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

✨ 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

🧬 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

🐛 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

🧬 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

🐛 Bug Fixes

• Fix search issue in SV table when site1 gene is missing @alisman (cbioportal-frontend#4752)
• Patient page: fix Clinical Events table search (handle numerical data) @alisman (cbioportal-frontend#4751)

👷‍♀️ Testing, Configuration & Deployment

• Configure left logo in the cBioPortal header via 'skin.left_logo' property @pvannierop (cbioportal-frontend#4747)
• Fix context initialization when property 'dat.method' is missing @pvannierop (#10423)
• Use RSA256 algorithm for SAML2 authN statement singing @pvannierop (#10387)

🖊️ Data Importer & Validator

• Replace DB Prop Assertion with Warning @averyniceday (#10424)

🕵️‍♀️ Full commit logs

• Backend: v5.4.4...v5.4.5
• Frontend: cBioPortal/cbioportal-frontend@v5.4.4...v5.4.5

🏷Notes on versioning and release procedure

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

🧬 Features

• Enable Results View Structural Variants Tab @inodb (cbioportal-frontend#4745)

✨ Enhancements

• On patient page, default to SBS mutational signatures @alisman (cbioportal-frontend#4748)

🐛 Bug Fixes

• StudyView: in manual submit mode, prevent user from clearing with UI @alisman (cbioportal-frontend#4738)
• Resolve fetching genomic chart datatype for logged in user @kalletlak (cbioportal-frontend#4742)
• Enable server public key retrieval in python scripts @pvannierop (#10413)

🎨 Style Tweaks

• Update home page citation @dippindots (cbioportal-frontend#4741)

📘 Documentation

• Improve keycloak configuration docs @forus (#10238)

👷‍♀️ Testing, Configuration & Deployment

• Add 'skin.left_logo' property @pvannierop (#10412)
• [RFC68] Enable Struct Var table feature on Study View with 'skin.study_view.show_sv_table' property @pvannierop (cbioportal-frontend#4744)

🕵️‍♀️ Full commit logs

• Backend: v5.4.3...v5.4.4
• Frontend: cBioPortal/cbioportal-frontend@v5.4.3...v5.4.4

🏷Notes on versioning and release procedure

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

✨ Enhancements

• [RFC 76] Redesign oncoprint annotation menu @BasLee (cbioportal-frontend#4709)

🐛 Bug Fixes

• Fix SV pane search box: Only filter genes when present @BasLee (cbioportal-frontend#4711)

🎨 Style Tweaks

• Remove revue from Annotation column sorting @leexgh (cbioportal-frontend#4739)

📐 Prototype (Internal Use)

• (GSoC) Generic Assay Categorical/Binary data implementation Frontend @Djokovic0311 (cbioportal-frontend#4686)

📘 Documentation

• Add some more info to getting started docs @inodb (#10399)
• Update News-Genie.md @ritikakundra (#10394)

👷‍♀️ Testing, Configuration & Deployment

• [RFC68] Add 'skin.study_view.show_sv_table' property @pvannierop (#10405)

🕵️‍♀️ Full commit logs

• Backend: v5.4.2...v5.4.3
• Frontend: cBioPortal/cbioportal-frontend@v5.4.2...v5.4.3

🏷Notes on versioning and release procedure

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

🐛 Bug Fixes

• (JSP) Fix broken global parameter @dippindots (#10381)
• Fix disabling SSL for MySQL connection @pvannierop @dippindots (#10353)
• search returns false for bad regex @jfkonecn (cbioportal-frontend#4719)

📘 Documentation

• Update faq.md @jagnathan (#10380)

👷‍♀️ Testing, Configuration & Deployment

• Update google analytics implementation @alisman (cbioportal-frontend#4718)

🖊️ Data Importer & Validator

• Improve validation of Entity Stable ID @oplantalech (#10365)
• Fixed an error in naming alleles for the mutation file checks in SNP, DNP, and TNP @sowmiyaa-kumar (#10235)

🧰 Maintenance

• Update yarn lock file @dippindots (cbioportal-frontend#4722)
• Bump semver from 5.6.0 to 5.7.2 @dependabot (cbioportal-frontend#4664)
• Bump word-wrap from 1.2.3 to 1.2.4 @dependabot (cbioportal-frontend#4668)

🕵️‍♀️ Full commit logs

• Backend: v5.4.1...v5.4.2
• Frontend: cBioPortal/cbioportal-frontend@v5.4.1...v5.4.2

🏷Notes on versioning and release procedure

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

🧬 Features

• Add higher granularity CNA charts on Study View @h164654156465 (cbioportal-frontend#4706)

✨ Enhancements

• Add property to define custom sample type colors in patient view @BasLee (cbioportal-frontend#4704)
• Improve non-profiled gene panel links in oncoprint tooltip @BasLee (cbioportal-frontend#4701)
• Fix hidden non-genomic data when excluding VUS in oncoprint @BasLee (cbioportal-frontend#4712)
• Extend sample type colors in patient view @BasLee (cbioportal-frontend#4679)

🏎 Performance Tweaks

• Reduce loading time for mutations table in comparison page @gblaih (cbioportal-frontend#4714)

👷‍♀️ Testing, Configuration & Deployment

• Update API clients and fix screenshots after Oncobk update @alisman (cbioportal-frontend#4715)
• Add e2e tests for Interactive Web Tour @Beking0912 (cbioportal-frontend#4700)
• Add json prop for custom patient view sample type colors @BasLee (#10336)

🕵️‍♀️ Full commit logs

• Backend: v5.4.0...v5.4.1
• Frontend: cBioPortal/cbioportal-frontend@v5.4.0...v5.4.1

🏷Notes on versioning and release procedure

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