nesp marine hub scripts

scripts/RestClient/nesp/marine/Marine_Biodiversity_Hub_Projects_tab.txt

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+hub_name	associatedProgram	associatedSubProgram	projectSiteId	projectType	organisationId	organisationName	organisationUrl	organisationLogo	projectName	aim	description	plannedStartDate	plannedEndDate	ecoScienceType	isExternal	status	manager	countries	uNRegions	banner_image	projectUrl	associatedOrgs	contactMail	keywords	termsOfUseAgreement	embeddedVideo	embeddedVideoTitle
+nesp-marine	NESP 1 - Marine Biodiversity Hub	Theme A - Threatened and migratory species		Ecological or biological survey / assessment (not citizen science)	4a3929aa-5d64-4c96-9e03-4ade85d5f9f1	Charles Darwin University			Project A1 - Northern Australian hotspots for the recovery of threatened euryhaline species	Australia's northern rivers and estuaries are important to sustaining sawfish and river shark species listed under the EPBC Act. This project will provide the Department of the Environment with information to improve management and facilitate the recovery of these species.	"Australia's northern rivers and estuaries are important to sustaining sawfish and river shark species listed under Australia's<em> Environment Protection and Biodiversity Conservation Act 1999</em> (EPBC Act). This project will provide the Department of the Environment with information to improve management and facilitate the recovery of these species.<p>Acoustic telemetry, molecular research, life history studies and Indigenous engagement and education will be central to determining the status of threatened river sharks, and establishing monitoring, management and protection. Following are the key research activities.</p><h2>Monitoring and understanding</h2><p>More than 200 tagged animals will be monitored (via an acoustic array established in earlier research) for mortality estimates, movement patterns and habitat use, acoustic receiver arrays will be designed to measure long term movement and mortality in NT, QLD and WA rivers, and statistical methods developed for estimating annual juvenile mortality.</p><p>Thirty neonate <em>Glyphis glyphis</em> (Speartooth Sharks) will be tagged for mortality estimates and large sub-adult <em>G. glyphis</em> will be tagged to investigate adult distribution, reproductive philopatry and mortality (Adelaide River) and the age structure of <em>G. glyphis</em> will be determined for demographic models.</p><p><em>G. garricki</em> (Northern River Shark) tissue samples will be collected in unsurveyed NT habitat (including the Daly, Finniss, Fitzmaurice, Victoria, Keep rivers) and in WA (Cambridge Gulf, King Sound) in partnership with Indigenous Ranger Groups, Murdoch University and NT Fisheries. <em>G. garricki</em> population structure will be examined and close-kin mark recapture used to establish a lower bound population size estimate.</p><p>Marine Biodiversity Hub research on habitat use, long-term movements and biologically important areas will be synthesised and recovery-directed research prioritised, and&nbsp;new information will be&nbsp;provided&nbsp;for updating the&nbsp;EPBC status of river sharks.</p><h2>Indigenous partnerships for management</h2><p>Key components of this project are being undertaken in partnership with Indigenous organisations, communities and ranger groups. Partnerships will assess Indigenous cultural use and knowledge of sawfish, and develop a sawfish education package for communities.</p><p>The Northern Australian Indigenous Land and Sea Management Alliance is a project partner and Indigenous land councils will be consulted to evaluate engagement and partnership opportunities.</p><p>Malak Malak Rangers (NT) and Dambi-Mangari Rangers (WA) among other ranger groups are assisting with field research, and protocols and methodologies are being developed for an annual Malak Malak <em>Pristis pristis</em> (Largetooth Sawfish) survey.</p><p><strong>Related information</strong></p><ul><li><a href=https://www.nespmarine.edu.au/news/sampling-speartooth-sharks-remote-lower-ord-river"">Sampling Speartooth Sharks on the remote Lower Ord River</a></li><li><a href=""https://www.nespmarine.edu.au/news/fishers-offer-narrow-sawfish-helping-hand"">Fishers offer Narrow Sawfish a helping hand</a></li><li><a href=""https://www.nespmarine.edu.au/news/largetooth-sawfish-found-rock-art-500-kilometres-sea"">Largetooth Sawfish found in rock art 500 kilometres from the sea</a></li><li><a href=""https://www.nespmarine.edu.au/news/making-art-videos-signs-and-steps-save-sawfish-australias-northern-rivers"">Making art, videos, signs and steps to save sawfish in Australia's northern rivers</a></li><li>S<a href=""http://www.nespmarine.edu.au/sawfish"">awfish and river shark research</a> undertaken during the National Environmental Research Program&nbsp; (NERP) 2011-2014&nbsp;</li></ul>"	7/01/2016	8/01/2016		TRUE	Completed	Peter Kyne	Australia	Oceania	https://www.nespmarine.edu.au/sites/default/files/sawfish%20rock%20art%20Peter%20Kyne%20carousel_0.png	https://www.nespmarine.edu.au/project/project-a1-northern-australian-hotspots-recovery-threatened-euryhaline-species		peter.kyne@cdu.edu.au	"Euryhaline sharks,Glyphis garricki,Glyphis glyphis,Indigenous engagement,Largetooth Sawfish,Malak Malak Rangers,northern river sharks,Pristis pristis,Speartooth Shark"	TRUE		

scripts/RestClient/nesp/marine/document.js

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+var document =
+    {
+      "labels" : [ ],
+      "dateCreated" : "",
+      "lastUpdated" : "",
+      "isPrimaryProjectImage" : true,
+      "documentId" : "",
+      "filepath" : "2021-11",
+      "thirdPartyConsentDeclarationMade" : false,
+      "projectActivityId" : "",
+      "role" : "mainImage",
+      "name" : "",
+      "type" : "image",
+      "status" : "active",
+      "filename" : "",
+      "isSciStarter" : false,
+      "projectId" : "",
+      "readOnly" : false,
+      "filesize" : 104117,
+      "contentType" : "image/jpeg"
+}
+
+/*
+var document =
+{
+  "documentId" : "",
+  "filename" : "",
+  "filepath" : "2021-02",
+  "isPrimaryProjectImage" : true,
+  "isSciStarter" : false,
+  "labels" : [ ],
+  "name" : "",
+  "projectId" : "",
+  "role" : "mainImage",
+  "status" : "active",
+  "thirdPartyConsentDeclarationMade" : false,
+  "type" : "image",
+  "lng" : "",
+  "filesize" : 104117,
+  "public" : true,
+  "contentType" : "image/jpeg",
+  "lat" : "",
+  "projectActivityId" : "",
+  "roles" : [
+    {
+      "name" : "Information",
+      "id" : "information"
+    },
+    {
+      "name" : "Embedded Video",
+      "id" : "embeddedVideo"
+    },
+    {
+      "name" : "Exceedance Report",
+      "id" : "exceedanceReport"
+    },
+    {
+      "name" : "Photo",
+      "id" : "photo"
+    },
+    {
+      "name" : "Project Plan / Work plan",
+      "id" : "projectPlan"
+    },
+    {
+      "name" : "Project Variation",
+      "id" : "projectVariation"
+    },
+    {
+      "name" : "Project Highlight Report",
+      "id" : "projectHighlightReport"
+    },
+    {
+      "name" : "Other Project document",
+      "id" : "other"
+    }
+  ],
+  "fileReady" : true,
+  "thirdPartyConsentDeclarationRequired" : true,
+  "embeddedVideoVisible" : false,
+  "settings" : {
+    "thirdPartyDeclarationTextSelector" : "#thirdPartyDeclarationText",
+    "roles" : [
+      {
+        "name" : "Information",
+        "id" : "information"
+      },
+      {
+        "name" : "Embedded Video",
+        "id" : "embeddedVideo"
+      },
+      {
+        "name" : "Exceedance Report",
+        "id" : "exceedanceReport"
+      },
+      {
+        "name" : "Photo",
+        "id" : "photo"
+      },
+      {
+        "name" : "Project Plan / Work plan",
+        "id" : "projectPlan"
+      },
+      {
+        "name" : "Project Variation",
+        "id" : "projectVariation"
+      },
+      {
+        "name" : "Project Highlight Report",
+        "id" : "projectHighlightReport"
+      },
+      {
+        "name" : "Other Project document",
+        "id" : "other"
+      }
+    ],
+    "showSettings" : true,
+    "imageLocation" : "/assets/"
+  },
+  "hasPreview" : false,
+  "fileButtonText" : "Change file",
+  "readOnly" : false,
+  "saveHelp" : "You must accept the Privacy Declaration before an image can be made viewable by everyone",
+  "fileLabel" : "",
+  "progress" : 0,
+  "complete" : false,
+  "saveEnabled" : false
+};
+*/

scripts/RestClient/nesp/marine/import.js

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+print("Imported started");
+var path = '';
+load(path + "document.js")
+load(path+"testExample.js");
+load(path+'uuid.js');
+load(path+'siteTemplate.js');
+
+print("Loaded all dependent files...");
+
+/*
+//Prod
+var projectSiteId = "75e5599b-44f2-4ffa-975a-e7900839ae35" //https://biocollect.ala.org.au/nesp/site/index/75e5599b-44f2-4ffa-975a-e7900839ae35
+// https://biocollect.ala.org.au/nesp/project/index/e7e0fe1a-315d-4485-84ef-73276a812dac
+*/
+
+// Test
+// Test Project https://biocollect-test.ala.org.au/nesp/project/index/a833ad82-bc3b-41f6-8d98-106df76a089c
+// Test Site https://biocollect-test.ala.org.au/biocollect-all/site/index/6d9270aa-6cdd-4cce-a319-5226e0affefc
+var hub_name = 0;
+var associatedProgram = hub_name + 1;
+var associatedSubProgram = associatedProgram + 1;
+var projectSiteId = associatedSubProgram + 1;
+var projectType = projectSiteId + 1;
+var organisationId = projectType + 1;
+var organisationName = organisationId + 1;
+var organisationUrl = organisationName + 1;
+var organisationLogo = organisationUrl + 1;
+var projectName = organisationLogo + 1;
+var aim = projectName + 1;
+var description = aim + 1;
+var plannedStartDate = description + 1;
+var plannedEndDate = plannedStartDate + 1;
+var ecoScienceType = plannedEndDate + 1
+var isExternal = ecoScienceType + 1;
+var status = isExternal + 1;
+var manager = status + 1;
+var countries = manager + 1;
+var uNRegions = countries + 1;
+var banner_image = uNRegions + 1;
+var projectUrl = banner_image + 1;
+var associatedOrgs = projectUrl + 1;
+var contactMail = associatedOrgs + 1;
+var keywords = contactMail + 1;
+var termsOfUseAgreement = keywords + 1;
+
+var csvData = cat(path+'Marine_Biodiversity_Hub_Projects_tab.txt');
+print("Loaded csv file");
+var csvRows = csvData.split('\r');
+print("Total rows "+ csvRows.length);
+
+// key value pairs of assoiated orgs
+var organisations = [
+    {name:"CSIRO", organisationId:"8c3a7806-6d5e-4b60-97d7-b76ba495750e"},
+    {name:"Charles Darwin University", organisationId:"9fe1c64f-ad8c-487d-b7f7-b975563d5e4b"},
+    {name:"Curtin University", organisationId:"sdsdc64f-ad8c-487d-b7f7-b975563d5e4b"},
+    {name:"Murdoch University", organisationId:"sddwc64f-ad8c-487d-b7f7-b975563d5e4b"}
+];
+
+for(var i = 1; i < csvRows.length; i++) {
+    print("PRINT "+csvRows.length)
+    var projectId = UUID.generate();
+    var siteId = UUID.generate();
+    var row = csvRows[i];
+    var fields = row.split('\t');
+
+    project.projectId = projectId;
+    project.urlWeb = fields[projectUrl];
+    project.projectSiteId = siteId
+    project.projectType = "ecoScience"
+    project.organisationId = "8a53da29-bbbe-4a76-81c8-13f0bafd2f85" // hub's organisation id
+
+    //When there are commas, tsv adds double quotes in the beginning and end of text, following string
+    //manipulations are done to avoid that
+    if(fields[contactMail].indexOf(',') != -1){
+        var tempManagerEmail = fields[contactMail].replace(/""/g, '"');
+        project.manager = tempManagerEmail.substring(1, tempManagerEmail.length-1);
+    }
+    else {
+        project.manager = fields[contactMail]
+    }
+
+    if(fields[manager].indexOf(',') != -1){
+        var tempManager = fields[manager].replace(/""/g, '"');
+        project.managerEmail = tempManager.substring(1, tempManager.length-1);
+    }
+    else {
+        project.managerEmail = fields[manager]
+    }
+
+    if(fields[description].indexOf(',') != -1){
+        var tempDescription = fields[description].replace(/""/g, '"');
+        project.description = tempDescription.substring(1, tempDescription.length-1);
+    }
+    else {
+        project.description = fields[description]
+    }
+
+    if(fields[aim].indexOf(',') != -1){
+        var tempAim = fields[aim].replace(/""/g, '"');
+        project.aim = tempAim.substring(1, tempAim.length-1);
+    }
+    else {
+        project.aim = fields[aim]
+    }
+
+    if(fields[projectName].indexOf(',') != -1){
+        var tempProjectName = fields[projectName];
+        project.name = tempProjectName.substring(1, tempProjectName.length-1);
+    }
+    else {
+        project.name = fields[projectName]
+    }
+
+    project.associatedProgram = fields[associatedProgram]
+
+    if(fields[associatedSubProgram].indexOf(',') != -1){
+        var tempAssociatedSubProgram = fields[associatedSubProgram];
+        project.associatedSubProgram = tempAssociatedSubProgram.substring(1, tempAssociatedSubProgram.length-1);
+    }
+    else {
+        project.associatedSubProgram = fields[associatedSubProgram]
+    }
+
+    //Handle associated orgs
+    project.associatedOrgs = []
+
+    var tempAssociatedOrgsArr = []
+    var tempAssociatedOrgs = "";
+    var tempStr = "";
+
+    //get comma separated values from associatedOrgs field in excelsheet
+    if(fields[associatedOrgs]) {
+        tempAssociatedOrgs = fields[associatedOrgs].replace(/""/g, '"');
+        tempStr = tempAssociatedOrgs.substring(1, tempAssociatedOrgs.length - 1);
+    }
+
+    if (tempStr) {
+        tempAssociatedOrgsArr = tempStr.split(',');
+    }
+
+    for (var k = 0; k < tempAssociatedOrgsArr.length; k++) {
+        var org = organisations.find(obj => obj.name === tempAssociatedOrgsArr[k]);
+        project.associatedOrgs.push({organisationId: org.organisationId});
+    }
+
+    //assign organisationId from excelsheet for the first organisationName in excelsheet
+    project.associatedOrgs.push({organisationId: fields[organisationId]});
+
+    var tempKeywords = fields[keywords].replace(/""/g, '"');
+    project.keywords = tempKeywords.substring(1, tempKeywords.length-1);
+
+    var startDate = fields[plannedStartDate] ? fields[plannedStartDate].split('/') : '';
+    var endDate = fields[plannedEndDate]  ? fields[plannedEndDate].split('/') : '';
+
+    if(!startDate || startDate == undefined || startDate == "" || startDate.length == 0 || startDate.length < 3) {
+        var dd = "01";
+        var mm = "01";
+        var yy = "2000";
+        startDate = ""+yy+"-"+mm+"-"+dd+"T00:00:00Z"+"";
+        project.plannedStartDate = ISODate(startDate);
+    } else {
+        startDate = ""+startDate[2]+"-"+("0" + startDate[1]).slice(-2)+"-"+("0" + startDate[0]).slice(-2)+"T00:00:00Z"+"";
+        project.plannedStartDate = ISODate(startDate);
+    }
+
+    if(!endDate || endDate == undefined || endDate == "" || endDate.length == 0 || endDate.length < 3) {
+        //print("Invalid project end date");
+    } else {
+        endDate = endDate[2] + "-" + ("0" + endDate[1]).slice(-2)+"-"+("0" + endDate[0]).slice(-2)+"T00:00:00Z"+"";
+        project.plannedEndDate = ISODate(endDate);
+    }
+
+    project.ecoScienceType = [];
+    if(fields[ecoScienceType]) {
+        project.ecoScienceType << fields[ecoScienceType]
+    }
+
+    var today = new ISODate();
+    var dd = today.getDate();
+    var mm = today.getMonth() + 1; //January is 0!
+    var yyyy = today.getFullYear();
+    var dateUTC = yyyy+"-"+("0" + mm).slice(-2)+"-"+("0" + dd).slice(-2)+"T00:00:00Z";
+
+    project.dateCreated = ISODate(dateUTC);
+    project.lastUpdated = ISODate(dateUTC);
+
+    if(siteMap) {
+        siteMap.projects = [];
+        siteMap.projects.push(projectId);
+        siteMap.siteId = siteId;
+        siteMap.lastUpdated = ISODate(dateUTC);
+        siteMap.dateCreated = ISODate(dateUTC);
+    }
+
+    if(fields[banner_image]) {
+        var imageUrl = fields[banner_image]
+        var urlSplitBySlash = imageUrl.split('/')
+        var fileName = urlSplitBySlash[urlSplitBySlash.length-1]
+
+        var contentType = "image/jpg"
+
+        if(fileName.endsWith(".png")) {
+            contentType = "image/png"
+        }
+
+        document.filename = fileName
+        document.name = fileName
+        document.documentId = UUID.generate()
+        document.projectId = project.projectId
+        document.contentType = contentType
+        document.fileLabel = fileName
+        document.dateCreated = ISODate(dateUTC);
+        document.lastUpdated = ISODate(dateUTC);
+    }
+
+    var userPermission = {};
+    userPermission.accessLevel = 'admin';
+    userPermission.entityId = project.projectId;
+    userPermission.userId = '8443';
+    userPermission.entityType = 'au.org.ala.ecodata.Project';
+
+    var documentResult = db.document.insert(document);
+    var siteResult = db.site.insert(siteMap);
+    var projectResult = db.project.insert(project);
+    var permissionResult = db.userPermission.insert(userPermission);
+
+    //print(JSON.stringify(project,null,"\t"));
+    print("Project is "+project.projectId + "," + project.name);
+    print("siteResult"+siteResult)
+    print("projectResult"+projectResult)
+    print("permissionResult"+permissionResult)
+    print("documentResult"+documentResult)
+}
+
+
+print(">>>>>>>>>>>>>>>>>>>>")
+print("Created " + (i-1) + " projects");
+print("<<<<<<<<<<<<<<<<<<<")