v2.3.2

Change Log:

• Set minimum stability to stable for composer packages. (57188f2)
• Synchronise networks that are not locally present. (3894d9a)
• Replaced NetworkRequest model with new adapter class. (82b7273)
• Added NetworkRequest status constants. (e48ca94)
• Added config node to composer.json. (3d48a22)

Bug Fix:

• Fixed a bug in validating Justification in network request creation. (69bb83b)
• Fixed a bug in reading file name as subject ID. (850484a)
• Fixed object type in ValidationHelper. (63c9b8b)
• Fixed a bug in validating elements of $_POST. (f9ed0e1)

v2.3.1

Change Log:

• Update to CI 4.3 with composer dependencies. (ceaa1ad)
• Deleted old CI test files. (c33fee1)
• Created unit test classes.
• Added DeleteDirectory() to FileMan class. (ae73b55)
• Made basePath nullable in constructor signature. (6d253d8)
• Changed canvas width in portal. (00e6f1a)
• Re-ordered constructor logic in UploadFileMan class. (30162f7)
• Removed getFileStack() from UploadFileMan class. (9183b89)
• Improved getMaximumAllowedUploadSize(). (82969ce)
• Added return type to GetAllowedDataFileFormats(). (d023bcc)
• Removed SaveAll() from UploadFileMan class. (88c33d7)
• Created QueryGeneretaor class to create Beacon V2 queries. (3ee9a3d)
• Replaced deprecated model instances with data adapter class instances. (ea6736b)
• Added App path to psr-4 autoload. (d1f93a1)
• Added _remap() to pass network key to endpoints. (6b620c6)
• Added Date Time type for attributes and automatic recognition of it.
• Added logic to delete user interface index upon source deletion. (de97d92)
• Added logic to make sure network indices get updated in case sources get modified. (92580bf)

Bug Fix:

• Various bugs in InsertPort() function. (94cc80b)
• Added a conditional to throw exception on a failed decryption. (aa5bf4f)
• Fixed a bug in formatting sizes over a GB. (d441ad3)
• Fixed return message in getPostAuthenticanPolicy(). (e940e0d)
• Fixed logic in GetFileMimeType() and getMimeType(). (2fc4c76)
• Fixed logic in GetFileExtension() and getExtension(). (4b44cfe)
• Fixed a bug in closing file handles. (d38a740)
• Fixed the logic for handle destruction in isValid(). (369c4bb)
• Fixed extension filters for non recursive mode. (b81be91)
• Fixed side effect for returning files in getFiles. (35e47f7)
• Fixed path concatenation in Save(). (e569f73)
• Fixed bugs in reading attribute properties. (5f9b7f4)
• Added reference to NullEntity in ValueFactory class.(14358b5)
• Fixed a bug in loaded users associated with a group. (2577167)

v2.3.0

Change log:

• Session Hijacking Prevention is added into .htaccess (49b7eb8)
• Default password for admin user is removed due to OWASP A07:2021(bcccb71)
• Updated security directions in .htaccess to block access to sensitive files and directories. (e4aac02)
• Created Attribute entity class and moved CRUD to its data adapter class.
• Created DataFile entity class and moved CRUD to its data adapter class. This replaces Upload model.
• Created EAV entity class and moved CRUD to its data adapter class.
• Created Pipeline entity class and moved CRUD to its data adapter class.
• Created Setting entity class and moved CRUD to its data adapter class.
• Created Source entity class and moved CRUD to its data adapter class.
• Created Subject entity class and moved CRUD to its data adapter class.
• Created Group entity class and moved CRUD to its data adapter class.
• Created Value entity class and moved CRUD to its data adapter class.
• Created Task entity class and moved CRUD to its data adapter class.
• Added entity primary key in list for ReadAll(). (70e3a05)
• Merge pull request #25 from CafeVariomeUoL/OWASP_top10_2021 (3dbd205)
• Updated Demon structure and moved all action with regards to Task entities.
• Created message classes for communication with Demon.
• Added display_name to source definition. (b70a03f)
• Updated meta values passed to views. (a4b9438)
• Created new uploader/importer interface under DataFile controller and views.
• Marked VCFDataInput as deprecated.
• Added Demon Start/Stop button in admin dashboard. (1e4ceba)
• Added view model capability to data adapter layer. (63cfbc1)
• Added InputValidation filter class to sanitize incoming data through post.
• Added privacy policy file to the UI. (a161b02)
• Added support for batch processing of uploaded/imported files.

Bug fix:

• Multiple bug fixes in PhenoPacketDataInput class.
• Fixed README.md links (b780515)
• Fixed icon in Single Sign-on Provider create view. (1d3330b)
• Fixed UI bugs in Elasticsearch and Neo4J views. (9903bf4)

v2.2.2

Change log:

• Added a new data adapter layer to interact with MySQL (Entity classes and their Adapters)
• Added factory classes for Entity class instantiation.
• Added Server entity with CRUD.
• Added Credential entity with CRUD.
• Added ProxyServer entity with CRUD.
• Added SingleSignOnProvider entity with CRUD.
• Added support for multiple authentication server (95c6a2f).
• Removed League OAuth and League Keycloak PHP libraries.
• Added ext-sodium to composer dependencies.
• Added ext-gd to composer dependencies.
• Added types to attributes of File and FileMan classes.
• Added diskName attribute to File to allow for saving files with system generated names (0241c24).
• Increased admin dashboard left side menu width from 14rem to 15rem (0bd3669).
• Created URLHelper class (282facb).
• Added constants for authentication session names (591215c).
• Marked UserModel, AuthAdapter, KeyCloak, and OAuth classes as deprecated.
• Added new upload directories in writable (d8b6a6a).
• Modified installer script to set permissions for new directories (fa9967d).
• Updated to CodeIgniter 4.2 (268d0a1).

Bug fix:

• Added autocomplete key-value pairs to settings table in the database schema.
• Fixed a bug in array intersection of clauses with AND logic (19bd96f)
• Fixed a bug in getting request type in TaskFilter (5bca1b2).
• Updated minimum PHP version in installer script to 8.0 (472984e).
• Added code to read .env file for database credentials.

v2.2.1

Change log:

• Started using endpoint settings in user interface for auto-complete.
• Created UserInterfaceAPI to load JavaScript in pages.
• Set JavaScript constants at the beginning of layouts.

Bug Fix:

• Fixed select2 auto-complete via AJAX calls for ORPHA codes.

v2.2.0

Change log:

• Profile page now opens in a new tab when Keycloak is in use.
• Added Cancel button for queries.
• Set minimum similarity measures to 0.5 for ORPHA and HPO
• Updated placeholder of HPO terms container in query builder page.
• Added source UID to HPO and ORPHA similarity queries.
• Added bcmath to composer requirements.
• Added version to CafeVariome class and dashboard footer

Bug Fix:

• Fixed source name description in create and update.
• Fixed a bug in creation of subject nodes in Neo4J that does not create duplicates but updates source related attributes if necessary. (See #19 )
• Trimmed attribute and values before creation to make sure no trailing space characters go in the database.
• Fixed a null reference pointer bug in Neo4J transaction destruction.
• Replaced double precision floating point comparisons with bccomp().
• Fixed a bug in ORPHA similarity queries that prevented exact match to be executed at the beginning regardless of similarity measures.
• Fixed various bugs in PhenoPacket import pipeline.
• Fixed a bug in validation of pipeline input data on create and update that separately checks for Expansion Policy.

v2.1.0

Change log:

• Added expansion capability to pipelines.

Bug Fix:

• Fixed a bug in processing spreadsheet files when subject ID is not in the file
• Fixed a bug in source deletion

Initial Release - v2.0.0

This is the initial alpha release of Cafe Variome 2.

Documentation can be found at Cafe Variome main portal.