Icgc

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- Retrieving software download versions from artifactory is now done over HTTPS.
- Updates to the Collaboratory page.
- Elasticsearch Facet API has been completely replaced with the newer Aggregations API.
- Fix to allow the enabling of experimental features through query parameters.
- Improvements to resizing behaviour of Genome Viewer.
- Bug fix for Collaboratory manifest IDs mistakenly being resolved as AWS-Virginia manifest IDs.
- Bug fixes to Advanced Search links in Phenotype and Enrichment Analysis.
- Misc bug fixes to API, UI, and build process.

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- Functional Impact filter now applies to gene and mutation tracks in the Genome Viewer.
- Functional Imapct filter now also applies to the compound page.
- Increased size of protein viewer and made it resize based on page width.
- Various Front End Bug Fixes.
- Removed SwaggerUI static assets used in the Portal API documetation (this is now centralized at http://docs.icgc.org/)
- Updates to some Portal UI docs.

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- Refactored the repositories API to support changes in document structure in Elasticsearch.
- Added `IS NOT` support for Facets, this functionality is hidden behind a feature flag.
- EntitySetIds are now part of entity id list in JQL. Olds style JQL for entitySetIds is still supported.
- Various UI Bug Fixes.
- Added UI.md (UI Getting Started Developer Guide), CONTRIBUTING.md (Making Contributions to the Source Guide) and GPL3 Licenses to UI code. Changed links to point to newly created ICGC Document site developed in parallel to this release.
- Filters are now managed by a seperate Angular Service to simplify interaction with UI logic.
- Changed directory structure of UI (flattened out unneccessary nesting) to simplify it for future extension.

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- Refactored Advanced Search Front end to render tabs and facets only when required - performance boost is the result.
- Decorated Restangular to provide support for cancelling ajax requests.
- Draft of front end developer conventions in progress - README.md
- Updated build tools on front end.
- Added JS Source Maps Support for extra debugging convenience.

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- New drug/compound entity page which correlates targeted genes and provides context into clinical trials.
- Drug/Compound integration in gene info pages.
- Quick search support added for Compounds/Drugs.
- Bug fixes for genome map viewer including support for tooltip descriptions in fullscreen.
- Reactome Pathway viewer from enrichment analysis now supports the ability to identify overlapping genes (ICGC vs input gene sets).
- Refactored Pathway Viewer into more angular-ized components.
- iobio integration added to AWS/Collaboratory repository pages.

3.8.18.x
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- Added tooltip information for Data Type in External Repository
- Added Analysis Software facet in External Repository
- Updated Genome Viewer to handle new API format
- Bug fixes to mutation counts and text rendering in Pathway Viewer
- Custom Copy to Clipboard Component added throuhgout application.
- Improved performance of the Advanced Search page.
- Released ICGC in the Cloud Universal Guide for AWS and Collaboratory.
- Released ICGC in the Cloud Repository showcase pages for AWS and Collaboratory.
- Separated DCC data releases from the external file repository page.
- Various portal UI bug fixes.
- Fixed mailer for error reporting on the data portal.
- Enrichment Analysis enhancements utilizing the Pathway Viewer for Reactome Pathways.
- Some additional improvements and optimizations introduced to front-end build process.

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- Updated d3 to fix minor error with Pathway Viewer
- Fixed issue that caused Pie Chart colouring from not being correctly assigned to new Projects on Cancer Projects page.
- In Phenotype Analysis, results of 0 should no longer link to advanced search
- When navigating to Genome Viewer from Donor Entity page, the mutation sorting and filter will be carried over
- Corrected the filter used in querying mutations for the Reactome Pathway Viewer
- Fixed bug that caused the Project Sample Sheet to return empty
- Refactored Browser API to fix various problems that could result in error 500s being returned
- Significantly reduced the load time of stacked bar chart in Project Summary page.
- Enhanced data repositories.
- Introduced in Pathway Viewer page relating to Enrichment Analysis
- Added filtering on Reactome ID’s in new Pathway Viewer page.
- Promoted featurePortal service to a Provider so it can be used in config angular modules (useful for altering angular routes or angular ui-router state templates).
- Added ICGC in the Cloud pages including (currently disabled as changes are being done to the documents):
- Logo addition on ICGC Portal Home Page
- ICGC In the Cloud Landing Page
- Preliminary User Guide for AWS-Virginia
- Added a generalized page to be able to model the info regarding associated ICGC Repositories (similar to the PCAWG Page).
- Fixed Grunt Bower service from running multiple times during build
- Added injectable Grunt Front-end Developer Profile so there is no more need to modify the application’s app.js when doing front-end development via ‘grunt server’.
- Updated ICGC Data Portal Team Page to reflect the current Project Team as well as to publicly acknowledge some important contributing parties to the ICGC Portal.