if("Left"==t.direction){if(e.index==e.elements.length-1)return W(g);e.nextSlide()}if("Right"==t.direction){if(0==e.index)return W(g);e.prevSlide()}}}});e.events.touch=q}var H=function(){function e(i,n){var s=this,l=arguments.length>2&&void 0!==arguments[2]?arguments[2]:null;if(t(this,e),this.img=i,this.slide=n,this.onclose=l,this.img.setZoomEvents)return!1;this.active=!1,this.zoomedIn=!1,this.dragging=!1,this.currentX=null,this.currentY=null,this.initialX=null,this.initialY=null,this.xOffset=0,this.yOffset=0,this.img.addEventListener("mousedown",(function(e){return s.dragStart(e)}),!1),this.img.addEventListener("mouseup",(function(e){return s.dragEnd(e)}),!1),this.img.addEventListener("mousemove",(function(e){return s.drag(e)}),!1),this.img.addEventListener("click",(function(e){return s.slide.classList.contains("dragging-nav")?(s.zoomOut(),!1):s.zoomedIn?void(s.zoomedIn&&!s.dragging&&s.zoomOut()):s.zoomIn()}),!1),this.img.setZoomEvents=!0}return n(e,[{key:"zoomIn",value:function(){var e=this.widowWidth();if(!(this.zoomedIn||e<=768)){var t=this.img;if(t.setAttribute("data-style",t.getAttribute("style")),t.style.maxWidth=t.naturalWidth+"px",t.style.maxHeight=t.naturalHeight+"px",t.naturalWidth>e){var i=e/2-t.naturalWidth/2;this.setTranslate(this.img.parentNode,i,0)}this.slide.classList.add("zoomed"),this.zoomedIn=!0}}},{key:"zoomOut",value:function(){this.img.parentNode.setAttribute("style",""),this.img.setAttribute("style",this.img.getAttribute("data-style")),this.slide.classList.remove("zoomed"),this.zoomedIn=!1,this.currentX=null,this.currentY=null,this.initialX=null,this.initialY=null,this.xOffset=0,this.yOffset=0,this.onclose&&"function"==typeof this.onclose&&this.onclose()}},{key:"dragStart",value:function(e){e.preventDefault(),this.zoomedIn?("touchstart"===e.type?(this.initialX=e.touches[0].clientX-this.xOffset,this.initialY=e.touches[0].clientY-this.yOffset):(this.initialX=e.clientX-this.xOffset,this.initialY=e.clientY-this.yOffset),e.target===this.img&&(this.active=!0,this.img.classList.add("dragging"))):this.active=!1}},{key:"dragEnd",value:function(e){var t=this;e.preventDefault(),this.initialX=this.currentX,this.initialY=this.currentY,this.active=!1,setTimeout((function(){t.dragging=!1,t.img.isDragging=!1,t.img.classList.remove("dragging")}),100)}},{key:"drag",value:function(e){this.active&&(e.preventDefault(),"touchmove"===e.type?(this.currentX=e.touches[0].clientX-this.initialX,this.currentY=e.touches[0].clientY-this.initialY):(this.currentX=e.clientX-this.initialX,this.currentY=e.clientY-this.initialY),this.xOffset=this.currentX,this.yOffset=this.currentY,this.img.isDragging=!0,this.dragging=!0,this.setTranslate(this.img,this.currentX,this.currentY))}},{key:"onMove",value:function(e){if(this.zoomedIn){var t=e.clientX-this.img.naturalWidth/2,i=e.clientY-this.img.naturalHeight/2;this.setTranslate(this.img,t,i)}}},{key:"setTranslate",value:function(e,t,i){e.style.transform="translate3d("+t+"px, "+i+"px, 0)"}},{key:"widowWidth",value:function(){return window.innerWidth||document.documentElement.clientWidth||document.body.clientWidth}}]),e}(),V=function(){function e(){var i=this,n=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{};t(this,e);var s=n.dragEl,l=n.toleranceX,o=void 0===l?40:l,r=n.toleranceY,a=void 0===r?65:r,h=n.slide,d=void 0===h?null:h,c=n.instance,u=void 0===c?null:c;this.el=s,this.active=!1,this.dragging=!1,this.currentX=null,this.currentY=null,this.initialX=null,this.initialY=null,this.xOffset=0,this.yOffset=0,this.direction=null,this.lastDirection=null,this.toleranceX=o,this.toleranceY=a,this.toleranceReached=!1,this.dragContainer=this.el,this.slide=d,this.instance=u,this.el.addEventListener("mousedown",(function(e){return i.dragStart(e)}),!1),this.el.addEventListener("mouseup",(function(e){return i.dragEnd(e)}),!1),this.el.addEventListener("mousemove",(function(e){return i.drag(e)}),!1)}return n(e,[{key:"dragStart",value:function(e){if(this.slide.classList.contains("zoomed"))this.active=!1;else{"touchstart"===e.type?(this.initialX=e.touches[0].clientX-this.xOffset,this.initialY=e.touches[0].clientY-this.yOffset):(this.initialX=e.clientX-this.xOffset,this.initialY=e.clientY-this.yOffset);var t=e.target.nodeName.toLowerCase();e.target.classList.contains("nodrag")||u(e.target,".nodrag")||-1!==["input","select","textarea","button","a"].indexOf(t)?this.active=!1:(e.preventDefault(),(e.target===this.el||"img"!==t&&u(e.target,".gslide-inline"))&&(this.active=!0,this.el.classList.add("dragging"),this.dragContainer=u(e.target,".ginner-container")))}}},{key:"dragEnd",value:function(e){var t=this;e&&e.preventDefault(),this.initialX=0,this.initialY=0,this.currentX=null,this.currentY=null,this.initialX=null,this.initialY=null,this.xOffset=0,this.yOffset=0,this.active=!1,this.doSlideChange&&(this.instance.preventOutsideClick=!0,"right"==this.doSlideChange&&this.instance.prevSlide(),"left"==this.doSlideChange&&this.instance.nextSlide()),this.doSlideClose&&this.instance.close(),this.toleranceReached||this.setTranslate(this.dragContainer,0,0,!0),setTimeout((function(){t.instance.preventOutsideClick=!1,t.toleranceReached=!1,t.lastDirection=null,t.dragging=!1,t.el.isDragging=!1,t.el.classList.remove("dragging"),t.slide.classList.remove("dragging-nav"),t.dragContainer.style.transform="",t.dragContainer.style.transition=""}),100)}},{key:"drag",value:function(e){if(this.active){e.preventDefault(),this.slide.classList.add("dragging-nav"),"touchmove"===e.type?(this.currentX=e.touches[0].clientX-this.initialX,this.currentY=e.touches[0].clientY-this.initialY):(this.currentX=e.clientX-this.initialX,this.currentY=e.clientY-this.initialY),this.xOffset=this.currentX,this.yOffset=this.currentY,this.el.isDragging=!0,this.dragging=!0,this.doSlideChange=!1,this.doSlideClose=!1;var t=Math.abs(this.currentX),i=Math.abs(this.currentY);if(t>0&&t>=Math.abs(this.currentY)&&(!this.lastDirection||"x"==this.lastDirection)){this.yOffset=0,this.lastDirection="x",this.setTranslate(this.dragContainer,this.currentX,0);var n=this.shouldChange();if(!this.instance.settings.dragAutoSnap&&n&&(this.doSlideChange=n),this.instance.settings.dragAutoSnap&&n)return this.instance.preventOutsideClick=!0,this.toleranceReached=!0,this.active=!1,this.instance.preventOutsideClick=!0,this.dragEnd(null),"right"==n&&this.instance.prevSlide(),void("left"==n&&this.instance.nextSlide())}if(this.toleranceY>0&&i>0&&i>=t&&(!this.lastDirection||"y"==this.lastDirection)){this.xOffset=0,this.lastDirection="y",this.setTranslate(this.dragContainer,0,this.currentY);var s=this.shouldClose();return!this.instance.settings.dragAutoSnap&&s&&(this.doSlideClose=!0),void(this.instance.settings.dragAutoSnap&&s&&this.instance.close())}}}},{key:"shouldChange",value:function(){var e=!1;if(Math.abs(this.currentX)>=this.toleranceX){var t=this.currentX>0?"right":"left";("left"==t&&this.slide!==this.slide.parentNode.lastChild||"right"==t&&this.slide!==this.slide.parentNode.firstChild)&&(e=t)}return e}},{key:"shouldClose",value:function(){var e=!1;return Math.abs(this.currentY)>=this.toleranceY&&(e=!0),e}},{key:"setTranslate",value:function(e,t,i){var n=arguments.length>3&&void 0!==arguments[3]&&arguments[3];e.style.transition=n?"all .2s ease":"",e.style.transform="translate3d(".concat(t,"px, ").concat(i,"px, 0)")}}]),e}();function j(e,t,i,n){var s=e.querySelector(".gslide-media"),l=new Image,o="gSlideTitle_"+i,r="gSlideDesc_"+i;l.addEventListener("load",(function(){T(n)&&n()}),!1),l.src=t.href,""!=t.sizes&&""!=t.srcset&&(l.sizes=t.sizes,l.srcset=t.srcset),l.alt="",I(t.alt)||""===t.alt||(l.alt=t.alt),""!==t.title&&l.setAttribute("aria-labelledby",o),""!==t.description&&l.setAttribute("aria-describedby",r),t.hasOwnProperty("_hasCustomWidth")&&t._hasCustomWidth&&(l.style.width=t.width),t.hasOwnProperty("_hasCustomHeight")&&t._hasCustomHeight&&(l.style.height=t.height),s.insertBefore(l,s.firstChild)}function F(e,t,i,n){var s=this,l=e.querySelector(".ginner-container"),o="gvideo"+i,r=e.querySelector(".gslide-media"),a=this.getAllPlayers();h(l,"gvideo-container"),r.insertBefore(m('
    '),r.firstChild);var d=e.querySelector(".gvideo-wrapper");S(this.settings.plyr.css,"Plyr");var c=t.href,u=null==t?void 0:t.videoProvider,g=!1;r.style.maxWidth=t.width,S(this.settings.plyr.js,"Plyr",(function(){if(!u&&c.match(/vimeo\.com\/([0-9]*)/)&&(u="vimeo"),!u&&(c.match(/(youtube\.com|youtube-nocookie\.com)\/watch\?v=([a-zA-Z0-9\-_]+)/)||c.match(/youtu\.be\/([a-zA-Z0-9\-_]+)/)||c.match(/(youtube\.com|youtube-nocookie\.com)\/embed\/([a-zA-Z0-9\-_]+)/))&&(u="youtube"),"local"===u||!u){u="local";var l='")}var r=g||m('
    '));h(d,"".concat(u,"-video gvideo")),d.appendChild(r),d.setAttribute("data-id",o),d.setAttribute("data-index",i);var v=O(s.settings.plyr,"config")?s.settings.plyr.config:{},f=new Plyr("#"+o,v);f.on("ready",(function(e){a[o]=e.detail.plyr,T(n)&&n()})),b((function(){return e.querySelector("iframe")&&"true"==e.querySelector("iframe").dataset.ready}),(function(){s.resize(e)})),f.on("enterfullscreen",R),f.on("exitfullscreen",R)}))}function R(e){var t=u(e.target,".gslide-media");"enterfullscreen"===e.type&&h(t,"fullscreen"),"exitfullscreen"===e.type&&d(t,"fullscreen")}function G(e,t,i,n){var s,l=this,o=e.querySelector(".gslide-media"),r=!(!O(t,"href")||!t.href)&&t.href.split("#").pop().trim(),d=!(!O(t,"content")||!t.content)&&t.content;if(d&&(C(d)&&(s=m('
    '.concat(d,"
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t=e;if(null!==(e=e.toLowerCase()).match(/\.(jpeg|jpg|jpe|gif|png|apn|webp|avif|svg)/))return"image";if(e.match(/(youtube\.com|youtube-nocookie\.com)\/watch\?v=([a-zA-Z0-9\-_]+)/)||e.match(/youtu\.be\/([a-zA-Z0-9\-_]+)/)||e.match(/(youtube\.com|youtube-nocookie\.com)\/embed\/([a-zA-Z0-9\-_]+)/))return"video";if(e.match(/vimeo\.com\/([0-9]*)/))return"video";if(null!==e.match(/\.(mp4|ogg|webm|mov)/))return"video";if(null!==e.match(/\.(mp3|wav|wma|aac|ogg)/))return"audio";if(e.indexOf("#")>-1&&""!==t.split("#").pop().trim())return"inline";return e.indexOf("goajax=true")>-1?"ajax":"external"}},{key:"parseConfig",value:function(e,t){var i=this,n=l({descPosition:t.descPosition},this.defaults);if(L(e)&&!k(e)){O(e,"type")||(O(e,"content")&&e.content?e.type="inline":O(e,"href")&&(e.type=this.sourceType(e.href)));var s=l(n,e);return this.setSize(s,t),s}var r="",a=e.getAttribute("data-glightbox"),h=e.nodeName.toLowerCase();if("a"===h&&(r=e.href),"img"===h&&(r=e.src,n.alt=e.alt),n.href=r,o(n,(function(s,l){O(t,l)&&"width"!==l&&(n[l]=t[l]);var o=e.dataset[l];I(o)||(n[l]=i.sanitizeValue(o))})),n.content&&(n.type="inline"),!n.type&&r&&(n.type=this.sourceType(r)),I(a)){if(!n.title&&"a"==h){var d=e.title;I(d)||""===d||(n.title=d)}if(!n.title&&"img"==h){var c=e.alt;I(c)||""===c||(n.title=c)}}else{var u=[];o(n,(function(e,t){u.push(";\\s?"+t)})),u=u.join("\\s?:|"),""!==a.trim()&&o(n,(function(e,t){var s=a,l=new RegExp("s?"+t+"s?:s?(.*?)("+u+"s?:|$)"),o=s.match(l);if(o&&o.length&&o[1]){var r=o[1].trim().replace(/;\s*$/,"");n[t]=i.sanitizeValue(r)}}))}if(n.description&&"."===n.description.substring(0,1)){var g;try{g=document.querySelector(n.description).innerHTML}catch(e){if(!(e instanceof DOMException))throw e}g&&(n.description=g)}if(!n.description){var v=e.querySelector(".glightbox-desc");v&&(n.description=v.innerHTML)}return this.setSize(n,t,e),this.slideConfig=n,n}},{key:"setSize",value:function(e,t){var i=arguments.length>2&&void 0!==arguments[2]?arguments[2]:null,n="video"==e.type?this.checkSize(t.videosWidth):this.checkSize(t.width),s=this.checkSize(t.height);return e.width=O(e,"width")&&""!==e.width?this.checkSize(e.width):n,e.height=O(e,"height")&&""!==e.height?this.checkSize(e.height):s,i&&"image"==e.type&&(e._hasCustomWidth=!!i.dataset.width,e._hasCustomHeight=!!i.dataset.height),e}},{key:"checkSize",value:function(e){return M(e)?"".concat(e,"px"):e}},{key:"sanitizeValue",value:function(e){return"true"!==e&&"false"!==e?e:"true"===e}}]),e}(),$=function(){function e(i,n,s){t(this,e),this.element=i,this.instance=n,this.index=s}return n(e,[{key:"setContent",value:function(){var e=this,t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:null,i=arguments.length>1&&void 0!==arguments[1]&&arguments[1];if(c(t,"loaded"))return!1;var n=this.instance.settings,s=this.slideConfig,l=w();T(n.beforeSlideLoad)&&n.beforeSlideLoad({index:this.index,slide:t,player:!1});var o=s.type,r=s.descPosition,a=t.querySelector(".gslide-media"),d=t.querySelector(".gslide-title"),u=t.querySelector(".gslide-desc"),g=t.querySelector(".gdesc-inner"),v=i,f="gSlideTitle_"+this.index,p="gSlideDesc_"+this.index;if(T(n.afterSlideLoad)&&(v=function(){T(i)&&i(),n.afterSlideLoad({index:e.index,slide:t,player:e.instance.getSlidePlayerInstance(e.index)})}),""==s.title&&""==s.description?g&&g.parentNode.parentNode.removeChild(g.parentNode):(d&&""!==s.title?(d.id=f,d.innerHTML=s.title):d.parentNode.removeChild(d),u&&""!==s.description?(u.id=p,l&&n.moreLength>0?(s.smallDescription=this.slideShortDesc(s.description,n.moreLength,n.moreText),u.innerHTML=s.smallDescription,this.descriptionEvents(u,s)):u.innerHTML=s.description):u.parentNode.removeChild(u),h(a.parentNode,"desc-".concat(r)),h(g.parentNode,"description-".concat(r))),h(a,"gslide-".concat(o)),h(t,"loaded"),"video"!==o){if("external"!==o)return"inline"===o?(G.apply(this.instance,[t,s,this.index,v]),void(s.draggable&&new V({dragEl:t.querySelector(".gslide-inline"),toleranceX:n.dragToleranceX,toleranceY:n.dragToleranceY,slide:t,instance:this.instance}))):void("image"!==o?T(v)&&v():j(t,s,this.index,(function(){var i=t.querySelector("img");s.draggable&&new V({dragEl:i,toleranceX:n.dragToleranceX,toleranceY:n.dragToleranceY,slide:t,instance:e.instance}),s.zoomable&&i.naturalWidth>i.offsetWidth&&(h(i,"zoomable"),new H(i,t,(function(){e.instance.resize()}))),T(v)&&v()})));Z.apply(this,[t,s,this.index,v])}else F.apply(this.instance,[t,s,this.index,v])}},{key:"slideShortDesc",value:function(e){var t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:50,i=arguments.length>2&&void 0!==arguments[2]&&arguments[2],n=document.createElement("div");n.innerHTML=e;var s=n.innerText,l=i;if((e=s.trim()).length<=t)return e;var o=e.substr(0,t-1);return l?(n=null,o+'... 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n=e.getAttribute("data-gallery");n&&(this.fullElementsList=this.elements,this.elements=this.getGalleryElements(this.elements,n)),I(i)&&(i=this.getElementIndex(e))<0&&(i=0)}M(i)||(i=0),this.build(),g(this.overlay,"none"===this.settings.openEffect?"none":this.settings.cssEfects.fade.in);var s=document.body,l=window.innerWidth-document.documentElement.clientWidth;if(l>0){var o=document.createElement("style");o.type="text/css",o.className="gcss-styles",o.innerText=".gscrollbar-fixer {margin-right: ".concat(l,"px}"),document.head.appendChild(o),h(s,"gscrollbar-fixer")}h(s,"glightbox-open"),h(Q,"glightbox-open"),J&&(h(document.body,"glightbox-mobile"),this.settings.slideEffect="slide"),this.showSlide(i,!0),1===this.elements.length?(h(this.prevButton,"glightbox-button-hidden"),h(this.nextButton,"glightbox-button-hidden")):(d(this.prevButton,"glightbox-button-hidden"),d(this.nextButton,"glightbox-button-hidden")),this.lightboxOpen=!0,this.trigger("open"),T(this.settings.onOpen)&&this.settings.onOpen(),K&&this.settings.touchNavigation&&B(this),this.settings.keyboardNavigation&&X(this)}},{key:"openAt",value:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:0;this.open(null,e)}},{key:"showSlide",value:function(){var e=this,t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:0,i=arguments.length>1&&void 0!==arguments[1]&&arguments[1];f(this.loader),this.index=parseInt(t);var n=this.slidesContainer.querySelector(".current");n&&d(n,"current"),this.slideAnimateOut();var s=this.slidesContainer.querySelectorAll(".gslide")[t];if(c(s,"loaded"))this.slideAnimateIn(s,i),p(this.loader);else{f(this.loader);var l=this.elements[t],o={index:this.index,slide:s,slideNode:s,slideConfig:l.slideConfig,slideIndex:this.index,trigger:l.node,player:null};this.trigger("slide_before_load",o),l.instance.setContent(s,(function(){p(e.loader),e.resize(),e.slideAnimateIn(s,i),e.trigger("slide_after_load",o)}))}this.slideDescription=s.querySelector(".gslide-description"),this.slideDescriptionContained=this.slideDescription&&c(this.slideDescription.parentNode,"gslide-media"),this.settings.preload&&(this.preloadSlide(t+1),this.preloadSlide(t-1)),this.updateNavigationClasses(),this.activeSlide=s}},{key:"preloadSlide",value:function(e){var t=this;if(e<0||e>this.elements.length-1)return!1;if(I(this.elements[e]))return!1;var i=this.slidesContainer.querySelectorAll(".gslide")[e];if(c(i,"loaded"))return!1;var n=this.elements[e],s=n.type,l={index:e,slide:i,slideNode:i,slideConfig:n.slideConfig,slideIndex:e,trigger:n.node,player:null};this.trigger("slide_before_load",l),"video"===s||"external"===s?setTimeout((function(){n.instance.setContent(i,(function(){t.trigger("slide_after_load",l)}))}),200):n.instance.setContent(i,(function(){t.trigger("slide_after_load",l)}))}},{key:"prevSlide",value:function(){this.goToSlide(this.index-1)}},{key:"nextSlide",value:function(){this.goToSlide(this.index+1)}},{key:"goToSlide",value:function(){var e=arguments.length>0&&void 0!==arguments[0]&&arguments[0];if(this.prevActiveSlide=this.activeSlide,this.prevActiveSlideIndex=this.index,!this.loop()&&(e<0||e>this.elements.length-1))return!1;e<0?e=this.elements.length-1:e>=this.elements.length&&(e=0),this.showSlide(e)}},{key:"insertSlide",value:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:-1;t<0&&(t=this.elements.length);var i=new $(e,this,t),n=i.getConfig(),s=l({},n),o=i.create(),r=this.elements.length-1;s.index=t,s.node=!1,s.instance=i,s.slideConfig=n,this.elements.splice(t,0,s);var a=null,h=null;if(this.slidesContainer){if(t>r)this.slidesContainer.appendChild(o);else{var d=this.slidesContainer.querySelectorAll(".gslide")[t];this.slidesContainer.insertBefore(o,d)}(this.settings.preload&&0==this.index&&0==t||this.index-1==t||this.index+1==t)&&this.preloadSlide(t),0===this.index&&0===t&&(this.index=1),this.updateNavigationClasses(),a=this.slidesContainer.querySelectorAll(".gslide")[t],h=this.getSlidePlayerInstance(t),s.slideNode=a}this.trigger("slide_inserted",{index:t,slide:a,slideNode:a,slideConfig:n,slideIndex:t,trigger:null,player:h}),T(this.settings.slideInserted)&&this.settings.slideInserted({index:t,slide:a,player:h})}},{key:"removeSlide",value:function(){var e=arguments.length>0&&void 0!==arguments[0]?arguments[0]:-1;if(e<0||e>this.elements.length-1)return!1;var t=this.slidesContainer&&this.slidesContainer.querySelectorAll(".gslide")[e];t&&(this.getActiveSlideIndex()==e&&(e==this.elements.length-1?this.prevSlide():this.nextSlide()),t.parentNode.removeChild(t)),this.elements.splice(e,1),this.trigger("slide_removed",e),T(this.settings.slideRemoved)&&this.settings.slideRemoved(e)}},{key:"slideAnimateIn",value:function(e,t){var i=this,n=e.querySelector(".gslide-media"),s=e.querySelector(".gslide-description"),l={index:this.prevActiveSlideIndex,slide:this.prevActiveSlide,slideNode:this.prevActiveSlide,slideIndex:this.prevActiveSlide,slideConfig:I(this.prevActiveSlideIndex)?null:this.elements[this.prevActiveSlideIndex].slideConfig,trigger:I(this.prevActiveSlideIndex)?null:this.elements[this.prevActiveSlideIndex].node,player:this.getSlidePlayerInstance(this.prevActiveSlideIndex)},o={index:this.index,slide:this.activeSlide,slideNode:this.activeSlide,slideConfig:this.elements[this.index].slideConfig,slideIndex:this.index,trigger:this.elements[this.index].node,player:this.getSlidePlayerInstance(this.index)};if(n.offsetWidth>0&&s&&(p(s),s.style.display=""),d(e,this.effectsClasses),t)g(e,this.settings.cssEfects[this.settings.openEffect].in,(function(){i.settings.autoplayVideos&&i.slidePlayerPlay(e),i.trigger("slide_changed",{prev:l,current:o}),T(i.settings.afterSlideChange)&&i.settings.afterSlideChange.apply(i,[l,o])}));else{var r=this.settings.slideEffect,a="none"!==r?this.settings.cssEfects[r].in:r;this.prevActiveSlideIndex>this.index&&"slide"==this.settings.slideEffect&&(a=this.settings.cssEfects.slideBack.in),g(e,a,(function(){i.settings.autoplayVideos&&i.slidePlayerPlay(e),i.trigger("slide_changed",{prev:l,current:o}),T(i.settings.afterSlideChange)&&i.settings.afterSlideChange.apply(i,[l,o])}))}setTimeout((function(){i.resize(e)}),100),h(e,"current")}},{key:"slideAnimateOut",value:function(){if(!this.prevActiveSlide)return!1;var e=this.prevActiveSlide;d(e,this.effectsClasses),h(e,"prev");var t=this.settings.slideEffect,i="none"!==t?this.settings.cssEfects[t].out:t;this.slidePlayerPause(e),this.trigger("slide_before_change",{prev:{index:this.prevActiveSlideIndex,slide:this.prevActiveSlide,slideNode:this.prevActiveSlide,slideIndex:this.prevActiveSlideIndex,slideConfig:I(this.prevActiveSlideIndex)?null:this.elements[this.prevActiveSlideIndex].slideConfig,trigger:I(this.prevActiveSlideIndex)?null:this.elements[this.prevActiveSlideIndex].node,player:this.getSlidePlayerInstance(this.prevActiveSlideIndex)},current:{index:this.index,slide:this.activeSlide,slideNode:this.activeSlide,slideIndex:this.index,slideConfig:this.elements[this.index].slideConfig,trigger:this.elements[this.index].node,player:this.getSlidePlayerInstance(this.index)}}),T(this.settings.beforeSlideChange)&&this.settings.beforeSlideChange.apply(this,[{index:this.prevActiveSlideIndex,slide:this.prevActiveSlide,player:this.getSlidePlayerInstance(this.prevActiveSlideIndex)},{index:this.index,slide:this.activeSlide,player:this.getSlidePlayerInstance(this.index)}]),this.prevActiveSlideIndex>this.index&&"slide"==this.settings.slideEffect&&(i=this.settings.cssEfects.slideBack.out),g(e,i,(function(){var t=e.querySelector(".ginner-container"),i=e.querySelector(".gslide-media"),n=e.querySelector(".gslide-description");t.style.transform="",i.style.transform="",d(i,"greset"),i.style.opacity="",n&&(n.style.opacity=""),d(e,"prev")}))}},{key:"getAllPlayers",value:function(){return this.videoPlayers}},{key:"getSlidePlayerInstance",value:function(e){var t="gvideo"+e,i=this.getAllPlayers();return!(!O(i,t)||!i[t])&&i[t]}},{key:"stopSlideVideo",value:function(e){if(k(e)){var t=e.querySelector(".gvideo-wrapper");t&&(e=t.getAttribute("data-index"))}console.log("stopSlideVideo is deprecated, use slidePlayerPause");var i=this.getSlidePlayerInstance(e);i&&i.playing&&i.pause()}},{key:"slidePlayerPause",value:function(e){if(k(e)){var t=e.querySelector(".gvideo-wrapper");t&&(e=t.getAttribute("data-index"))}var i=this.getSlidePlayerInstance(e);i&&i.playing&&i.pause()}},{key:"playSlideVideo",value:function(e){if(k(e)){var t=e.querySelector(".gvideo-wrapper");t&&(e=t.getAttribute("data-index"))}console.log("playSlideVideo is deprecated, use slidePlayerPlay");var i=this.getSlidePlayerInstance(e);i&&!i.playing&&i.play()}},{key:"slidePlayerPlay",value:function(e){var t;if(!J||null!==(t=this.settings.plyr.config)&&void 0!==t&&t.muted){if(k(e)){var i=e.querySelector(".gvideo-wrapper");i&&(e=i.getAttribute("data-index"))}var n=this.getSlidePlayerInstance(e);n&&!n.playing&&(n.play(),this.settings.autofocusVideos&&n.elements.container.focus())}}},{key:"setElements",value:function(e){var t=this;this.settings.elements=!1;var i=[];e&&e.length&&o(e,(function(e,n){var s=new $(e,t,n),o=s.getConfig(),r=l({},o);r.slideConfig=o,r.instance=s,r.index=n,i.push(r)})),this.elements=i,this.lightboxOpen&&(this.slidesContainer.innerHTML="",this.elements.length&&(o(this.elements,(function(){var e=m(t.settings.slideHTML);t.slidesContainer.appendChild(e)})),this.showSlide(0,!0)))}},{key:"getElementIndex",value:function(e){var t=!1;return o(this.elements,(function(i,n){if(O(i,"node")&&i.node==e)return t=n,!0})),t}},{key:"getElements",value:function(){var e=this,t=[];this.elements=this.elements?this.elements:[],!I(this.settings.elements)&&E(this.settings.elements)&&this.settings.elements.length&&o(this.settings.elements,(function(i,n){var s=new $(i,e,n),o=s.getConfig(),r=l({},o);r.node=!1,r.index=n,r.instance=s,r.slideConfig=o,t.push(r)}));var i=!1;return this.getSelector()&&(i=document.querySelectorAll(this.getSelector())),i?(o(i,(function(i,n){var s=new $(i,e,n),o=s.getConfig(),r=l({},o);r.node=i,r.index=n,r.instance=s,r.slideConfig=o,r.gallery=i.getAttribute("data-gallery"),t.push(r)})),t):t}},{key:"getGalleryElements",value:function(e,t){return e.filter((function(e){return 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n=O(this.settings.svg,"next")?this.settings.svg.next:"",s=O(this.settings.svg,"prev")?this.settings.svg.prev:"",l=O(this.settings.svg,"close")?this.settings.svg.close:"",r=this.settings.lightboxHTML;r=m(r=(r=(r=r.replace(/{nextSVG}/g,n)).replace(/{prevSVG}/g,s)).replace(/{closeSVG}/g,l)),document.body.appendChild(r);var d=document.getElementById("glightbox-body");this.modal=d;var 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t=e.state,n=e.name,r=t.rects.reference,o=t.rects.popper,i=t.modifiersData.preventOverflow,a=J(t,{elementContext:"reference"}),s=J(t,{altBoundary:!0}),f=ve(a,r),c=ve(s,o,i),p=ye(f),u=ye(c);t.modifiersData[n]={referenceClippingOffsets:f,popperEscapeOffsets:c,isReferenceHidden:p,hasPopperEscaped:u},t.attributes.popper=Object.assign({},t.attributes.popper,{"data-popper-reference-hidden":p,"data-popper-escaped":u})}},be=Z({defaultModifiers:[ee,te,oe,ie]}),xe=[ee,te,oe,ie,ae,le,he,me,ge],we=Z({defaultModifiers:xe});e.applyStyles=ie,e.arrow=me,e.computeStyles=oe,e.createPopper=we,e.createPopperLite=be,e.defaultModifiers=xe,e.detectOverflow=J,e.eventListeners=ee,e.flip=le,e.hide=ge,e.offset=ae,e.popperGenerator=Z,e.popperOffsets=te,e.preventOverflow=he,Object.defineProperty(e,"__esModule",{value:!0})})); + diff --git a/site_libs/quarto-html/quarto-syntax-highlighting-dark.css b/site_libs/quarto-html/quarto-syntax-highlighting-dark.css new file mode 100644 index 0000000..343d2f8 --- /dev/null +++ b/site_libs/quarto-html/quarto-syntax-highlighting-dark.css @@ -0,0 +1,189 @@ +/* quarto syntax highlight colors */ +:root { + --quarto-hl-al-color: #f07178; + --quarto-hl-an-color: #d4d0ab; + --quarto-hl-at-color: #00e0e0; + --quarto-hl-bn-color: #d4d0ab; + --quarto-hl-bu-color: #abe338; + --quarto-hl-ch-color: #abe338; + --quarto-hl-co-color: #f8f8f2; + --quarto-hl-cv-color: #ffd700; + --quarto-hl-cn-color: #ffd700; + --quarto-hl-cf-color: #ffa07a; + --quarto-hl-dt-color: #ffa07a; + --quarto-hl-dv-color: #d4d0ab; + --quarto-hl-do-color: #f8f8f2; + --quarto-hl-er-color: #f07178; + --quarto-hl-ex-color: #00e0e0; + --quarto-hl-fl-color: #d4d0ab; + --quarto-hl-fu-color: #ffa07a; + --quarto-hl-im-color: #abe338; + --quarto-hl-in-color: #d4d0ab; + --quarto-hl-kw-color: #ffa07a; + --quarto-hl-op-color: #ffa07a; + --quarto-hl-ot-color: #00e0e0; + --quarto-hl-pp-color: #dcc6e0; + --quarto-hl-re-color: #00e0e0; + --quarto-hl-sc-color: #abe338; + --quarto-hl-ss-color: #abe338; + --quarto-hl-st-color: #abe338; + --quarto-hl-va-color: #00e0e0; + --quarto-hl-vs-color: #abe338; + --quarto-hl-wa-color: #dcc6e0; +} + +/* other quarto variables */ +:root { + --quarto-font-monospace: SFMono-Regular, Menlo, Monaco, Consolas, "Liberation Mono", "Courier New", monospace; +} + +code span.al { + background-color: #2a0f15; + font-weight: bold; + color: #f07178; +} + +code span.an { + color: #d4d0ab; +} + +code span.at { + color: #00e0e0; +} + +code span.bn { + color: #d4d0ab; +} + +code span.bu { + color: #abe338; +} + +code span.ch { + color: #abe338; +} + +code span.co { + font-style: italic; + color: #f8f8f2; +} + +code span.cv { + color: #ffd700; +} + +code span.cn { + color: #ffd700; +} + +code span.cf { + font-weight: bold; + color: #ffa07a; +} + +code span.dt { + color: #ffa07a; +} + +code span.dv { + color: #d4d0ab; +} + +code span.do { + color: #f8f8f2; +} + +code span.er { + color: #f07178; + text-decoration: underline; +} + +code span.ex { + font-weight: bold; + color: #00e0e0; +} + +code span.fl { + color: #d4d0ab; +} + +code span.fu { + color: #ffa07a; +} + +code span.im { + color: #abe338; +} + +code span.in { + color: #d4d0ab; +} + +code span.kw { + font-weight: bold; + color: #ffa07a; +} + +pre > code.sourceCode > span { + color: #f8f8f2; +} + +code span { + color: #f8f8f2; +} + +code.sourceCode > span { + color: #f8f8f2; +} + +div.sourceCode, +div.sourceCode pre.sourceCode { + color: #f8f8f2; +} + +code span.op { + color: #ffa07a; +} + +code span.ot { + color: #00e0e0; +} + +code span.pp { + color: #dcc6e0; +} + +code span.re { + background-color: #f8f8f2; + color: #00e0e0; +} + +code span.sc { + color: #abe338; +} + +code span.ss { + color: #abe338; +} + +code span.st { + color: #abe338; +} + +code span.va { + color: #00e0e0; +} + +code span.vs { + color: #abe338; +} + +code span.wa { + color: #dcc6e0; +} + +.prevent-inlining { + content: " code.sourceCode > span { + color: #003B4F; +} + +code span { + color: #003B4F; +} + +code.sourceCode > span { + color: #003B4F; +} + +div.sourceCode, +div.sourceCode pre.sourceCode { + color: #003B4F; +} + +code span.ot { + color: #003B4F; + font-style: inherit; +} + +code span.at { + color: #657422; + font-style: inherit; +} + +code span.ss { + color: #20794D; + font-style: inherit; +} + +code span.an { + color: #5E5E5E; + font-style: inherit; +} + +code span.fu { + color: #4758AB; + font-style: inherit; +} + +code span.st { + color: #20794D; + font-style: inherit; +} + +code span.cf { + color: #003B4F; + font-style: inherit; +} + +code span.op { + color: #5E5E5E; + font-style: inherit; +} + +code span.er { + color: #AD0000; + font-style: inherit; +} + +code span.bn { + color: #AD0000; + font-style: inherit; +} + +code span.al { + color: #AD0000; + font-style: inherit; +} + +code span.va { + color: #111111; + font-style: inherit; +} + +code span.bu { + font-style: inherit; +} + +code span.ex { + font-style: inherit; +} + +code span.pp { + color: #AD0000; + font-style: inherit; +} + +code span.in { + color: #5E5E5E; + font-style: inherit; +} + +code span.vs { + color: #20794D; + font-style: inherit; +} + +code span.wa { + color: #5E5E5E; + font-style: italic; +} + +code span.do { + color: #5E5E5E; + font-style: italic; +} + +code span.im { + color: #00769E; + font-style: inherit; +} + +code span.ch { + color: #20794D; + font-style: inherit; +} + +code span.dt { + color: #AD0000; + font-style: inherit; +} + +code span.fl { + color: #AD0000; + font-style: inherit; +} + +code span.co { + color: #5E5E5E; + font-style: inherit; +} + +code span.cv { + color: #5E5E5E; + font-style: italic; +} + +code span.cn { + color: #8f5902; + font-style: inherit; +} + +code span.sc { + color: #5E5E5E; + font-style: inherit; +} + +code span.dv { + color: #AD0000; + font-style: inherit; +} + +code span.kw { + color: #003B4F; + font-style: inherit; +} + +.prevent-inlining { + content: " { + // Find any conflicting margin elements and add margins to the + // top to prevent overlap + const marginChildren = window.document.querySelectorAll( + ".column-margin.column-container > *, .margin-caption, .aside" + ); + + let lastBottom = 0; + for (const marginChild of marginChildren) { + if (marginChild.offsetParent !== null) { + // clear the top margin so we recompute it + marginChild.style.marginTop = null; + const top = marginChild.getBoundingClientRect().top + window.scrollY; + if (top < lastBottom) { + const marginChildStyle = window.getComputedStyle(marginChild); + const marginBottom = parseFloat(marginChildStyle["marginBottom"]); + const margin = lastBottom - top + marginBottom; + marginChild.style.marginTop = `${margin}px`; + } + const styles = window.getComputedStyle(marginChild); + const marginTop = parseFloat(styles["marginTop"]); + lastBottom = top + marginChild.getBoundingClientRect().height + marginTop; + } + } +}; + +window.document.addEventListener("DOMContentLoaded", function (_event) { + // Recompute the position of margin elements anytime the body size changes + if (window.ResizeObserver) { + const resizeObserver = new window.ResizeObserver( + throttle(() => { + layoutMarginEls(); + if ( + window.document.body.getBoundingClientRect().width < 990 && + isReaderMode() + ) { + quartoToggleReader(); + } + }, 50) + ); + resizeObserver.observe(window.document.body); + } + + const tocEl = window.document.querySelector('nav.toc-active[role="doc-toc"]'); + const sidebarEl = window.document.getElementById("quarto-sidebar"); + const leftTocEl = window.document.getElementById("quarto-sidebar-toc-left"); + const marginSidebarEl = window.document.getElementById( + "quarto-margin-sidebar" + ); + // function to determine whether the element has a previous sibling that is active + const prevSiblingIsActiveLink = (el) => { + const sibling = el.previousElementSibling; + if (sibling && sibling.tagName === "A") { + return sibling.classList.contains("active"); + } else { + return false; + } + }; + + // fire slideEnter for bootstrap tab activations (for htmlwidget resize behavior) + function fireSlideEnter(e) { + const event = window.document.createEvent("Event"); + event.initEvent("slideenter", true, true); + window.document.dispatchEvent(event); + } + const tabs = window.document.querySelectorAll('a[data-bs-toggle="tab"]'); + tabs.forEach((tab) => { + tab.addEventListener("shown.bs.tab", fireSlideEnter); + }); + + // fire slideEnter for tabby tab activations (for htmlwidget resize behavior) + document.addEventListener("tabby", fireSlideEnter, false); + + // Track scrolling and mark TOC links as active + // get table of contents and sidebar (bail if we don't have at least one) + const tocLinks = tocEl + ? [...tocEl.querySelectorAll("a[data-scroll-target]")] + : []; + const makeActive = (link) => tocLinks[link].classList.add("active"); + const removeActive = (link) => tocLinks[link].classList.remove("active"); + const removeAllActive = () => + [...Array(tocLinks.length).keys()].forEach((link) => removeActive(link)); + + // activate the anchor for a section associated with this TOC entry + tocLinks.forEach((link) => { + link.addEventListener("click", () => { + if (link.href.indexOf("#") !== -1) { + const anchor = link.href.split("#")[1]; + const heading = window.document.querySelector( + `[data-anchor-id=${anchor}]` + ); + if (heading) { + // Add the class + heading.classList.add("reveal-anchorjs-link"); + + // function to show the anchor + const handleMouseout = () => { + heading.classList.remove("reveal-anchorjs-link"); + heading.removeEventListener("mouseout", handleMouseout); + }; + + // add a function to clear the anchor when the user mouses out of it + heading.addEventListener("mouseout", handleMouseout); + } + } + }); + }); + + const sections = tocLinks.map((link) => { + const target = link.getAttribute("data-scroll-target"); + if (target.startsWith("#")) { + return window.document.getElementById(decodeURI(`${target.slice(1)}`)); + } else { + return window.document.querySelector(decodeURI(`${target}`)); + } + }); + + const sectionMargin = 200; + let currentActive = 0; + // track whether we've initialized state the first time + let init = false; + + const updateActiveLink = () => { + // The index from bottom to top (e.g. reversed list) + let sectionIndex = -1; + if ( + window.innerHeight + window.pageYOffset >= + window.document.body.offsetHeight + ) { + sectionIndex = 0; + } else { + sectionIndex = [...sections].reverse().findIndex((section) => { + if (section) { + return window.pageYOffset >= section.offsetTop - sectionMargin; + } else { + return false; + } + }); + } + if (sectionIndex > -1) { + const current = sections.length - sectionIndex - 1; + if (current !== currentActive) { + removeAllActive(); + currentActive = current; + makeActive(current); + if (init) { + window.dispatchEvent(sectionChanged); + } + init = true; + } + } + }; + + const inHiddenRegion = (top, bottom, hiddenRegions) => { + for (const region of hiddenRegions) { + if (top <= region.bottom && bottom >= region.top) { + return true; + } + } + return false; + }; + + const categorySelector = "header.quarto-title-block .quarto-category"; + const activateCategories = (href) => { + // Find any categories + // Surround them with a link pointing back to: + // #category=Authoring + try { + const categoryEls = window.document.querySelectorAll(categorySelector); + for (const categoryEl of categoryEls) { + const categoryText = categoryEl.textContent; + if (categoryText) { + const link = `${href}#category=${encodeURIComponent(categoryText)}`; + const linkEl = window.document.createElement("a"); + linkEl.setAttribute("href", link); + for (const child of categoryEl.childNodes) { + linkEl.append(child); + } + categoryEl.appendChild(linkEl); + } + } + } catch { + // Ignore errors + } + }; + function hasTitleCategories() { + return window.document.querySelector(categorySelector) !== null; + } + + function offsetRelativeUrl(url) { + const offset = getMeta("quarto:offset"); + return offset ? offset + url : url; + } + + function offsetAbsoluteUrl(url) { + const offset = getMeta("quarto:offset"); + const baseUrl = new URL(offset, window.location); + + const projRelativeUrl = url.replace(baseUrl, ""); + if (projRelativeUrl.startsWith("/")) { + return projRelativeUrl; + } else { + return "/" + projRelativeUrl; + } + } + + // read a meta tag value + function getMeta(metaName) { + const metas = window.document.getElementsByTagName("meta"); + for (let i = 0; i < metas.length; i++) { + if (metas[i].getAttribute("name") === metaName) { + return metas[i].getAttribute("content"); + } + } + return ""; + } + + async function findAndActivateCategories() { + const currentPagePath = offsetAbsoluteUrl(window.location.href); + const response = await fetch(offsetRelativeUrl("listings.json")); + if (response.status == 200) { + return response.json().then(function (listingPaths) { + const listingHrefs = []; + for (const listingPath of listingPaths) { + const pathWithoutLeadingSlash = listingPath.listing.substring(1); + for (const item of listingPath.items) { + if ( + item === currentPagePath || + item === currentPagePath + "index.html" + ) { + // Resolve this path against the offset to be sure + // we already are using the correct path to the listing + // (this adjusts the listing urls to be rooted against + // whatever root the page is actually running against) + const relative = offsetRelativeUrl(pathWithoutLeadingSlash); + const baseUrl = window.location; + const resolvedPath = new URL(relative, baseUrl); + listingHrefs.push(resolvedPath.pathname); + break; + } + } + } + + // Look up the tree for a nearby linting and use that if we find one + const nearestListing = findNearestParentListing( + offsetAbsoluteUrl(window.location.pathname), + listingHrefs + ); + if (nearestListing) { + activateCategories(nearestListing); + } else { + // See if the referrer is a listing page for this item + const referredRelativePath = offsetAbsoluteUrl(document.referrer); + const referrerListing = listingHrefs.find((listingHref) => { + const isListingReferrer = + listingHref === referredRelativePath || + listingHref === referredRelativePath + "index.html"; + return isListingReferrer; + }); + + if (referrerListing) { + // Try to use the referrer if possible + activateCategories(referrerListing); + } else if (listingHrefs.length > 0) { + // Otherwise, just fall back to the first listing + activateCategories(listingHrefs[0]); + } + } + }); + } + } + if (hasTitleCategories()) { + findAndActivateCategories(); + } + + const findNearestParentListing = (href, listingHrefs) => { + if (!href || !listingHrefs) { + return undefined; + } + // Look up the tree for a nearby linting and use that if we find one + const relativeParts = href.substring(1).split("/"); + while (relativeParts.length > 0) { + const path = relativeParts.join("/"); + for (const listingHref of listingHrefs) { + if (listingHref.startsWith(path)) { + return listingHref; + } + } + relativeParts.pop(); + } + + return undefined; + }; + + const manageSidebarVisiblity = (el, placeholderDescriptor) => { + let isVisible = true; + let elRect; + + return (hiddenRegions) => { + if (el === null) { + return; + } + + // Find the last element of the TOC + const lastChildEl = el.lastElementChild; + + if (lastChildEl) { + // Converts the sidebar to a menu + const convertToMenu = () => { + for (const child of el.children) { + child.style.opacity = 0; + child.style.overflow = "hidden"; + } + + nexttick(() => { + const toggleContainer = window.document.createElement("div"); + toggleContainer.style.width = "100%"; + toggleContainer.classList.add("zindex-over-content"); + toggleContainer.classList.add("quarto-sidebar-toggle"); + toggleContainer.classList.add("headroom-target"); // Marks this to be managed by headeroom + toggleContainer.id = placeholderDescriptor.id; + toggleContainer.style.position = "fixed"; + + const toggleIcon = window.document.createElement("i"); + toggleIcon.classList.add("quarto-sidebar-toggle-icon"); + toggleIcon.classList.add("bi"); + toggleIcon.classList.add("bi-caret-down-fill"); + + const toggleTitle = window.document.createElement("div"); + const titleEl = window.document.body.querySelector( + placeholderDescriptor.titleSelector + ); + if (titleEl) { + toggleTitle.append( + titleEl.textContent || titleEl.innerText, + toggleIcon + ); + } + toggleTitle.classList.add("zindex-over-content"); + toggleTitle.classList.add("quarto-sidebar-toggle-title"); + toggleContainer.append(toggleTitle); + + const toggleContents = window.document.createElement("div"); + toggleContents.classList = el.classList; + toggleContents.classList.add("zindex-over-content"); + toggleContents.classList.add("quarto-sidebar-toggle-contents"); + for (const child of el.children) { + if (child.id === "toc-title") { + continue; + } + + const clone = child.cloneNode(true); + clone.style.opacity = 1; + clone.style.display = null; + toggleContents.append(clone); + } + toggleContents.style.height = "0px"; + const positionToggle = () => { + // position the element (top left of parent, same width as parent) + if (!elRect) { + elRect = el.getBoundingClientRect(); + } + toggleContainer.style.left = `${elRect.left}px`; + toggleContainer.style.top = `${elRect.top}px`; + toggleContainer.style.width = `${elRect.width}px`; + }; + positionToggle(); + + toggleContainer.append(toggleContents); + el.parentElement.prepend(toggleContainer); + + // Process clicks + let tocShowing = false; + // Allow the caller to control whether this is dismissed + // when it is clicked (e.g. sidebar navigation supports + // opening and closing the nav tree, so don't dismiss on click) + const clickEl = placeholderDescriptor.dismissOnClick + ? toggleContainer + : toggleTitle; + + const closeToggle = () => { + if (tocShowing) { + toggleContainer.classList.remove("expanded"); + toggleContents.style.height = "0px"; + tocShowing = false; + } + }; + + // Get rid of any expanded toggle if the user scrolls + window.document.addEventListener( + "scroll", + throttle(() => { + closeToggle(); + }, 50) + ); + + // Handle positioning of the toggle + window.addEventListener( + "resize", + throttle(() => { + elRect = undefined; + positionToggle(); + }, 50) + ); + + window.addEventListener("quarto-hrChanged", () => { + elRect = undefined; + }); + + // Process the click + clickEl.onclick = () => { + if (!tocShowing) { + toggleContainer.classList.add("expanded"); + toggleContents.style.height = null; + tocShowing = true; + } else { + closeToggle(); + } + }; + }); + }; + + // Converts a sidebar from a menu back to a sidebar + const convertToSidebar = () => { + for (const child of el.children) { + child.style.opacity = 1; + child.style.overflow = null; + } + + const placeholderEl = window.document.getElementById( + placeholderDescriptor.id + ); + if (placeholderEl) { + placeholderEl.remove(); + } + + el.classList.remove("rollup"); + }; + + if (isReaderMode()) { + convertToMenu(); + isVisible = false; + } else { + // Find the top and bottom o the element that is being managed + const elTop = el.offsetTop; + const elBottom = + elTop + lastChildEl.offsetTop + lastChildEl.offsetHeight; + + if (!isVisible) { + // If the element is current not visible reveal if there are + // no conflicts with overlay regions + if (!inHiddenRegion(elTop, elBottom, hiddenRegions)) { + convertToSidebar(); + isVisible = true; + } + } else { + // If the element is visible, hide it if it conflicts with overlay regions + // and insert a placeholder toggle (or if we're in reader mode) + if (inHiddenRegion(elTop, elBottom, hiddenRegions)) { + convertToMenu(); + isVisible = false; + } + } + } + } + }; + }; + + const tabEls = document.querySelectorAll('a[data-bs-toggle="tab"]'); + for (const tabEl of tabEls) { + const id = tabEl.getAttribute("data-bs-target"); + if (id) { + const columnEl = document.querySelector( + `${id} .column-margin, .tabset-margin-content` + ); + if (columnEl) + tabEl.addEventListener("shown.bs.tab", function (event) { + const el = event.srcElement; + if (el) { + const visibleCls = `${el.id}-margin-content`; + // walk up until we find a parent tabset + let panelTabsetEl = el.parentElement; + while (panelTabsetEl) { + if (panelTabsetEl.classList.contains("panel-tabset")) { + break; + } + panelTabsetEl = panelTabsetEl.parentElement; + } + + if (panelTabsetEl) { + const prevSib = panelTabsetEl.previousElementSibling; + if ( + prevSib && + prevSib.classList.contains("tabset-margin-container") + ) { + const childNodes = prevSib.querySelectorAll( + ".tabset-margin-content" + ); + for (const childEl of childNodes) { + if (childEl.classList.contains(visibleCls)) { + childEl.classList.remove("collapse"); + } else { + childEl.classList.add("collapse"); + } + } + } + } + } + + layoutMarginEls(); + }); + } + } + + // Manage the visibility of the toc and the sidebar + const marginScrollVisibility = manageSidebarVisiblity(marginSidebarEl, { + id: "quarto-toc-toggle", + titleSelector: "#toc-title", + dismissOnClick: true, + }); + const sidebarScrollVisiblity = manageSidebarVisiblity(sidebarEl, { + id: "quarto-sidebarnav-toggle", + titleSelector: ".title", + dismissOnClick: false, + }); + let tocLeftScrollVisibility; + if (leftTocEl) { + tocLeftScrollVisibility = manageSidebarVisiblity(leftTocEl, { + id: "quarto-lefttoc-toggle", + titleSelector: "#toc-title", + dismissOnClick: true, + }); + } + + // Find the first element that uses formatting in special columns + const conflictingEls = window.document.body.querySelectorAll( + '[class^="column-"], [class*=" column-"], aside, [class*="margin-caption"], [class*=" margin-caption"], [class*="margin-ref"], [class*=" margin-ref"]' + ); + + // Filter all the possibly conflicting elements into ones + // the do conflict on the left or ride side + const arrConflictingEls = Array.from(conflictingEls); + const leftSideConflictEls = arrConflictingEls.filter((el) => { + if (el.tagName === "ASIDE") { + return false; + } + return Array.from(el.classList).find((className) => { + return ( + className !== "column-body" && + className.startsWith("column-") && + !className.endsWith("right") && + !className.endsWith("container") && + className !== "column-margin" + ); + }); + }); + const rightSideConflictEls = arrConflictingEls.filter((el) => { + if (el.tagName === "ASIDE") { + return true; + } + + const hasMarginCaption = Array.from(el.classList).find((className) => { + return className == "margin-caption"; + }); + if (hasMarginCaption) { + return true; + } + + return Array.from(el.classList).find((className) => { + return ( + className !== "column-body" && + !className.endsWith("container") && + className.startsWith("column-") && + !className.endsWith("left") + ); + }); + }); + + const kOverlapPaddingSize = 10; + function toRegions(els) { + return els.map((el) => { + const boundRect = el.getBoundingClientRect(); + const top = + boundRect.top + + document.documentElement.scrollTop - + kOverlapPaddingSize; + return { + top, + bottom: top + el.scrollHeight + 2 * kOverlapPaddingSize, + }; + }); + } + + let hasObserved = false; + const visibleItemObserver = (els) => { + let visibleElements = [...els]; + const intersectionObserver = new IntersectionObserver( + (entries, _observer) => { + entries.forEach((entry) => { + if (entry.isIntersecting) { + if (visibleElements.indexOf(entry.target) === -1) { + visibleElements.push(entry.target); + } + } else { + visibleElements = visibleElements.filter((visibleEntry) => { + return visibleEntry !== entry; + }); + } + }); + + if (!hasObserved) { + hideOverlappedSidebars(); + } + hasObserved = true; + }, + {} + ); + els.forEach((el) => { + intersectionObserver.observe(el); + }); + + return { + getVisibleEntries: () => { + return visibleElements; + }, + }; + }; + + const rightElementObserver = visibleItemObserver(rightSideConflictEls); + const leftElementObserver = visibleItemObserver(leftSideConflictEls); + + const hideOverlappedSidebars = () => { + marginScrollVisibility(toRegions(rightElementObserver.getVisibleEntries())); + sidebarScrollVisiblity(toRegions(leftElementObserver.getVisibleEntries())); + if (tocLeftScrollVisibility) { + tocLeftScrollVisibility( + toRegions(leftElementObserver.getVisibleEntries()) + ); + } + }; + + window.quartoToggleReader = () => { + // Applies a slow class (or removes it) + // to update the transition speed + const slowTransition = (slow) => { + const manageTransition = (id, slow) => { + const el = document.getElementById(id); + if (el) { + if (slow) { + el.classList.add("slow"); + } else { + el.classList.remove("slow"); + } + } + }; + + manageTransition("TOC", slow); + manageTransition("quarto-sidebar", slow); + }; + const readerMode = !isReaderMode(); + setReaderModeValue(readerMode); + + // If we're entering reader mode, slow the transition + if (readerMode) { + slowTransition(readerMode); + } + highlightReaderToggle(readerMode); + hideOverlappedSidebars(); + + // If we're exiting reader mode, restore the non-slow transition + if (!readerMode) { + slowTransition(!readerMode); + } + }; + + const highlightReaderToggle = (readerMode) => { + const els = document.querySelectorAll(".quarto-reader-toggle"); + if (els) { + els.forEach((el) => { + if (readerMode) { + el.classList.add("reader"); + } else { + el.classList.remove("reader"); + } + }); + } + }; + + const setReaderModeValue = (val) => { + if (window.location.protocol !== "file:") { + window.localStorage.setItem("quarto-reader-mode", val); + } else { + localReaderMode = val; + } + }; + + const isReaderMode = () => { + if (window.location.protocol !== "file:") { + return window.localStorage.getItem("quarto-reader-mode") === "true"; + } else { + return localReaderMode; + } + }; + let localReaderMode = null; + + const tocOpenDepthStr = tocEl?.getAttribute("data-toc-expanded"); + const tocOpenDepth = tocOpenDepthStr ? Number(tocOpenDepthStr) : 1; + + // Walk the TOC and collapse/expand nodes + // Nodes are expanded if: + // - they are top level + // - they have children that are 'active' links + // - they are directly below an link that is 'active' + const walk = (el, depth) => { + // Tick depth when we enter a UL + if (el.tagName === "UL") { + depth = depth + 1; + } + + // It this is active link + let isActiveNode = false; + if (el.tagName === "A" && el.classList.contains("active")) { + isActiveNode = true; + } + + // See if there is an active child to this element + let hasActiveChild = false; + for (child of el.children) { + hasActiveChild = walk(child, depth) || hasActiveChild; + } + + // Process the collapse state if this is an UL + if (el.tagName === "UL") { + if (tocOpenDepth === -1 && depth > 1) { + el.classList.add("collapse"); + } else if ( + depth <= tocOpenDepth || + hasActiveChild || + prevSiblingIsActiveLink(el) + ) { + el.classList.remove("collapse"); + } else { + el.classList.add("collapse"); + } + + // untick depth when we leave a UL + depth = depth - 1; + } + return hasActiveChild || isActiveNode; + }; + + // walk the TOC and expand / collapse any items that should be shown + + if (tocEl) { + walk(tocEl, 0); + updateActiveLink(); + } + + // Throttle the scroll event and walk peridiocally + window.document.addEventListener( + "scroll", + throttle(() => { + if (tocEl) { + updateActiveLink(); + walk(tocEl, 0); + } + if (!isReaderMode()) { + hideOverlappedSidebars(); + } + }, 5) + ); + window.addEventListener( + "resize", + throttle(() => { + if (!isReaderMode()) { + hideOverlappedSidebars(); + } + }, 10) + ); + hideOverlappedSidebars(); + highlightReaderToggle(isReaderMode()); +}); + +// grouped tabsets +window.addEventListener("pageshow", (_event) => { + function getTabSettings() { + const data = localStorage.getItem("quarto-persistent-tabsets-data"); + if (!data) { + localStorage.setItem("quarto-persistent-tabsets-data", "{}"); + return {}; + } + if (data) { + return JSON.parse(data); + } + } + + function setTabSettings(data) { + localStorage.setItem( + "quarto-persistent-tabsets-data", + JSON.stringify(data) + ); + } + + function setTabState(groupName, groupValue) { + const data = getTabSettings(); + data[groupName] = groupValue; + setTabSettings(data); + } + + function toggleTab(tab, active) { + const tabPanelId = tab.getAttribute("aria-controls"); + const tabPanel = document.getElementById(tabPanelId); + if (active) { + tab.classList.add("active"); + tabPanel.classList.add("active"); + } else { + tab.classList.remove("active"); + tabPanel.classList.remove("active"); + } + } + + function toggleAll(selectedGroup, selectorsToSync) { + for (const [thisGroup, tabs] of Object.entries(selectorsToSync)) { + const active = selectedGroup === thisGroup; + for (const tab of tabs) { + toggleTab(tab, active); + } + } + } + + function findSelectorsToSyncByLanguage() { + const result = {}; + const tabs = Array.from( + document.querySelectorAll(`div[data-group] a[id^='tabset-']`) + ); + for (const item of tabs) { + const div = item.parentElement.parentElement.parentElement; + const group = div.getAttribute("data-group"); + if (!result[group]) { + result[group] = {}; + } + const selectorsToSync = result[group]; + const value = item.innerHTML; + if (!selectorsToSync[value]) { + selectorsToSync[value] = []; + } + selectorsToSync[value].push(item); + } + return result; + } + + function setupSelectorSync() { + const selectorsToSync = findSelectorsToSyncByLanguage(); + Object.entries(selectorsToSync).forEach(([group, tabSetsByValue]) => { + Object.entries(tabSetsByValue).forEach(([value, items]) => { + items.forEach((item) => { + item.addEventListener("click", (_event) => { + setTabState(group, value); + toggleAll(value, selectorsToSync[group]); + }); + }); + }); + }); + return selectorsToSync; + } + + const selectorsToSync = setupSelectorSync(); + for (const [group, selectedName] of Object.entries(getTabSettings())) { + const selectors = selectorsToSync[group]; + // it's possible that stale state gives us empty selections, so we explicitly check here. + if (selectors) { + toggleAll(selectedName, selectors); + } + } +}); + +function throttle(func, wait) { + let waiting = false; + return function () { + if (!waiting) { + func.apply(this, arguments); + waiting = true; + setTimeout(function () { + waiting = false; + }, wait); + } + }; +} + +function nexttick(func) { + return setTimeout(func, 0); +} diff --git a/site_libs/quarto-html/tippy.css b/site_libs/quarto-html/tippy.css new file mode 100644 index 0000000..e6ae635 --- /dev/null +++ b/site_libs/quarto-html/tippy.css @@ -0,0 +1 @@ +.tippy-box[data-animation=fade][data-state=hidden]{opacity:0}[data-tippy-root]{max-width:calc(100vw - 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b/site_libs/quarto-listing/list.min.js new file mode 100644 index 0000000..8131881 --- /dev/null +++ b/site_libs/quarto-listing/list.min.js @@ -0,0 +1,2 @@ +var List;List=function(){var t={"./src/add-async.js":function(t){t.exports=function(t){return function e(r,n,s){var i=r.splice(0,50);s=(s=s||[]).concat(t.add(i)),r.length>0?setTimeout((function(){e(r,n,s)}),1):(t.update(),n(s))}}},"./src/filter.js":function(t){t.exports=function(t){return t.handlers.filterStart=t.handlers.filterStart||[],t.handlers.filterComplete=t.handlers.filterComplete||[],function(e){if(t.trigger("filterStart"),t.i=1,t.reset.filter(),void 0===e)t.filtered=!1;else{t.filtered=!0;for(var r=t.items,n=0,s=r.length;nv.page,a=new g(t[s],void 0,n),v.items.push(a),r.push(a)}return v.update(),r}m(t.slice(0),e)}},this.show=function(t,e){return this.i=t,this.page=e,v.update(),v},this.remove=function(t,e,r){for(var n=0,s=0,i=v.items.length;s-1&&r.splice(n,1),v},this.trigger=function(t){for(var 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+ setCategoryHash(category); + } +}; + +window["quarto-listing-loaded"] = () => { + // Process any existing hash + const hash = getHash(); + + if (hash) { + // If there is a category, switch to that + if (hash.category) { + activateCategory(hash.category); + } + // Paginate a specific listing + const listingIds = Object.keys(window["quarto-listings"]); + for (const listingId of listingIds) { + const page = hash[getListingPageKey(listingId)]; + if (page) { + showPage(listingId, page); + } + } + } + + const listingIds = Object.keys(window["quarto-listings"]); + for (const listingId of listingIds) { + // The actual list + const list = window["quarto-listings"][listingId]; + + // Update the handlers for pagination events + refreshPaginationHandlers(listingId); + + // Render any visible items that need it + renderVisibleProgressiveImages(list); + + // Whenever the list is updated, we also need to + // attach handlers to the new pagination elements + // and refresh any newly visible items. + list.on("updated", function () { + renderVisibleProgressiveImages(list); + setTimeout(() => refreshPaginationHandlers(listingId)); + + // Show or hide the no matching message + toggleNoMatchingMessage(list); + }); + } +}; + +window.document.addEventListener("DOMContentLoaded", function (_event) { + // Attach click handlers to categories + const categoryEls = window.document.querySelectorAll( + ".quarto-listing-category .category" + ); + + for (const categoryEl of categoryEls) { + const category = categoryEl.getAttribute("data-category"); + categoryEl.onclick = () => { + activateCategory(category); + setCategoryHash(category); + }; + } + + // Attach a click handler to the category title + // (there should be only one, but since it is a class name, handle N) + const categoryTitleEls = window.document.querySelectorAll( + ".quarto-listing-category-title" + ); + for (const categoryTitleEl of categoryTitleEls) { + categoryTitleEl.onclick = () => { + activateCategory(""); + setCategoryHash(""); + }; + } + + categoriesLoaded = true; +}); + +function toggleNoMatchingMessage(list) { + const selector = `#${list.listContainer.id} .listing-no-matching`; + const noMatchingEl = window.document.querySelector(selector); + if (noMatchingEl) { + if (list.visibleItems.length === 0) { + noMatchingEl.classList.remove("d-none"); + } else { + if (!noMatchingEl.classList.contains("d-none")) { + noMatchingEl.classList.add("d-none"); + } + } + } +} + +function setCategoryHash(category) { + setHash({ category }); +} + +function setPageHash(listingId, page) { + const currentHash = getHash() || {}; + currentHash[getListingPageKey(listingId)] = page; + setHash(currentHash); +} + +function getListingPageKey(listingId) { + return `${listingId}-page`; +} + +function refreshPaginationHandlers(listingId) { + const listingEl = window.document.getElementById(listingId); + const paginationEls = listingEl.querySelectorAll( + ".pagination li.page-item:not(.disabled) .page.page-link" + ); + for (const paginationEl of paginationEls) { + paginationEl.onclick = (sender) => { + setPageHash(listingId, sender.target.getAttribute("data-i")); + showPage(listingId, sender.target.getAttribute("data-i")); + return false; + }; + } +} + +function renderVisibleProgressiveImages(list) { + // Run through the visible items and render any progressive images + for (const item of list.visibleItems) { + const itemEl = item.elm; + if (itemEl) { + const progressiveImgs = itemEl.querySelectorAll( + `img[${kProgressiveAttr}]` + ); + for (const progressiveImg of progressiveImgs) { + const srcValue = progressiveImg.getAttribute(kProgressiveAttr); + if (srcValue) { + progressiveImg.setAttribute("src", srcValue); + } + progressiveImg.removeAttribute(kProgressiveAttr); + } + } + } +} + +function getHash() { + // Hashes are of the form + // #name:value|name1:value1|name2:value2 + const currentUrl = new URL(window.location); + const hashRaw = currentUrl.hash ? currentUrl.hash.slice(1) : undefined; + return parseHash(hashRaw); +} + +const kAnd = "&"; +const kEquals = "="; + +function parseHash(hash) { + if (!hash) { + return undefined; + } + const hasValuesStrs = hash.split(kAnd); + const hashValues = hasValuesStrs + .map((hashValueStr) => { + const vals = hashValueStr.split(kEquals); + if (vals.length === 2) { + return { name: vals[0], value: vals[1] }; + } else { + return undefined; + } + }) + .filter((value) => { + return value !== undefined; + }); + + const hashObj = {}; + hashValues.forEach((hashValue) => { + hashObj[hashValue.name] = decodeURIComponent(hashValue.value); + }); + return hashObj; +} + +function makeHash(obj) { + return Object.keys(obj) + .map((key) => { + return `${key}${kEquals}${obj[key]}`; + }) + .join(kAnd); +} + +function setHash(obj) { + const hash = makeHash(obj); + window.history.pushState(null, null, `#${hash}`); +} + +function showPage(listingId, page) { + const list = window["quarto-listings"][listingId]; + if (list) { + list.show((page - 1) * list.page + 1, list.page); + } +} + +function activateCategory(category) { + // Deactivate existing categories + const activeEls = window.document.querySelectorAll( + ".quarto-listing-category .category.active" + ); + for (const activeEl of activeEls) { + activeEl.classList.remove("active"); + } + + // Activate this category + const categoryEl = window.document.querySelector( + `.quarto-listing-category .category[data-category='${category}'` + ); + if (categoryEl) { + categoryEl.classList.add("active"); + } + + // Filter the listings to this category + filterListingCategory(category); +} + +function filterListingCategory(category) { + const listingIds = Object.keys(window["quarto-listings"]); + for (const listingId of listingIds) { + const list = window["quarto-listings"][listingId]; + if (list) { + if (category === "") { + // resets the filter + list.filter(); + } else { + // filter to this category + list.filter(function (item) { + const itemValues = item.values(); + if (itemValues.categories !== null) { + const categories = itemValues.categories.split(","); + return categories.includes(category); + } else { + return false; + } + }); + } + } + } +} diff --git a/site_libs/quarto-nav/headroom.min.js b/site_libs/quarto-nav/headroom.min.js new file mode 100644 index 0000000..b08f1df --- /dev/null +++ b/site_libs/quarto-nav/headroom.min.js @@ -0,0 +1,7 @@ +/*! + * headroom.js v0.12.0 - Give your page some headroom. 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b/site_libs/quarto-nav/quarto-nav.js @@ -0,0 +1,289 @@ +const headroomChanged = new CustomEvent("quarto-hrChanged", { + detail: {}, + bubbles: true, + cancelable: false, + composed: false, +}); + +window.document.addEventListener("DOMContentLoaded", function () { + let init = false; + + // Manage the back to top button, if one is present. + let lastScrollTop = window.pageYOffset || document.documentElement.scrollTop; + const scrollDownBuffer = 5; + const scrollUpBuffer = 35; + const btn = document.getElementById("quarto-back-to-top"); + const hideBackToTop = () => { + btn.style.display = "none"; + }; + const showBackToTop = () => { + btn.style.display = "inline-block"; + }; + if (btn) { + window.document.addEventListener( + "scroll", + function () { + const currentScrollTop = + window.pageYOffset || document.documentElement.scrollTop; + + // Shows and hides the button 'intelligently' as the user scrolls + if (currentScrollTop - scrollDownBuffer > lastScrollTop) { + hideBackToTop(); + lastScrollTop = currentScrollTop <= 0 ? 0 : currentScrollTop; + } else if (currentScrollTop < lastScrollTop - scrollUpBuffer) { + showBackToTop(); + lastScrollTop = currentScrollTop <= 0 ? 0 : currentScrollTop; + } + + // Show the button at the bottom, hides it at the top + if (currentScrollTop <= 0) { + hideBackToTop(); + } else if ( + window.innerHeight + currentScrollTop >= + document.body.offsetHeight + ) { + showBackToTop(); + } + }, + false + ); + } + + function throttle(func, wait) { + var timeout; + return function () { + const context = this; + const args = arguments; + const later = function () { + clearTimeout(timeout); + timeout = null; + func.apply(context, args); + }; + + if (!timeout) { + timeout = setTimeout(later, wait); + } + }; + } + + function headerOffset() { + // Set an offset if there is are fixed top navbar + const headerEl = window.document.querySelector("header.fixed-top"); + if (headerEl) { + return headerEl.clientHeight; + } else { + return 0; + } + } + + function footerOffset() { + const footerEl = window.document.querySelector("footer.footer"); + if (footerEl) { + return footerEl.clientHeight; + } else { + return 0; + } + } + + function dashboardOffset() { + const dashboardNavEl = window.document.getElementById( + "quarto-dashboard-header" + ); + if (dashboardNavEl !== null) { + return dashboardNavEl.clientHeight; + } else { + return 0; + } + } + + function updateDocumentOffsetWithoutAnimation() { + updateDocumentOffset(false); + } + + function updateDocumentOffset(animated) { + // set body offset + const topOffset = headerOffset(); + const bodyOffset = topOffset + footerOffset() + dashboardOffset(); + const bodyEl = window.document.body; + bodyEl.setAttribute("data-bs-offset", topOffset); + bodyEl.style.paddingTop = topOffset + "px"; + + // deal with sidebar offsets + const sidebars = window.document.querySelectorAll( + ".sidebar, .headroom-target" + ); + sidebars.forEach((sidebar) => { + if (!animated) { + sidebar.classList.add("notransition"); + // Remove the no transition class after the animation has time to complete + setTimeout(function () { + sidebar.classList.remove("notransition"); + }, 201); + } + + if (window.Headroom && sidebar.classList.contains("sidebar-unpinned")) { + sidebar.style.top = "0"; + sidebar.style.maxHeight = "100vh"; + } else { + sidebar.style.top = topOffset + "px"; + sidebar.style.maxHeight = "calc(100vh - " + topOffset + "px)"; + } + }); + + // allow space for footer + const mainContainer = window.document.querySelector(".quarto-container"); + if (mainContainer) { + mainContainer.style.minHeight = "calc(100vh - " + bodyOffset + "px)"; + } + + // link offset + let linkStyle = window.document.querySelector("#quarto-target-style"); + if (!linkStyle) { + linkStyle = window.document.createElement("style"); + linkStyle.setAttribute("id", "quarto-target-style"); + window.document.head.appendChild(linkStyle); + } + while (linkStyle.firstChild) { + linkStyle.removeChild(linkStyle.firstChild); + } + if (topOffset > 0) { + linkStyle.appendChild( + window.document.createTextNode(` + section:target::before { + content: ""; + display: block; + height: ${topOffset}px; + margin: -${topOffset}px 0 0; + }`) + ); + } + if (init) { + window.dispatchEvent(headroomChanged); + } + init = true; + } + + // initialize headroom + var header = window.document.querySelector("#quarto-header"); + if (header && window.Headroom) { + const headroom = new window.Headroom(header, { + tolerance: 5, + onPin: function () { + const sidebars = window.document.querySelectorAll( + ".sidebar, .headroom-target" + ); + sidebars.forEach((sidebar) => { + sidebar.classList.remove("sidebar-unpinned"); + }); + updateDocumentOffset(); + }, + onUnpin: function () { + const sidebars = window.document.querySelectorAll( + ".sidebar, .headroom-target" + ); + sidebars.forEach((sidebar) => { + sidebar.classList.add("sidebar-unpinned"); + }); + updateDocumentOffset(); + }, + }); + headroom.init(); + + let frozen = false; + window.quartoToggleHeadroom = function () { + if (frozen) { + headroom.unfreeze(); + frozen = false; + } else { + headroom.freeze(); + frozen = true; + } + }; + } + + window.addEventListener( + "hashchange", + function (e) { + if ( + getComputedStyle(document.documentElement).scrollBehavior !== "smooth" + ) { + window.scrollTo(0, window.pageYOffset - headerOffset()); + } + }, + false + ); + + // Observe size changed for the header + const headerEl = window.document.querySelector("header.fixed-top"); + if (headerEl && window.ResizeObserver) { + const observer = new window.ResizeObserver(() => { + setTimeout(updateDocumentOffsetWithoutAnimation, 0); + }); + observer.observe(headerEl, { + attributes: true, + childList: true, + characterData: true, + }); + } else { + window.addEventListener( + "resize", + throttle(updateDocumentOffsetWithoutAnimation, 50) + ); + } + setTimeout(updateDocumentOffsetWithoutAnimation, 250); + + // fixup index.html links if we aren't on the filesystem + if (window.location.protocol !== "file:") { + const links = window.document.querySelectorAll("a"); + for (let i = 0; i < links.length; i++) { + if (links[i].href) { + links[i].dataset.originalHref = links[i].href; + links[i].href = links[i].href.replace(/\/index\.html/, "/"); + } + } + + // Fixup any sharing links that require urls + // Append url to any sharing urls + const sharingLinks = window.document.querySelectorAll( + "a.sidebar-tools-main-item, a.quarto-navigation-tool, a.quarto-navbar-tools, a.quarto-navbar-tools-item" + ); + for (let i = 0; i < sharingLinks.length; i++) { + const sharingLink = sharingLinks[i]; + const href = sharingLink.getAttribute("href"); + if (href) { + sharingLink.setAttribute( + "href", + href.replace("|url|", window.location.href) + ); + } + } + + // Scroll the active navigation item into view, if necessary + const navSidebar = window.document.querySelector("nav#quarto-sidebar"); + if (navSidebar) { + // Find the active item + const activeItem = navSidebar.querySelector("li.sidebar-item a.active"); + if (activeItem) { + // Wait for the scroll height and height to resolve by observing size changes on the + // nav element that is scrollable + const resizeObserver = new ResizeObserver((_entries) => { + // The bottom of the element + const elBottom = activeItem.offsetTop; + const viewBottom = navSidebar.scrollTop + navSidebar.clientHeight; + + // The element height and scroll height are the same, then we are still loading + if (viewBottom !== navSidebar.scrollHeight) { + // Determine if the item isn't visible and scroll to it + if (elBottom >= viewBottom) { + navSidebar.scrollTop = elBottom; + } + + // stop observing now since we've completed the scroll + resizeObserver.unobserve(navSidebar); + } + }); + resizeObserver.observe(navSidebar); + } + } + } +}); diff --git a/site_libs/quarto-search/autocomplete.umd.js b/site_libs/quarto-search/autocomplete.umd.js new file mode 100644 index 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Apache Software License 2.0 + * + * http://www.apache.org/licenses/LICENSE-2.0 + */ +var e,t;e=this,t=function(){"use strict";function e(e,t){var n=Object.keys(e);if(Object.getOwnPropertySymbols){var r=Object.getOwnPropertySymbols(e);t&&(r=r.filter((function(t){return Object.getOwnPropertyDescriptor(e,t).enumerable}))),n.push.apply(n,r)}return n}function t(t){for(var n=1;ne.length)&&(t=e.length);for(var n=0,r=new Array(t);n0&&void 0!==arguments[0]?arguments[0]:1,t=arguments.length>1&&void 0!==arguments[1]?arguments[1]:3,n=new Map,r=Math.pow(10,t);return{get:function(t){var i=t.match(C).length;if(n.has(i))return n.get(i);var o=1/Math.pow(i,.5*e),c=parseFloat(Math.round(o*r)/r);return n.set(i,c),c},clear:function(){n.clear()}}}var $=function(){function e(){var t=arguments.length>0&&void 0!==arguments[0]?arguments[0]:{},n=t.getFn,i=void 0===n?I.getFn:n,o=t.fieldNormWeight,c=void 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a/site_libs/quarto-search/quarto-search.js b/site_libs/quarto-search/quarto-search.js new file mode 100644 index 0000000..5f723d7 --- /dev/null +++ b/site_libs/quarto-search/quarto-search.js @@ -0,0 +1,1286 @@ +const kQueryArg = "q"; +const kResultsArg = "show-results"; + +// If items don't provide a URL, then both the navigator and the onSelect +// function aren't called (and therefore, the default implementation is used) +// +// We're using this sentinel URL to signal to those handlers that this +// item is a more item (along with the type) and can be handled appropriately +const kItemTypeMoreHref = "0767FDFD-0422-4E5A-BC8A-3BE11E5BBA05"; + +window.document.addEventListener("DOMContentLoaded", function (_event) { + // Ensure that search is available on this page. If it isn't, + // should return early and not do anything + var searchEl = window.document.getElementById("quarto-search"); + if (!searchEl) return; + + const { autocomplete } = window["@algolia/autocomplete-js"]; + + let quartoSearchOptions = {}; + let language = {}; + const searchOptionEl = window.document.getElementById( + "quarto-search-options" + ); + if (searchOptionEl) { + const jsonStr = searchOptionEl.textContent; + quartoSearchOptions = JSON.parse(jsonStr); + language = quartoSearchOptions.language; + } + + // note the search mode + if (quartoSearchOptions.type === "overlay") { + searchEl.classList.add("type-overlay"); + } else { + searchEl.classList.add("type-textbox"); + } + + // Used to determine highlighting behavior for this page + // A `q` query param is expected when the user follows a search + // to this page + const currentUrl = new URL(window.location); + const query = currentUrl.searchParams.get(kQueryArg); + const showSearchResults = currentUrl.searchParams.get(kResultsArg); + const mainEl = window.document.querySelector("main"); + + // highlight matches on the page + if (query && mainEl) { + // perform any highlighting + highlight(escapeRegExp(query), mainEl); + + // fix up the URL to remove the q query param + const replacementUrl = new URL(window.location); + replacementUrl.searchParams.delete(kQueryArg); + window.history.replaceState({}, "", replacementUrl); + } + + // function to clear highlighting on the page when the search query changes + // (e.g. if the user edits the query or clears it) + let highlighting = true; + const resetHighlighting = (searchTerm) => { + if (mainEl && highlighting && query && searchTerm !== query) { + clearHighlight(query, mainEl); + highlighting = false; + } + }; + + // Clear search highlighting when the user scrolls sufficiently + const resetFn = () => { + resetHighlighting(""); + window.removeEventListener("quarto-hrChanged", resetFn); + window.removeEventListener("quarto-sectionChanged", resetFn); + }; + + // Register this event after the initial scrolling and settling of events + // on the page + window.addEventListener("quarto-hrChanged", resetFn); + window.addEventListener("quarto-sectionChanged", resetFn); + + // Responsively switch to overlay mode if the search is present on the navbar + // Note that switching the sidebar to overlay mode requires more coordinate (not just + // the media query since we generate different HTML for sidebar overlays than we do + // for sidebar input UI) + const detachedMediaQuery = + quartoSearchOptions.type === "overlay" ? "all" : "(max-width: 991px)"; + + // If configured, include the analytics client to send insights + const plugins = configurePlugins(quartoSearchOptions); + + let lastState = null; + const { setIsOpen, setQuery, setCollections } = autocomplete({ + container: searchEl, + detachedMediaQuery: detachedMediaQuery, + defaultActiveItemId: 0, + panelContainer: "#quarto-search-results", + panelPlacement: quartoSearchOptions["panel-placement"], + debug: false, + openOnFocus: true, + plugins, + classNames: { + form: "d-flex", + }, + placeholder: language["search-text-placeholder"], + translations: { + clearButtonTitle: language["search-clear-button-title"], + detachedCancelButtonText: language["search-detached-cancel-button-title"], + submitButtonTitle: language["search-submit-button-title"], + }, + initialState: { + query, + }, + getItemUrl({ item }) { + return item.href; + }, + onStateChange({ state }) { + // If this is a file URL, note that + + // Perhaps reset highlighting + resetHighlighting(state.query); + + // If the panel just opened, ensure the panel is positioned properly + if (state.isOpen) { + if (lastState && !lastState.isOpen) { + setTimeout(() => { + positionPanel(quartoSearchOptions["panel-placement"]); + }, 150); + } + } + + // Perhaps show the copy link + showCopyLink(state.query, quartoSearchOptions); + + lastState = state; + }, + reshape({ sources, state }) { + return sources.map((source) => { + try { + const items = source.getItems(); + + // Validate the items + validateItems(items); + + // group the items by document + const groupedItems = new Map(); + items.forEach((item) => { + const hrefParts = item.href.split("#"); + const baseHref = hrefParts[0]; + const isDocumentItem = hrefParts.length === 1; + + const items = groupedItems.get(baseHref); + if (!items) { + groupedItems.set(baseHref, [item]); + } else { + // If the href for this item matches the document + // exactly, place this item first as it is the item that represents + // the document itself + if (isDocumentItem) { + items.unshift(item); + } else { + items.push(item); + } + groupedItems.set(baseHref, items); + } + }); + + const reshapedItems = []; + let count = 1; + for (const [_key, value] of groupedItems) { + const firstItem = value[0]; + reshapedItems.push({ + ...firstItem, + type: kItemTypeDoc, + }); + + const collapseMatches = quartoSearchOptions["collapse-after"]; + const collapseCount = + typeof collapseMatches === "number" ? collapseMatches : 1; + + if (value.length > 1) { + const target = `search-more-${count}`; + const isExpanded = + state.context.expanded && + state.context.expanded.includes(target); + + const remainingCount = value.length - collapseCount; + + for (let i = 1; i < value.length; i++) { + if (collapseMatches && i === collapseCount) { + reshapedItems.push({ + target, + title: isExpanded + ? language["search-hide-matches-text"] + : remainingCount === 1 + ? `${remainingCount} ${language["search-more-match-text"]}` + : `${remainingCount} ${language["search-more-matches-text"]}`, + type: kItemTypeMore, + href: kItemTypeMoreHref, + }); + } + + if (isExpanded || !collapseMatches || i < collapseCount) { + reshapedItems.push({ + ...value[i], + type: kItemTypeItem, + target, + }); + } + } + } + count += 1; + } + + return { + ...source, + getItems() { + return reshapedItems; + }, + }; + } catch (error) { + // Some form of error occurred + return { + ...source, + getItems() { + return [ + { + title: error.name || "An Error Occurred While Searching", + text: + error.message || + "An unknown error occurred while attempting to perform the requested search.", + type: kItemTypeError, + }, + ]; + }, + }; + } + }); + }, + navigator: { + navigate({ itemUrl }) { + if (itemUrl !== offsetURL(kItemTypeMoreHref)) { + window.location.assign(itemUrl); + } + }, + navigateNewTab({ itemUrl }) { + if (itemUrl !== offsetURL(kItemTypeMoreHref)) { + const windowReference = window.open(itemUrl, "_blank", "noopener"); + if (windowReference) { + windowReference.focus(); + } + } + }, + navigateNewWindow({ itemUrl }) { + if (itemUrl !== offsetURL(kItemTypeMoreHref)) { + window.open(itemUrl, "_blank", "noopener"); + } + }, + }, + getSources({ state, setContext, setActiveItemId, refresh }) { + return [ + { + sourceId: "documents", + getItemUrl({ item }) { + if (item.href) { + return offsetURL(item.href); + } else { + return undefined; + } + }, + onSelect({ + item, + state, + setContext, + setIsOpen, + setActiveItemId, + refresh, + }) { + if (item.type === kItemTypeMore) { + toggleExpanded(item, state, setContext, setActiveItemId, refresh); + + // Toggle more + setIsOpen(true); + } + }, + getItems({ query }) { + if (query === null || query === "") { + return []; + } + + const limit = quartoSearchOptions.limit; + if (quartoSearchOptions.algolia) { + return algoliaSearch(query, limit, quartoSearchOptions.algolia); + } else { + // Fuse search options + const fuseSearchOptions = { + isCaseSensitive: false, + shouldSort: true, + minMatchCharLength: 2, + limit: limit, + }; + + return readSearchData().then(function (fuse) { + return fuseSearch(query, fuse, fuseSearchOptions); + }); + } + }, + templates: { + noResults({ createElement }) { + const hasQuery = lastState.query; + + return createElement( + "div", + { + class: `quarto-search-no-results${ + hasQuery ? "" : " no-query" + }`, + }, + language["search-no-results-text"] + ); + }, + header({ items, createElement }) { + // count the documents + const count = items.filter((item) => { + return item.type === kItemTypeDoc; + }).length; + + if (count > 0) { + return createElement( + "div", + { class: "search-result-header" }, + `${count} ${language["search-matching-documents-text"]}` + ); + } else { + return createElement( + "div", + { class: "search-result-header-no-results" }, + `` + ); + } + }, + footer({ _items, createElement }) { + if ( + quartoSearchOptions.algolia && + quartoSearchOptions.algolia["show-logo"] + ) { + const libDir = quartoSearchOptions.algolia["libDir"]; + const logo = createElement("img", { + src: offsetURL( + `${libDir}/quarto-search/search-by-algolia.svg` + ), + class: "algolia-search-logo", + }); + return createElement( + "a", + { href: "http://www.algolia.com/" }, + logo + ); + } + }, + + item({ item, createElement }) { + return renderItem( + item, + createElement, + state, + setActiveItemId, + setContext, + refresh, + quartoSearchOptions + ); + }, + }, + }, + ]; + }, + }); + + window.quartoOpenSearch = () => { + setIsOpen(false); + setIsOpen(true); + focusSearchInput(); + }; + + document.addEventListener("keyup", (event) => { + const { key } = event; + const kbds = quartoSearchOptions["keyboard-shortcut"]; + const focusedEl = document.activeElement; + + const isFormElFocused = [ + "input", + "select", + "textarea", + "button", + "option", + ].find((tag) => { + return focusedEl.tagName.toLowerCase() === tag; + }); + + if ( + kbds && + kbds.includes(key) && + !isFormElFocused && + !document.activeElement.isContentEditable + ) { + event.preventDefault(); + window.quartoOpenSearch(); + } + }); + + // Remove the labeleledby attribute since it is pointing + // to a non-existent label + if (quartoSearchOptions.type === "overlay") { + const inputEl = window.document.querySelector( + "#quarto-search .aa-Autocomplete" + ); + if (inputEl) { + inputEl.removeAttribute("aria-labelledby"); + } + } + + function throttle(func, wait) { + let waiting = false; + return function () { + if (!waiting) { + func.apply(this, arguments); + waiting = true; + setTimeout(function () { + waiting = false; + }, wait); + } + }; + } + + // If the main document scrolls dismiss the search results + // (otherwise, since they're floating in the document they can scroll with the document) + window.document.body.onscroll = throttle(() => { + // Only do this if we're not detached + // Bug #7117 + // This will happen when the keyboard is shown on ios (resulting in a scroll) + // which then closed the search UI + if (!window.matchMedia(detachedMediaQuery).matches) { + setIsOpen(false); + } + }, 50); + + if (showSearchResults) { + setIsOpen(true); + focusSearchInput(); + } +}); + +function configurePlugins(quartoSearchOptions) { + const autocompletePlugins = []; + const algoliaOptions = quartoSearchOptions.algolia; + if ( + algoliaOptions && + algoliaOptions["analytics-events"] && + algoliaOptions["search-only-api-key"] && + algoliaOptions["application-id"] + ) { + const apiKey = algoliaOptions["search-only-api-key"]; + const appId = algoliaOptions["application-id"]; + + // Aloglia insights may not be loaded because they require cookie consent + // Use deferred loading so events will start being recorded when/if consent + // is granted. + const algoliaInsightsDeferredPlugin = deferredLoadPlugin(() => { + if ( + window.aa && + window["@algolia/autocomplete-plugin-algolia-insights"] + ) { + window.aa("init", { + appId, + apiKey, + useCookie: true, + }); + + const { createAlgoliaInsightsPlugin } = + window["@algolia/autocomplete-plugin-algolia-insights"]; + // Register the insights client + const algoliaInsightsPlugin = createAlgoliaInsightsPlugin({ + insightsClient: window.aa, + onItemsChange({ insights, insightsEvents }) { + const events = insightsEvents.flatMap((event) => { + // This API limits the number of items per event to 20 + const chunkSize = 20; + const itemChunks = []; + const eventItems = event.items; + for (let i = 0; i < eventItems.length; i += chunkSize) { + itemChunks.push(eventItems.slice(i, i + chunkSize)); + } + // Split the items into multiple events that can be sent + const events = itemChunks.map((items) => { + return { + ...event, + items, + }; + }); + return events; + }); + + for (const event of events) { + insights.viewedObjectIDs(event); + } + }, + }); + return algoliaInsightsPlugin; + } + }); + + // Add the plugin + autocompletePlugins.push(algoliaInsightsDeferredPlugin); + return autocompletePlugins; + } +} + +// For plugins that may not load immediately, create a wrapper +// plugin and forward events and plugin data once the plugin +// is initialized. This is useful for cases like cookie consent +// which may prevent the analytics insights event plugin from initializing +// immediately. +function deferredLoadPlugin(createPlugin) { + let plugin = undefined; + let subscribeObj = undefined; + const wrappedPlugin = () => { + if (!plugin && subscribeObj) { + plugin = createPlugin(); + if (plugin && plugin.subscribe) { + plugin.subscribe(subscribeObj); + } + } + return plugin; + }; + + return { + subscribe: (obj) => { + subscribeObj = obj; + }, + onStateChange: (obj) => { + const plugin = wrappedPlugin(); + if (plugin && plugin.onStateChange) { + plugin.onStateChange(obj); + } + }, + onSubmit: (obj) => { + const plugin = wrappedPlugin(); + if (plugin && plugin.onSubmit) { + plugin.onSubmit(obj); + } + }, + onReset: (obj) => { + const plugin = wrappedPlugin(); + if (plugin && plugin.onReset) { + plugin.onReset(obj); + } + }, + getSources: (obj) => { + const plugin = wrappedPlugin(); + if (plugin && plugin.getSources) { + return plugin.getSources(obj); + } else { + return Promise.resolve([]); + } + }, + data: (obj) => { + const plugin = wrappedPlugin(); + if (plugin && plugin.data) { + plugin.data(obj); + } + }, + }; +} + +function validateItems(items) { + // Validate the first item + if (items.length > 0) { + const item = items[0]; + const missingFields = []; + if (item.href == undefined) { + missingFields.push("href"); + } + if (!item.title == undefined) { + missingFields.push("title"); + } + if (!item.text == undefined) { + missingFields.push("text"); + } + + if (missingFields.length === 1) { + throw { + name: `Error: Search index is missing the ${missingFields[0]} field.`, + message: `The items being returned for this search do not include all the required fields. Please ensure that your index items include the ${missingFields[0]} field or use index-fields in your _quarto.yml file to specify the field names.`, + }; + } else if (missingFields.length > 1) { + const missingFieldList = missingFields + .map((field) => { + return `${field}`; + }) + .join(", "); + + throw { + name: `Error: Search index is missing the following fields: ${missingFieldList}.`, + message: `The items being returned for this search do not include all the required fields. Please ensure that your index items includes the following fields: ${missingFieldList}, or use index-fields in your _quarto.yml file to specify the field names.`, + }; + } + } +} + +let lastQuery = null; +function showCopyLink(query, options) { + const language = options.language; + lastQuery = query; + // Insert share icon + const inputSuffixEl = window.document.body.querySelector( + ".aa-Form .aa-InputWrapperSuffix" + ); + + if (inputSuffixEl) { + let copyButtonEl = window.document.body.querySelector( + ".aa-Form .aa-InputWrapperSuffix .aa-CopyButton" + ); + + if (copyButtonEl === null) { + copyButtonEl = window.document.createElement("button"); + copyButtonEl.setAttribute("class", "aa-CopyButton"); + copyButtonEl.setAttribute("type", "button"); + copyButtonEl.setAttribute("title", language["search-copy-link-title"]); + copyButtonEl.onmousedown = (e) => { + e.preventDefault(); + e.stopPropagation(); + }; + + const linkIcon = "bi-clipboard"; + const checkIcon = "bi-check2"; + + const shareIconEl = window.document.createElement("i"); + shareIconEl.setAttribute("class", `bi ${linkIcon}`); + copyButtonEl.appendChild(shareIconEl); + inputSuffixEl.prepend(copyButtonEl); + + const clipboard = new window.ClipboardJS(".aa-CopyButton", { + text: function (_trigger) { + const copyUrl = new URL(window.location); + copyUrl.searchParams.set(kQueryArg, lastQuery); + copyUrl.searchParams.set(kResultsArg, "1"); + return copyUrl.toString(); + }, + }); + clipboard.on("success", function (e) { + // Focus the input + + // button target + const button = e.trigger; + const icon = button.querySelector("i.bi"); + + // flash "checked" + icon.classList.add(checkIcon); + icon.classList.remove(linkIcon); + setTimeout(function () { + icon.classList.remove(checkIcon); + icon.classList.add(linkIcon); + }, 1000); + }); + } + + // If there is a query, show the link icon + if (copyButtonEl) { + if (lastQuery && options["copy-button"]) { + copyButtonEl.style.display = "flex"; + } else { + copyButtonEl.style.display = "none"; + } + } + } +} + +/* Search Index Handling */ +// create the index +var fuseIndex = undefined; +var shownWarning = false; + +// fuse index options +const kFuseIndexOptions = { + keys: [ + { name: "title", weight: 20 }, + { name: "section", weight: 20 }, + { name: "text", weight: 10 }, + ], + ignoreLocation: true, + threshold: 0.1, +}; + +async function readSearchData() { + // Initialize the search index on demand + if (fuseIndex === undefined) { + if (window.location.protocol === "file:" && !shownWarning) { + window.alert( + "Search requires JavaScript features disabled when running in file://... URLs. In order to use search, please run this document in a web server." + ); + shownWarning = true; + return; + } + const fuse = new window.Fuse([], kFuseIndexOptions); + + // fetch the main search.json + const response = await fetch(offsetURL("search.json")); + if (response.status == 200) { + return response.json().then(function (searchDocs) { + searchDocs.forEach(function (searchDoc) { + fuse.add(searchDoc); + }); + fuseIndex = fuse; + return fuseIndex; + }); + } else { + return Promise.reject( + new Error( + "Unexpected status from search index request: " + response.status + ) + ); + } + } + + return fuseIndex; +} + +function inputElement() { + return window.document.body.querySelector(".aa-Form .aa-Input"); +} + +function focusSearchInput() { + setTimeout(() => { + const inputEl = inputElement(); + if (inputEl) { + inputEl.focus(); + } + }, 50); +} + +/* Panels */ +const kItemTypeDoc = "document"; +const kItemTypeMore = "document-more"; +const kItemTypeItem = "document-item"; +const kItemTypeError = "error"; + +function renderItem( + item, + createElement, + state, + setActiveItemId, + setContext, + refresh, + quartoSearchOptions +) { + switch (item.type) { + case kItemTypeDoc: + return createDocumentCard( + createElement, + "file-richtext", + item.title, + item.section, + item.text, + item.href, + item.crumbs, + quartoSearchOptions + ); + case kItemTypeMore: + return createMoreCard( + createElement, + item, + state, + setActiveItemId, + setContext, + refresh + ); + case kItemTypeItem: + return createSectionCard( + createElement, + item.section, + item.text, + item.href + ); + case kItemTypeError: + return createErrorCard(createElement, item.title, item.text); + default: + return undefined; + } +} + +function createDocumentCard( + createElement, + icon, + title, + section, + text, + href, + crumbs, + quartoSearchOptions +) { + const iconEl = createElement("i", { + class: `bi bi-${icon} search-result-icon`, + }); + const titleEl = createElement("p", { class: "search-result-title" }, title); + const titleContents = [iconEl, titleEl]; + const showParent = quartoSearchOptions["show-item-context"]; + if (crumbs && showParent) { + let crumbsOut = undefined; + const crumbClz = ["search-result-crumbs"]; + if (showParent === "root") { + crumbsOut = crumbs.length > 1 ? crumbs[0] : undefined; + } else if (showParent === "parent") { + crumbsOut = crumbs.length > 1 ? crumbs[crumbs.length - 2] : undefined; + } else { + crumbsOut = crumbs.length > 1 ? crumbs.join(" > ") : undefined; + crumbClz.push("search-result-crumbs-wrap"); + } + + const crumbEl = createElement( + "p", + { class: crumbClz.join(" ") }, + crumbsOut + ); + titleContents.push(crumbEl); + } + + const titleContainerEl = createElement( + "div", + { class: "search-result-title-container" }, + titleContents + ); + + const textEls = []; + if (section) { + const sectionEl = createElement( + "p", + { class: "search-result-section" }, + section + ); + textEls.push(sectionEl); + } + const descEl = createElement("p", { + class: "search-result-text", + dangerouslySetInnerHTML: { + __html: text, + }, + }); + textEls.push(descEl); + + const textContainerEl = createElement( + "div", + { class: "search-result-text-container" }, + textEls + ); + + const containerEl = createElement( + "div", + { + class: "search-result-container", + }, + [titleContainerEl, textContainerEl] + ); + + const linkEl = createElement( + "a", + { + href: offsetURL(href), + class: "search-result-link", + }, + containerEl + ); + + const classes = ["search-result-doc", "search-item"]; + if (!section) { + classes.push("document-selectable"); + } + + return createElement( + "div", + { + class: classes.join(" "), + }, + linkEl + ); +} + +function createMoreCard( + createElement, + item, + state, + setActiveItemId, + setContext, + refresh +) { + const moreCardEl = createElement( + "div", + { + class: "search-result-more search-item", + onClick: (e) => { + // Handle expanding the sections by adding the expanded + // section to the list of expanded sections + toggleExpanded(item, state, setContext, setActiveItemId, refresh); + e.stopPropagation(); + }, + }, + item.title + ); + + return moreCardEl; +} + +function toggleExpanded(item, state, setContext, setActiveItemId, refresh) { + const expanded = state.context.expanded || []; + if (expanded.includes(item.target)) { + setContext({ + expanded: expanded.filter((target) => target !== item.target), + }); + } else { + setContext({ expanded: [...expanded, item.target] }); + } + + refresh(); + setActiveItemId(item.__autocomplete_id); +} + +function createSectionCard(createElement, section, text, href) { + const sectionEl = createSection(createElement, section, text, href); + return createElement( + "div", + { + class: "search-result-doc-section search-item", + }, + sectionEl + ); +} + +function createSection(createElement, title, text, href) { + const descEl = createElement("p", { + class: "search-result-text", + dangerouslySetInnerHTML: { + __html: text, + }, + }); + + const titleEl = createElement("p", { class: "search-result-section" }, title); + const linkEl = createElement( + "a", + { + href: offsetURL(href), + class: "search-result-link", + }, + [titleEl, descEl] + ); + return linkEl; +} + +function createErrorCard(createElement, title, text) { + const descEl = createElement("p", { + class: "search-error-text", + dangerouslySetInnerHTML: { + __html: text, + }, + }); + + const titleEl = createElement("p", { + class: "search-error-title", + dangerouslySetInnerHTML: { + __html: ` ${title}`, + }, + }); + const errorEl = createElement("div", { class: "search-error" }, [ + titleEl, + descEl, + ]); + return errorEl; +} + +function positionPanel(pos) { + const panelEl = window.document.querySelector( + "#quarto-search-results .aa-Panel" + ); + const inputEl = window.document.querySelector( + "#quarto-search .aa-Autocomplete" + ); + + if (panelEl && inputEl) { + panelEl.style.top = `${Math.round(panelEl.offsetTop)}px`; + if (pos === "start") { + panelEl.style.left = `${Math.round(inputEl.left)}px`; + } else { + panelEl.style.right = `${Math.round(inputEl.offsetRight)}px`; + } + } +} + +/* Highlighting */ +// highlighting functions +function highlightMatch(query, text) { + if (text) { + const start = text.toLowerCase().indexOf(query.toLowerCase()); + if (start !== -1) { + const startMark = ""; + const endMark = ""; + + const end = start + query.length; + text = + text.slice(0, start) + + startMark + + text.slice(start, end) + + endMark + + text.slice(end); + const startInfo = clipStart(text, start); + const endInfo = clipEnd( + text, + startInfo.position + startMark.length + endMark.length + ); + text = + startInfo.prefix + + text.slice(startInfo.position, endInfo.position) + + endInfo.suffix; + + return text; + } else { + return text; + } + } else { + return text; + } +} + +function clipStart(text, pos) { + const clipStart = pos - 50; + if (clipStart < 0) { + // This will just return the start of the string + return { + position: 0, + prefix: "", + }; + } else { + // We're clipping before the start of the string, walk backwards to the first space. + const spacePos = findSpace(text, pos, -1); + return { + position: spacePos.position, + prefix: "", + }; + } +} + +function clipEnd(text, pos) { + const clipEnd = pos + 200; + if (clipEnd > text.length) { + return { + position: text.length, + suffix: "", + }; + } else { + const spacePos = findSpace(text, clipEnd, 1); + return { + position: spacePos.position, + suffix: spacePos.clipped ? 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    Ucloud is an interactive online platform from the University of Southern Danmark eScience center that allows users to execute softwares and computer code directly from their browser. If you have an account from a danish university, hospital, and other institutions, you can access the platform for free and try the course.

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    Starting a session of the Introduction to NGS data analysis on uCloud

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      Log onto ucloud at the address http://cloud.sdu.dk using the university/institution credentials you possess.

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      If you are participating in the NGS Summer Course 2023 in Aarhus, click AFTER logging in on this link. You should see a message on your browser where you have to accept the invitation to the project. This will add you to a project on uCloud, where we have data and extra computing credit for the course.

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      Be sure to be in the right project. If you are participating in the NGS Summer Course 2023 in Aarhus, choose NGS Summer Course from the project menu (red circle). Afterwards, click on the App menu (green circle)

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    Note: The project My Workspace is instead your private space where you have some free hundreds of CPU hours and GBs of memory.

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    • Click on it. You will get into the settings window. Choose any Job Name (Nr 1 in the figure below), how many hours you want to use for the job (Nr 2, choose at least 2 hours, you can increase this later), and how many CPUs (Nr 3, choose at least 4 CPUs for the first three exercises, but use at least 8 CPUs to run the single cell analysis). Select the Introduction to NGS Data Analysis as course (Nr 4). Then click on Submit (Nr 5).
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    • You will now enter a waiting queue. When the session starts, the timer begins to count down (red circle). In a couple of minutes you should be able to open the interface through the button (green circle). Note the buttons to add time to your session (blue circle) and the button to stop the session when you are done (pink circle)
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    • You will be able to see jupyterlab in your browser. On the left side of the screen you can see various folders. You can find the exercises inside the folder Notebooks. You can download any file by right-clicking on it and choosing Download. You can also upload files by clicking on the Upload button on the top left corner of the screen, if you want to experiment with your own data!
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    Reuse your notebooks and data

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    The first time you run the Genomics Sandbox, you download data and notebooks. You can reuse them!

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    • Open the Genomics Sandbox App and use the settings to run it. You can click on your previous job name to recycle the settings (red circle).
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    You need to find a drive with your user name (red circle), written as Member Files: NameSurname#Number. Then, go into Jobs/Genomics Sandbox/JobID/Notebooks and choose the folder (green circle). JobID corresponds to the Job Name you used in the previous session, followed by some random number in parenthesis.

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    • Do the same procedure adding a folder again and finding Jobs/Genomics Sandbox/JobID/Data. At the end you should have two added folders like this:
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    • Click on Submit. Now you will be able to reuse data, results and exercises on which you worked before.
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    +Sandbox Workshop +

    +

    +Autumn 2023 +

    +

    +Welcome to the homepage for in-person workshops introducing the Health Data Science Sandbox to potential users. Thanks for joining us! +

    +

    !!! info “Upcoming Workshop at AAU” Intro to the Health Data Science Sandbox at Aalborg University

    +
    Interested in adding **new analysis techniques** to your health data science skill set? Curious about how to use Danish **supercomputing resources**? Looking for how to host **coding material for your own course** as an academic educator? Join our workshop for a demo of the Health Data Science Sandbox, a platform for training and research being built collaboratively across 5 universities. We will introduce our mission, network, and resources and then give you an opportunity to try out our omics-focused training module with **single cell RNA sequencing data** in a guided live session on UCloud (experience with R is a plus but not required). The workshop is open for students, researchers, and educators. 
+
+- Instructors: Sandbox Data Scientists Jakob Skelmose (AAU CLINDA) and Samuele Soraggi (AU BiRC)
+- Time: 6 December 2023, 1200-1600
+- Location: SLV249 moedelokale 11.01.032 at AAU SUND
+- Prerequisites: anyone can join for the first hour to hear about Sandbox resources, how to use them, and plans for the future. Some experience with R or Python will help you if you join the following transcriptomics app demo for the rest of the session (but all are welcome).
+- [Sign up](https://www.moodle.aau.dk/course/view.php?id=50047) on AAU's Moodle or [email the Sandbox](mailto:nhds_sandbox@sund.ku.dk) with questions
    +

    +Agenda +

    +
      +
    1. The Sandbox Concept - 30 minutes
      2. +
    2. Accessing Sandbox resources - 10 minutes
      3. +
    3. Try out our transcriptomics module - 2 hours
      4. +
    4. Discussion and feedback - 20 minutes
      5. +
    +
    +

    The Sandbox concept

    +

    The Health Data Science Sandbox aims to be a training resource for bioinformaticians, data scientists, and those generally curious about how to investigate large biomedical datasets. We are an active and developing project seeking interested users (both trainees and educators). All of our open-source materials are available on our Github page and much more information is available on the rest of the website you are currently visiting! We work with both UCloud and Computerome (major Danish academic supercomputers) - see our HPC Access page for more info on each set up.

    +
    +
    +

    Access Sandbox resources

    +

    We currently provide training materials and resources as topical apps on UCloud, the supercomputer located at the University of Southern Denmark. To use these resources, you’ll need the following:

    +
      +
    1. Log onto UCloud at the address http://cloud.sdu.dk using your university credentials.
      2. +
    2. the ability to navigate in linux / RStudio / Jupyter. You don’t need to be an expert, but it is beyond our ambitions (and course material) to teach you how to code and how to run analyses simultaneously. We recommend a basic R or Python course before diving in.
      3. +
    +

    Note:

    +
      +
    1. To use Sandbox materials outside of the workshop, you can request a project by clicking on apply for resources in your uCloud dashboard.
      2. +
    2. If you are a BSc or MSc student, you need a supervisor to apply on your behalf, or you can try to apply yourself mentioning the supervisor approval in the application.
      3. +
    3. Remember, however, that you have 1000Kr of computing credit, and around 50GB of free storage to work on uCLoud.
      4. +
    +
    +
    +

    Try out our transcriptomics module

    +

    So our Sandbox data scientists have finished their intro at the workshop? Great, now the brave ones in the audience can try out one of our apps in a live session. Today we are demoing:

    +

    Transcriptomics ### Transcriptomics If you’re interested in bulk or single cell RNA sequencing analysis and visualization, join Sandbox Data Scientist Samuele Soraggi from Aarhus University in testing out our Transcriptomics Sandbox app.

    +

    Follow these instructions to try our app:

    +
      +

    1. Click on the button below to join the project for today: <!DOCTYPE html>

      + + + + + +<p>Green Button</p> + + + + + +

      Go to Link

      + + +

      You should see a message on your browser where you have to accept the invitation to the project. This will add you to a project on uCloud, where we have data and extra computing credit for the course.

      2. +

    2. Be sure you have joined the project. Check if you have the project OMICS workshop from the project menu (red circle). Afterwards, click on the App menu (green circle)

      3. +
      3. +
      • Find the app Transcriptomics Sandbox (red circle), which is under the title Featured.
        • +
      4. +
    +

    +
      +
    • Click on it. You will get into the settings window. Choose any Job Name (Nr 1 in the figure below), how many hours you want to use for the job (Nr 2; choose at least 3 hours, you can increase this later), and how many CPUs (Nr 3, choose at least 4 CPUs). Choose the course RNAseq in RStudio from the drop-down menu (Nr 4). Finally, click on the blue button Add Folder.
      • +
    +

    +
      +
    • Now, click on the browsing bar that appears (red circle).
      • +
    +

    +
      +
    • In the appearing window, you should see already a folder called Intro_to_scRNAseq_R. Click on Use at its right (red circle)
      • +
    +

    +
      +
    • Afterwards, you should have something like this in the settings page:
      • +
    +

    +
      +

    • Now, click on Submit to start the app (the button is on the right side of the settings page)

      • +

    • You will now enter a waiting queue. When the session starts, the timer begins to count down (red circle), and you should be able to open the interface through the button (green circle). Note the buttons to add time to your session (blue circle) and the button to stop the session when you are done (pink circle)

      • +
    +

    +
      +

    • Open the interface by clicking on the button (green circle of figure above). Sometimes you are warned of a missing connection: simply refresh the page. You will enter Rstudio, well-known interface to code in R.

      • +

    • Run the following command to download the tutorial: download.file("https://raw.githubusercontent.com/hds-sandbox/ELIXIR-workshop/main/Notebooks/scRNAseq_Tutorial_R.Rmd", "tutorial_scrna.Rmd")

      • +

    • Open the file tutorial_scrnaR.Rmd that should now appear in the file browser of Rstudio. Click now on visual (on the tool bar) if you need to see the tutorial in a more readable format.

      • +

    • The executable code is inside chunks (called cells) to be executed in order from the first to the last using the little green arrow appearing on the right side of each code cell.

      • +

    • Read carefully through the tutorial and execute the code cells. You will see the outputs appearing as you proceed.

      • +
    +
    +
    +

    Discussion and feedback

    +

    We hope you enjoyed the live demo. If you have broader questions, suggestions, or concerns, now is the time to raise them! If you are totally toast for the day, remember that you can check out longer versions of our tutorials as well as other topics and tools in each of the Sandbox modules or join us for a multi-day in person course.

    +

    As data scientists, we also would be really happy for some quantifiable info and feedback - we want to build things that the Danish health data science community is excited to use. Please answer these 5 questions for us before you head out for the day (link activated on day of the workshop).

    +

    +Nice meeting you and we hope to see you again! +

    + + +
    + +
    + +
    + + + + + \ No newline at end of file diff --git a/workshop/workshop_Conference2023.html b/workshop/workshop_Conference2023.html new file mode 100644 index 0000000..6fba709 --- /dev/null +++ b/workshop/workshop_Conference2023.html @@ -0,0 +1,754 @@ + + + + + + + + + +Introduction to NGS data analysis + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    +
    + +
    + +
    + + + + +
    + + + + +

    +Sandbox Workshop +

    +

    +Autumn 2023 +

    +

    +Welcome to the homepage for in-person workshops introducing the Health Data Science Sandbox to potential users. Thanks for joining us! +

    +

    +Agenda +

    +
      +
    • The Sandbox Concept - 30 minutes
      • +
    • Accessing Sandbox resources - 10 minutes
      • +
    • Try out our transcriptomics module - 2 hours
      • +
    • Discussion and feedback - 20 minutes
      • +
    +
    +

    The Sandbox concept

    +

    The Health Data Science Sandbox aims to be a training resource for bioinformaticians, data scientists, and those generally curious about how to investigate large biomedical datasets. We are an active and developing project seeking interested users (both trainees and educators). All of our open-source materials are available on our Github page and much more information is available on the rest of the website you are currently visiting! We work with both UCloud and Computerome (major Danish academic supercomputers) - see our HPC Access page for more info on each set up.

    +
    +
    +

    Access Sandbox resources

    +

    We currently provide training materials and resources as topical apps on UCloud, the supercomputer located at the University of Southern Denmark. To use these resources, you’ll need the following:

    +
      +
    1. a Danish university ID so you can sign on to UCloud via WAYF. See this guide and/or follow along with our live demo.
      2. +
    2. the ability to navigate in linux / RStudio / Jupyter. You don’t need to be an expert, but it is beyond our ambitions (and course material) to teach you how to code and how to run analyses simultaneously. We recommend a basic R or Python course before diving in.
      3. +
    3. our invite link to the correct UCloud project that will be shared on the day of the workshop. This way, we can provide you compute resources for the active sessions of the workshop. To use Sandbox materials outside of the workshop, you’ll need to check with the local DeiC office at your university about how to request compute hours on UCloud.
      4. +
    +
    +
    +

    Try out a module

    +

    So our Sandbox data scientists have finished their intro at the workshop? Great, now it’s time to choose your poison (cough) topic of interest for today. Your options are below:

    +

    Genomics ### Genomics If you’re interested in NGS technologies and applications ranging from genome assembly to variant calling to metagenomics, join Sandbox Data Scientist Samuele Soraggi in testing out our Genomics Sandbox app. This app supports a semester-length course on NGS as well as a Population Genomics course run regularly at Aarhus University. Sign into UCloud and then click this invite link.

    +

    Transcriptomics ### Transcriptomics If you’re interested in bulk or single cell RNA sequencing analysis and visualization, join Sandbox Data Scientist Jose Alejandro Romero Herrera (Alex) in testing out our Transcriptomics Sandbox app. This app supports regular 3-4 day workshops at University of Copenhagen and provides stand-alone visualisation tools. Sign into UCloud and then click this invite link.

    +

    proteomics ### Proteomics Interested in modern methods for protein structure prediction? Join Sandbox Data Scientist Jacob Fredegaard Hansen as he walks you through how to use ColabFold on UCloud. Jacob can also demo our Proteomics Sandbox, which contains a suite of proteomics analysis tools that will support a future course in clinical proteomics but is already available on UCloud for interested users. Sign into UCloud and then click this invite link.

    +
    +
    +

    Discussion and feedback

    +

    We hope you enjoyed the live demo. If you have broader questions, suggestions, or concerns, now is the time to raise them! If you are totally toast for the day, remember that you can check out longer versions of our tutorials as well as other topics and tools in each of the Sandbox modules or join us for a multi-day in person course.

    +

    As data scientists, we also would be really happy for some quantifiable info and feedback - we want to build things that the Danish health data science community is excited to use. Please answer these 5 questions for us before you head out for the day (link activated on day of the workshop).

    +

    +Nice meeting you and we hope to see you again! +

    + + +
    + +
    + +
    + + + + + \ No newline at end of file diff --git a/workshop/workshop_april2024.html b/workshop/workshop_april2024.html new file mode 100644 index 0000000..8692354 --- /dev/null +++ b/workshop/workshop_april2024.html @@ -0,0 +1,948 @@ + + + + + + + + + +Introduction to NGS data analysis - Sandbox Workshop + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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    Sandbox Workshop

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    +Sandbox Workshop dates: 18-19 April 2024 +

    +

    +Welcome to the homepage for in-person workshops introducing the Health Data Science Sandbox to new users. Thanks for joining us! +

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    Agenda

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    Day 1

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    TimeActivity
    9:00Morning coffee (optional)
    9:30Introduction to the Sandbox project
    10:00Introduction to HPC: the basics
    10:30Coffee break
    10:45DK HPC resources, access, and intro to UCloud
    11:15UCloud demo: using apps and running jobs
    12:00Lunch break
    13:00Proteomics App
    14:15Coffee break
    14:30Proteomics App
    16:00End of day!
    +
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    Day 2

    + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
    TimeActivity
    9:00Morning coffee (optional)
    9:30RDM intro for health data science
    10:30Coffee break
    10:45Step-by-step guide: simple solutions
    12:00Lunch break
    13:00Transcriptomics App
    14:30Coffee break
    14:45Transcriptomics App
    15:45Wrap-up and feedback
    16:00End of day and goodbye!
    +
    +
    +
    +

    Workshop

    +

    The Health Data Science Sandbox aims to be a training resource for bioinformaticians, data scientists, and those generally curious about how to investigate large biomedical datasets. We are an active and developing project seeking interested users (both trainees and educators). All of our open-source materials are available on our Github page and can be used on a computing cluster! We work with both UCloud, GenomeDK and Computerome, the major Danish academic supercomputers. See our HPC Access page for more info on each setup.

    +
    +

    Access Sandbox resources

    +

    Our first choice is to provide all the training materials, tutorials, and tools as interactive apps on UCloud, the supercomputer located at the University of Southern Denmark. Anyone using these resources needs the following:

    +
      +
    1. a Danish university ID so you can sign on to UCloud via WAYF1.
      2. +
    +

     

    +

    + for UCloud Access click here +

    +

     

    +
      +

    1. basic ability to navigate in Linux/RStudio/Jupyter. You don’t need to be an expert, but it is beyond our ambitions (and course material) to teach you how to code from zero and how to run analyses simultaneously. We recommend a basic R or Python course before diving in.

      2. +

    2. For workshop participants: Use our invite link to the correct UCloud workspace that will be shared on the day of the workshop. This way, we can provide you with compute resources for the active sessions of the workshop2 Click the link below after your first uCloud access and accept the invite that shows.

      3. +
    +

     

    +

    + Invite link to uCloud workspace +

    +

       

    +
    +
    +
    + +
    +
    +Note +
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    +

    Our apps can run on other clusters, simply by pulling a so-called docker container. You only need to have either docker or singularity installed on the cluster. GenomeDK supports singularity and thus can run our learning material as well. Ask us if you want to help the apps out of uCloud. Instructions will soon be available within our HPC access instructions.

    +
    +
    +
    +
    +

    Our OMICS apps

    +

    The agenda starts with an introduction to High Performance Computing (HPC) and uCloud. You will try two apps during the workshop, but we are developing others, and have deployed three apps already.

    +

     

    +
    +Image +

    +Proteomics Sandbox: Our sandbox modern with a suite of proteomics analysis tools, used for example in clinical proteomics. This app is not alone, since our data scientist Jacob has also made the app ColabFold on UCloud, with methods for protein structure prediction. +

    +
    +

     

    +
    +Image +

    +Transcriptomics Sandbox : Our sandbox for bulk or single-cell RNA sequencing analysis and visualization - amongst others two regular workshops and provides stand-alone visualization tools. In the next update, we will introduce advanced tutorials for more complex single-cell RNA sequencing analysis from some of our supported courses. +

    +
    +

     

    +
    +Image +

    +Genomics Sandbox: Our sandbox NGS data analysis and applications range from genome assembly to variant calling to metagenomics. We have currently a semester-long population genomics course and an NGS course with many applications (alignment, VCF analysis, bulk-RNA data, single-cell RNA sequencing) +

    +
    +
    +
    +

    Discussion and feedback

    +

    We hope you enjoyed the live demo. If you have broader questions, suggestions, or concerns, now is the time to raise them! If you are totally toast for the day, remember that you can check out longer versions of our tutorials as well as other topics and tools in each of the Sandbox modules or join us for a multi-day in-person course (follow our news here).

    +

    As data scientists, we also would be really happy for some quantifiable info and feedback - we want to build things that the Danish health data science community is excited to use. Please answer these 5 questions for us before you head out for the day 3.

    +

     

    +
    +
    +
    + +
    +
    +

    +Nice meeting you and we hope to see you again! +

    +
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    +
    + + +
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    Footnotes

    + +
      +

    1. Other institutions (e.g. hospitals, libraries, …) can log on through WAYF. See all institutions here↩︎

      2. +

    2. To use Sandbox materials outside of the workshop: remember that each new user has hundreds of hours of free computing credit and around 50GB of free storage, which can be used to run any uCloud software. If you run out of credit (which takes a long time) you’ll need to check with the local DeiC office at your university about how to request compute hours on UCloud. Contact us at the Sandbox if you need help or want more information.↩︎

      3. +

    3. link activated on day one of the workshop.↩︎

      4. +
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