🧬 Features
Normalize survival status clinical data
As part of the effort to support multiple types of survival analyses including Progression Free Survival (PFS) and Disease Free Survival (DFS), the survival status related clinical data is normalized in v3.4.0. These are patient clinical attributes, such as OS_STATUS and DFS_STATUS. There were a variety of different values for these including DECEASED, Recurred/Progressed, Recurred, LIVING, DiseaseFree. To capture both the original value and the normalized value we decided to change the value to be prefixed with either 0: or 1:, for example: 0:LIVING, 0:DiseaseFree and 1:DECEASED. This allows one to get either the normalized boolean or the raw original text value. A script is included to move migrate data files to the new format
- Backend @dippindots (#7574)
- Frontend
- Handle the new format in various places on frontend @dippindots (#3257)
- (Patient page header) Remove prefix for OS_STATUS and DFS_STATUS @dippindots (#3260)
- Database migration @dippindots (migration.sql)
- Tool for migration of data files: @dippindots @rmadupuri (#15)
✨ Enhancements
- Combine Comparison and Survival buttons into one button "Comparison/Survival" @alisman (#3259)
- Pick default profile for any alteration types included in OQL @adamabeshouse (#3231)
🎨 Style Tweaks
- Show super small p/q values as <10^-x rather than 0 @kalletlak (#3235)
🐛 Bug Fixes
- Add updated forked dependency for live to support spring 5x @kalletlak (#7587)
- Fix error when clearing enriched groups selection @kalletlak (#3254)
- Fix relative path on institute image logo @alisman (#3249)
- Trim off html entities coming from NCI API @zhx828 (#3219)
- Check intragenic before regular fusion & Do not set intragenic as functionalFusion @zhx828 (#3244)
- Fix incorrect mapping of study to discrete CNA molecular profile @onursumer (#3243)
- oncoprint - make counts tracks (e.g. mutation spectrum) downloadable) @adamabeshouse (#3251)
⚙️ REST API Changes
- Github action to test performance of genie private portal @mandawilson (#7040)
- Set order of API Tags without alphabet prefix @inodb (#7565)
🗄 Database Migration
- Prototype: update and Propagate AlleleSpecificCopyNumber Models @averyniceday (#7582)
- Database migration for survival status related attributes @dippindots (migration.sql)
📘 Documentation
- Updated FAQ about zscores @jjgao (#7539)
- fix link broken in docker import data document @dippindots (#7563)
🧹 Cleanup & Refactoring 🔧
👷♀️ Testing, Configuration & Deployment
- Add a class to local dev banner @zhx828 (#7573)
- Github action to test performance of genie private portal @mandawilson (#7040)
🧰 Maintenance
- Disconnecting use of MutationRepositoryLegacy in business module. @n1zea144 (#7588)
- Disconnect gene panel code (importer) from business module. @n1zea144 (#7569)
- Update screenshots for release-3.4.0 @dippindots (#3258)
- Fix two tests which broken due to addition of new study @alisman (#3250)
- remove console log on comparison page @dippindots (#3253)
📐 Prototype (Internal Use)
- Update and Propagate AlleleSpecificCopyNumber Models @averyniceday (#7582)
🕵️♀️ Full commit logs
- Backend: v3.3.7...v3.4.0
- Frontend: cBioPortal/cbioportal-frontend@v3.3.7...v3.4.0
🏷Notes on versioning and release procedure
https://docs.cbioportal.org/4.-development/release-procedure#a-note-on-versioning