v6.0.5

🧬 Features

• Add plots tab to study view @gblaih (cbioportal-frontend#4802)
• Study view custom sample selection with multi study @7xuanlu (cbioportal-frontend#4867)

✨ Enhancements

• Added select all button and remove all button for columns on SV data @olzhasmukayev (cbioportal-frontend#4872)
• Added button to open iframe source @khaledfahmy123 (cbioportal-frontend#4874)

🐛 Bug Fixes

• 🔒 Update to allow for multiple Authentication Providers @haynescd (#10725)

🎨 Style Tweaks

• fix the padding on the new section @olzhasmukayev (cbioportal-frontend#4880)

👷‍♀️ Testing, Configuration & Deployment

• Update url navigation for e2e tests to first go to blank page @gblaih (cbioportal-frontend#4860)
• Update to remove legacy db properties @haynescd (cbioportal-frontend#4873)

🧰 Maintenance

• Update api clients after change for mutation data filter @alisman (cbioportal-frontend#4875)
• 🔧 Update keycloak image to quay.io @haynescd (cbioportal-frontend#4869)

🕵️‍♀️ Full commit logs

• Backend: v6.0.4...v6.0.5
• Frontend: cBioPortal/cbioportal-frontend@v6.0.4...v6.0.5

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/4.-development/release-procedure#a-note-on-versioning

v6.0.4

🐛 Bug Fixes

• Fix: groups and authorities filter issue @dippindots (#10700)
• Fix: Replace deprecated Spring Security class @haynescd (#10704)
• Fix Mutation Data Counts Endpoint on Mutation Tables and Rename Return Types @7xuanlu (#10665)
• Fix surivival chart for large cohort label overlap (number at risk) @TJMKuijpers (cbioportal-frontend#4833)

📘 Documentation

• Add release 15 for GENIE to news @ritikakundra (#10699)
• Update news 2023 - Mar 2024 @inodb (#10691)

🧹 Cleanup & Refactoring 🔧

• Delete requirements.txt @JREastonMarks (#10686)

👷‍♀️ Testing, Configuration & Deployment

• Update Saml Security Tests @haynescd (#10709)

🧰 Maintenance

• 🔧 Remove temp docker image @haynescd (#10713)
• ➖ Remove mockserver dep from production build @haynescd (#10707)
• 🐛 Update core version in dockerFile @haynescd (#10708)
• Dependencies Update Version of Core @JREastonMarks (#10693)

🕵️‍♀️ Full commit logs

• Backend: v6.0.3...v6.0.4
• Frontend: cBioPortal/cbioportal-frontend@v6.0.3...v6.0.4

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning

v6.0.3

🧬 Features

• Adding Customizable Custom Driver Column to Mutation, CNA, and SV Table @7xuanlu (cbioportal-frontend#4840)

✨ Enhancements

• 🔨Refactor code: retrieve ndex tooltip information dynamically @SAHU-01 (cbioportal-frontend#4847)

🐛 Bug Fixes

• PR for issue #10669 number at risk table @TJMKuijpers (cbioportal-frontend#4862)
• Fix issue with genie download tab loading slow @gblaih (cbioportal-frontend#4863)
• Fix: previous filters deselection upon each 'Select All' click @khaledfahmy123 (cbioportal-frontend#4854)

📘 Documentation

• Issue 10623 update documentation on deploy without docker @JREastonMarks (#10655)

👷‍♀️ Testing, Configuration & Deployment

• Fix localdb tests on the backend @gblaih (cbioportal-frontend#4853)
• Update screenshots after data change @alisman (cbioportal-frontend#4857)

🧰 Maintenance

• Update oncokb client after api change @alisman (cbioportal-frontend#4865)
• #10679 Fix: mysql-connector-java version update to avoid vulnerabilities @amanbhardwaj12072003 (#10681)

🕵️‍♀️ Full commit logs

• Backend: v6.0.2...v6.0.3
• Frontend: cBioPortal/cbioportal-frontend@v6.0.2...v6.0.3

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning

v6.0.2

🐛 Bug Fixes

• Fix News Page redirect @inodb (#10658)
• Fix custom MSK endpoints to include api-legacy @JREastonMarks (#10656)
• Add missing webAPI route @inodb (#10650)
• Fix Immutable List to Mutable List @JREastonMarks (#10639)
• Fix 5x errors on Study View for mutation type table @7xuanlu (#10633)
• Change List to Immutable List @JREastonMarks (#10629)
• Add /faq route @inodb (#10624)
• Fix bar plot changing color when a control is clicked @gblaih (cbioportal-frontend#4845)
• Add configuration for disabling study tag fetching (default to true) @alisman (cbioportal-frontend#4848)

📘 Documentation

• Fix docs redirects for application properties @inodb (#10657)
• Remove old info from deployment procedure @inodb (#10643)
• Add news until May 2023 @inodb (#10631)
• Support default_sort_column config for mutation, CNA, and SV tables @7xuanlu (#10630)
• Add document for inter-repository dependencies @sheridancbio (#10621)

🧰 Maintenance

• Update api clients @alisman (cbioportal-frontend#4850)

👷‍♀️ Testing, Configuration & Deployment

• Add configuration to disable study tags (#10637) @JREastonMarks (#10640)
• Update Security Integration test to remove selenium container @haynescd (#10615)

🕵️‍♀️ Full commit logs

• Backend: v6.0.1...v6.0.2
• Frontend: cBioPortal/cbioportal-frontend@v6.0.1...v6.0.2

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning

v6.0.1

🐛 Bug Fixes

• Changes Immutable List to Mutable List @JREastonMarks (#10620)
• Restore frontend app name property @alisman (#10619)
• fix migrate_db.py path in entrypoint @nr23730 (#10535)
• Fix tutorials @uklineale (#10614 #10606)
• fix structural variant count column on datasets page @uklineale (cbioportal-frontend#4832)

⚙️ REST API Changes

• New Mutation data counts per gene endpoint @7xuanlu (#10559)

📘 Documentation

• Update ER diagram to db schema 2.13.1 @forus (#10617)
• Update bravado documentation with persistent authorization @MatthijsPon (#10616)
• Customize Custom Driver Name in application.properties file @7xuanlu (#10611)

🧰 Maintenance

• JSP files deleted @amanbhardwaj12072003 (#10587)

🕵️‍♀️ Full commit logs

• Backend: v6.0.0...v6.0.1
• Frontend: cBioPortal/cbioportal-frontend@v6.0.0...v6.0.1

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning

v6.0.0

Overview Backend Changes

This release involves a major repackaging of the backend software to improve the development experience. The backend has been upgraded to use Java Spring Boot v3.1.4. The CORE and MAF modules have been moved to new repositories. All other modules have been compacted into a single source repository. We have also updated the JVM to 21 and many libraries have been updated to address security and performance issues.

More information about this can be found in the Migration Guide.

Module Compaction

As an example all code that was in the service module are now in the src folder. This compaction also means that we now have one pom file. The files in service/src/main/java/org/cbioportal/service are now in /src/main/java/org/cbioportal/service

Properties File Update

We have deprecated the portal.properties file and moved most of the configuration properties to application.properties. Additionally we have added a security.properties file for all security configurations.

Security Updates

Properties used to configure Security have changed, see security.properties reference.
The supported authentication values have been updated and are the following: false, oauth2, optional_oauth2, saml. The optional_oauth2 replaces social_auth. This option allows users to use the site without authentication, but they can optionally log in to save virtual studies and groups.

Developer Experience Improvements

• Update testing and code coverage to github processes (#10561, #10548, #10528)
• Enable hot reloading (#10555)

New Repositories

• CORE - https://github.com/cBioPortal/cbioportal-core
• MAF - https://github.com/cBioPortal/maf

Backend Upgrade Related Commits and Merges

• [RFC72] Spring Boot Upgrade @haynescd @JREastonMarks @inodb @pvannierop (#10425, cbioportal-frontend#4753)
• Update to make /api redirect to springdoc.swagger-ui.path @haynescd (#10533)
• Add Installations Map Redirect @haynescd (#10527)
• Add Sentry jar @haynescd (#10530)
• 6.0.0 fixes for issues identified during testing in prod @haynescd (#10579)
• Add Custom OAuth Authorization @haynescd (#10519)
• Fix CacheMapUtil configurations @haynescd (#10513)
• Fix Cache for StudyViewApplier @haynescd (#10593)
• Add /ln path and update proxy Controller @haynescd (#10531)
• Update to make /api redirect to springdoc.swagger-ui.path @haynescd (#10533)
• Add Installations Map Redirect @haynescd (#10527)
• Hot reloading and Formatting @JREastonMarks (#10555)
• Fix SonarCube Coverage @JREastonMarks (#10548, #10528)
• Fix Auth integration @haynescd @pvannierop (#10560)
• Add 401 response when not authorized exception is thrown instead of redirect @haynescd (#10590)
• Add UUID Dat Support @haynescd (cbioportal-frontend#4837)
• Release 6.0.0 Deployment Documentation @JREastonMarks (#10522)

Other Changes

🧬 Features

• Mutational signature plot with cosmic reference signature @TJMKuijpers (cbioportal-frontend#4771)
• Add structural variant count to datasets page @uklineale (#10582, #10547)

✨ Enhancements

• When bookmark url is too long, prompt user to create a virtual study instead @alisman (cbioportal-frontend#4807)
• Update NDex tooltip @inodb (cbioportal-frontend#4828)
• Change NDEx Tab name @inodb (cbioportal-frontend#4797)
• Add user color configuration for oncoprinter @gblaih (cbioportal-frontend#4817)
• Iframe loader should allow fullscreen functionality @alisman (cbioportal-frontend#4801)
• add arrow buttons to tooltip timeline @uklineale (cbioportal-frontend#4808)

🐛 Bug Fixes

• Show p/q-values in boxplots of comparison clinical tab @gblaih (cbioportal-frontend#4842)
• Update mobxpromise and fix circular dependency caused by onResult @alisman (cbioportal-frontend#4836)
• Prevent clicking within a tooltip from triggering row selection @onursumer (cbioportal-frontend#4821)
• Default visibility of p-value above legend SV plot @TJMKuijpers (cbioportal-frontend#4803)
• Update properties to fix cors issue in backend @haynescd (cbioportal-frontend#4819)
• Fix: data type filter set default value for checkbox @TJMKuijpers (cbioportal-frontend#4804)
• Enable study view action buttons earlier @alisman (cbioportal-frontend#4799)

⚙️ Changes to handle external APIs

• Update civic API @leexgh (cbioportal-frontend#4775)

👷‍♀️ Testing, Configuration & Deployment

• Update screenshots after data changes @alisman (cbioportal-frontend#4835)
• Update test for sample selector mutational signature @TJMKuijpers (cbioportal-frontend#4843)
• Remove demo-rfc72 dockerImage from localdb tests @haynescd (cbioportal-frontend#4805)
• Fix path to config_service for dev and dev builds @alisman (cbioportal-frontend#4824)

📘 Documentation

• Update Authenticating-Users-via-Tokens.md @scvannost (#10501)
• Update News Release - fix formatting @rmadupuri (#10509)
• Update News - Dec 29, 2023 data release @sbabyanusha (#10494)
• Fix link to Architecture overview @pieterlukasse (#10596)

🕵️‍♀️ Full commit logs

• Backend: v5.4.10...v6.0.0
• Frontend: cBioPortal/cbioportal-frontend@v5.4.10...v6.0.0

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning

v5.4.10

✨ Enhancements

• Add button in oncoprint tracks menu that adds toggled tracks @gblaih (cbioportal-frontend#4780)
• Update sample type values to show 'total RNA' or 'total DNA' in Patient view @jagnathan (cbioportal-frontend#4782)
• Removing the filtering of amino acid changes with '+' as not relevant anymore @sowmiyaa-kumar (#10487)

🐛 Bug Fixes

• Fix study view survival chart showing two info icons @gblaih (cbioportal-frontend#4793)

👷‍♀️ Testing, Configuration & Deployment

• Implement Custom Tabs mechanism for Study View @pvannierop (cbioportal-frontend#4776)
• Update screenshots after Oncokb update @alisman (cbioportal-frontend#4795)

🕵️‍♀️ Full commit logs

• Backend: v5.4.9...v5.4.10
• Frontend: cBioPortal/cbioportal-frontend@v5.4.9...v5.4.10

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning

v5.4.9

🧬 Features

• [RFC77] Filter buttons on the landing page study search menu @TJMKuijpers (cbioportal-frontend#4721)
• Add group percentages to oncoprint @alisman (cbioportal-frontend#4756)

✨ Enhancements

• Fix incorrect oncokb data and cancer type label used in mutations table @gblaih (cbioportal-frontend#4758)
• Add user color configuration for oncoprint @gblaih (cbioportal-frontend#4699)
• Change gene add behavior to improve user experience @alisman (cbioportal-frontend#4770)

🐛 Bug Fixes

• Clinical attribute types with priority of zero should not appear by default on study view @alisman (cbioportal-frontend#4768)
• Study view: fix comparison session generation from study view bin cha… @alisman (cbioportal-frontend#4767)
• Use appropriate genome-nexus url depending on study @kalletlak (cbioportal-frontend#4787)
• Restore asterisks in oncoprint track percentage labels @alisman (cbioportal-frontend#4779)
• Fix for endless loop preventing gene update using modify query interface (after direct load of results of view) @alisman (cbioportal-frontend#4778)

📘 Documentation

• Fix path typos in MSK-Maintenance.md @jamesqo (#10480)
• Update study view clinical charts documentation @dippindots (#10440)

👷‍♀️ Testing, Configuration & Deployment

• Update screenshots with civic disabled @alisman (cbioportal-frontend#4769)
• Update screenshots after oncokb update and pie chart label change @alisman (cbioportal-frontend#4766)
• Fix spec import that is currently breaking local db test report @alisman (cbioportal-frontend#4781)%
• Label checker action reruns when needed @Luke-Sikina (#10462)

🕵️‍♀️ Full commit logs

• Backend: v5.4.7...v5.4.9
• Frontend: cBioPortal/cbioportal-frontend@v5.4.7...v5.4.9

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning

v5.4.7

🐛 Bug Fixes

• Refactor to allow pie and table charts to download both full and summary data @alisman (cbioportal-frontend#4762)
• Fix SVG download (prevent embedding of css) @alisman (cbioportal-frontend#4761)
• Fix link to MKS Impact study agreement @alisman (cbioportal-frontend#4759)
• Add download data and PDF option @TJMKuijpers (cbioportal-frontend#4757)

🎨 Style Tweaks

• Patient timeline: Make sure sample acquisition track always appears above sequencing @alisman (cbioportal-frontend#4760)

🧰 Maintenance

• Update API clients @alisman (cbioportal-frontend#4765)

📘 Documentation

• Documentation for the 'priority_studies' feature in portal.properties @sowmiyaa-kumar (#10441)
• Improve timeline link docs @jagnathan (#10403)

🕵️‍♀️ Full commit logs

• Backend: v5.4.6...v5.4.7
• Frontend: cBioPortal/cbioportal-frontend@v5.4.6...v5.4.7

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning

v5.4.6

🧬 Features

• RFC69 : survival chart with landmark events and hazard ratio @TJMKuijpers (cbioportal-frontend#4740)
• match cna chart colors with oncoprint and adjust label colors according to slice brightness @h164654156465 (cbioportal-frontend#4750)

🎨 Style Tweaks

• Genie portal timeline: tweak track ordering for assessment tracks @alisman (cbioportal-frontend#4754)

🕵️‍♀️ Full commit logs

• Backend: v5.4.5...v5.4.6
• Frontend: cBioPortal/cbioportal-frontend@v5.4.5...v5.4.6

🏷Notes on versioning and release procedure

https://docs.cbioportal.org/development/release-procedure/#a-note-on-versioning