🧬 Features

• Pairwise plots @sowmiyaa-kumar (cbioportal-frontend#5148)

🐛 Bug Fixes

• Fix logout confirmation issue for saml_plus_basic @dippindots (#11469)

⚙️ REST API Changes

• RFC93: Custom variant annotation filter in study view page @FlorisVleugels (#11432)

🗄 Clickhouse Database Changes

• Add off_panel flag for genomic_event_derived table @fuzhaoyuan (#11477)

🧰 Maintenance

• Revert "Fix CDSA iframe url" @dippindots (cbioportal-frontend#5154)

📘 Documentation

• Replace Github Packages with Maven Central @zainasir (#11489)
• Update About-Us.md @oplantalech (#11491)
• Update Funders @inodb (#11483)
• add bluesky and linkedin newsletter to FAQ @tmazor (#11474)
• add migration guide for v6.0 to v6.1 @zainasir (#11467)

👷‍♀️ Testing, Configuration & Deployment

• Replace Github Packages with Maven Central @zainasir (#11489, cbioportal-frontend#5156)
• Migration of localdb tests to async @gblaih (cbioportal-frontend#5143)
• Stabilize query page reference genome test @gblaih (cbioportal-frontend#5155)
• Fix e2e remote quick search test @gblaih (cbioportal-frontend#5151)
• Screenshot updates for pairwise feature on plots tab @alisman (cbioportal-frontend#5149)
• Localdb screenshot tracking fix testing @gblaih (cbioportal-frontend#5146)

🎨 Style Tweaks

• remove quick search beta @inodb (cbioportal-frontend#5150)

🕵️‍♀️ Full commit logs

• Backend: v6.1.0...v6.1.1
• Frontend: cBioPortal/cbioportal-frontend@v6.1.0...v6.1.1

🏷Notes on versioning and release procedure

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

✨ Enhancements

• Add aria-labels to buttons on query page @alisman (cbioportal-frontend#5142)
• Improve layout of cancer summary page @gblaih (cbioportal-frontend#5133)

📘 Documentation

• Update PR section in CONTRIBUTING.md @dippindots (#11443)
• improve documentation for using github packages @zainasir (#11461)
• Replace Jitpack with Github Packages @zainasir (#11450)
• Fixed the path of Backend code organization File @gauravbyte (#11451)

👷‍♀️ Testing, Configuration & Deployment

• Replace Jitpack with Github Packages @zainasir (#11450)
• Replace Jitpack with Github Packages @zainasir (cbioportal-frontend#5128)
• Fix broken studyview e2e remote tests @gblaih (cbioportal-frontend#5139)
• Fix screenshot tracking in circleci localdb tests @zainasir (cbioportal-frontend#5127)
• fix screenshot tracking for backend localdb tests in circleci @zainasir (#11449)

🕵️‍♀️ Full commit logs

• Backend: v6.0.28...v6.0.29
• Frontend: cBioPortal/cbioportal-frontend@v6.0.28...v6.0.29

🏷Notes on versioning and release procedure

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

🐛 Bug Fixes

• Fix for frequency in multi-study view @eugeniomazzone (#11331)
• Update groupid for jitpack builds @zainasir (#11421)
• Remove NA label when NA=0 in filter chart @lllinging (cbioportal-frontend#5126)
• Fix the option to configure default view oncoprint @TJMKuijpers (cbioportal-frontend#5117)
• Improve loading behavior of charts on results comparison alterations tab @gblaih (cbioportal-frontend#5114)

✨ Enhancements

• feat : Added boxplot stats as tooltip for axis label @rishisulakhe (cbioportal-frontend#5125)
• Add sample and patient counts toggle for cancer summary chart tooltip @gblaih (cbioportal-frontend#5110)
• Add last updated time and embolden exact matches in cosmic column in mutations table @gblaih (cbioportal-frontend#5103)

👷‍♀️ Testing, Configuration & Deployment

• Fix e2e localdb results comparison alteration tests @gblaih (cbioportal-frontend#5121)
• Fix flaky e2e remote tests @gblaih (cbioportal-frontend#5119)
• Fix broken annotation filter localdb tests @gblaih (cbioportal-frontend#5107)

📘 Documentation

• Add Supported Data Types Docs @inodb (#11409)
• Fix file paths in the docker documentation @rmadupuri (#11414)
• add documentation for clickhouse mode setup for cbioportal docker compose @zainasir (#11433)
• add stacked bar chart sorting to news page @tmazor (#11434)
• Fix 11373 Standalone Deployment Documentation @JREastonMarks (#11427)
• Remove servlet-api dependency from mockserver-client-java @dippindots (#10844)

🧰 Maintenance

• Remove servlet-api dependency from mockserver-client-java @dippindots (#10844)

🕵️‍♀️ Full commit logs

• Backend: v6.0.27...v6.0.28
• Frontend: cBioPortal/cbioportal-frontend@v6.0.27...v6.0.28

🏷Notes on versioning and release procedure

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

🐛 Bug Fixes

• Update records to extend Serializable @haynescd (#11419)
• Update the names for oncoprint tracks and custom sample color @TJMKuijpers (#11400)

🧹 Cleanup & Refactoring 🔧

• Update logo image and add brand assets folder @alisman (cbioportal-frontend#5113)

🕵️‍♀️ Full commit logs

• Backend: v6.0.26...v6.0.27
• Frontend: cBioPortal/cbioportal-frontend@v6.0.26...v6.0.27

🏷Notes on versioning and release procedure

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

🐛 Bug Fixes

• Fix study view crash for clinical data only studies and no gene panel data @Aiosa (#11358)
• Fix Generic Assay show categorical patient counts - legacy @fuzhaoyuan (#11381)
• Add generic assay profiles checking in study view page @dippindots (#11370)
• Fix CDSA iframe url @alisman (cbioportal-frontend#5111)
• Fix comparison mutations tab not loading when no mutations selected @gblaih (cbioportal-frontend#5090)
• Timeline: hide superfluous drag-to-zoom button when zooming is disabled @FilledEther20 (cbioportal-frontend#5096)
• Fix compare button for treatment tables on study view @gblaih (cbioportal-frontend#5097)

✨ Enhancements

• Expand tooltip target for boxplot @alisman (cbioportal-frontend#5112)
• Add table visualisation for categorical values @pozhidaevak (cbioportal-frontend#5012)

🏎 Performance Tweaks

• Re-arrange joining on genetic_alteration table to optimize memory con… @alisman (#11374)

📘 Documentation

• Create Isolated Deployment (incl local OncoKB, Genome Nexus) @JREastonMarks (#11378)
• Clarify spring security configuration @inodb (#11388)
• Fix Load-Sample-Cancer-Study.md @VenkateshVishwas (#11288)
• Fix README.md for Windows users @KingAlex1985 (#11342)
• Fix typo in feature-development-guide.md @m12m3r (#10922)
• Update swagger URLs in notebook docs @er-abhijeet (#11363)

🧹 Cleanup & Refactoring 🔧

• Remove unneeded references to old tables @sheridancbio (#10875)
• Delete unused logfile in root directory @jamesqo (#10905)
• Update cBioPortal Architecture to start transition to clickhouse only implementation @haynescd (#11368)
• Add rfc80 clean arch @haynescd (#11396)

👷‍♀️ Testing, Configuration & Deployment

• Label new issues automatically @dippindots (#11383)
• Support custom springboot args for circleci api tests @zainasir (#11398)
• Update circleci localdb tests to use the new setup @zainasir (#11385)
• Fix local e2e @alisman (cbioportal-frontend#5102)
• Fix flaky test when inputting geneset @gblaih (cbioportal-frontend#5101)
• Refactor localdb tests @inodb (cbioportal-frontend#5078)
• Fix broken remote e2e tests @gblaih (cbioportal-frontend#5100)
• E2E: fix element selection for home.spec.test @alisman (cbioportal-frontend#5098)

🧰 Maintenance

• Update cache action version @inodb (#11397)
• Update docker build and push action to latest version @dippindots (#11147)

🕵️‍♀️ Full commit logs

• Backend: v6.0.25...v6.0.26
• Frontend: cBioPortal/cbioportal-frontend@v6.0.25...v6.0.26

🏷Notes on versioning and release procedure

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

🐛 Bug Fixes

• Fix legacy "not mutated" count error @fuzhaoyuan (#11341)
• Mutation tab: Handle missing functional impact data from GN gracefully @alisman (cbioportal-frontend#5092)
• Revert temp clinical data value casing workaround @onursumer (cbioportal-frontend#5074)

🧬 Features

• Add Stacked Bar Chart and sorting to Plots Tab @SURAJ-SHARMA27 (cbioportal-frontend#4960)

✨ Enhancements

• hide timeline events availability chart by default @ShahKirtan2003 (cbioportal-frontend#5066)

📘 Documentation

• Add migration guide for v6.0.24 @zainasir (#11346)

👷‍♀️ Testing, Configuration & Deployment

• Update e2e tests after hiding of default timeline events availability… @alisman (cbioportal-frontend#5094)
• Fix e2e @alisman (cbioportal-frontend#5091)

🕵️‍♀️ Full commit logs

• Backend: v6.0.24...v6.0.25
• Frontend: cBioPortal/cbioportal-frontend@v6.0.24...v6.0.25

🏷Notes on versioning and release procedure

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

✨ Enhancements

• Improve Homepage Search: Hide Dropdown on Typing @GarvitDadheech (cbioportal-frontend#4953)
• Add truncation of timeline label @jCHENEBY (cbioportal-frontend#4990)

🐛 Bug Fixes

• Study View Clin Data Pagination Fix @fuzhaoyuan (cbioportal-frontend#4909)
• Fix genie api page error @gblaih (#11336)
• Fix sv tab genome nexus client @fuzhaoyuan (cbioportal-frontend#5045)
• On Study View sort structural variant table by sample count @alisman (cbioportal-frontend#5046)
• Update function logScalePossible for generic assay negative data @TJMKuijpers (cbioportal-frontend#5084)
• Bugfix/hide empty resource tab @Nelliney (cbioportal-frontend#4969)
• Fix log scale breaking box plot in plots tab @gblaih (cbioportal-frontend#5079)

🧰 Maintenance

• Upgrade to spring boot 3.4 @gblaih (#11318)
• Update api client @dippindots (cbioportal-frontend#5082)

🏎 Performance Tweaks

• Defer loading of gene panel data until plots tab is shown @alisman (cbioportal-frontend#5087)
• Make XY plot data cacheable @onursumer (#11278)
• Reduce api calls for generic assay meta in study view page @dippindots (cbioportal-frontend#5019)

🧹 Cleanup & Refactoring 🔧

• Remove Heroku references @thepiyush-303 (cbioportal-frontend#5088)

📘 Documentation

• Update News-Genie.md @sbabyanusha (#11326)
• Fix the broken link on the ER Diagram page in docs @chandrikarj (#11309)

👷‍♀️ Testing, Configuration & Deployment

• Modify config service API response to return correct data type @arishta (#11323)
• Add security status badge @zainasir (#11335)
• Improve logging for security tests on circleci @zainasir (#11332)
• Improve circleci tests with reusable docker images @zainasir (#11328)
• Bin merge test & input validation @fuzhaoyuan (#11275)
• Upgrade circleci config version and improve api/security tests @zainasir (#11325)
• Integrate Docker Scout as part of security tests. @zainasir (#11324)
• Fix e2e tests to use CANCER_TYPE rather than tumor type @rishisulakhe (cbioportal-frontend#5077)
• Update screenshots for timeline @alisman (cbioportal-frontend#5085)
• Update screenshots, tests & api clients @alisman (cbioportal-frontend#5081)
• Fix localdb servdist @alisman (cbioportal-frontend#5080)
• Update screenshot after gene table update @inodb (cbioportal-frontend#5076)

🕵️‍♀️ Full commit logs

• Backend: v6.0.23...v6.0.24
• Frontend: cBioPortal/cbioportal-frontend@v6.0.23...v6.0.24

🏷Notes on versioning and release procedure

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

🧬 Features

• Opt-In Clickhouse mode of study view @alisman (#11224, cbioportal-frontend#5069)

✨ Enhancements

• Change file and links name to resource displayName @hweej (cbioportal-frontend#5061)
• Improve Parsing of Custom Selection @anshuman-rai-27 (cbioportal-frontend#5064)
• Add gene column in the Mutations table @arishta (cbioportal-frontend#5049)
• Show gene search icon on row hover @arishta (cbioportal-frontend#5059)

🐛 Bug Fixes

• Fix download button in clinical tab @arishta (cbioportal-frontend#5058)
• Use NP instead of NS for Mutations in Download tab @arishta (cbioportal-frontend#5057)

📘 Documentation

• Update Redis config source reference @emmanuel-ferdman (#11145)
• Add documentation for quick select on homepage @sowmiyaa-kumar (#10452)
• Update file paths in data import scripts documentation @zainasir (#11305)
• Add documentation for cBioPortal security measures. @zainasir (#11300)
• Update News.md @sbabyanusha (#11295)
• Add donate button config instructions @inodb (#11286)

👷‍♀️ Testing, Configuration & Deployment

• fix typo in github dependency graph action @zainasir (#11303)
• update github dependency graph with docker builds @zainasir (#11302)
• automate jitpack build and frontend version update for new releases @zainasir (cbioportal-frontend#5067)
• Update localdb screenshots @alisman (cbioportal-frontend#5068)

🕵️‍♀️ Full commit logs

• Backend: v6.0.22...v6.0.23
• Frontend: cBioPortal/cbioportal-frontend@v6.0.22...v6.0.23

🏷Notes on versioning and release procedure

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

✨ Enhancements

• add donate button @inodb (cbioportal-frontend#5065)
• Group comparison view: update boxplot info in clinical tab @TJMKuijpers (cbioportal-frontend#4924)

🐛 Bug Fixes

• Fix full data download failing with pie chart in study view @gblaih (#11239)

👷‍♀️ Testing, Configuration & Deployment

• eliminate code issues in jitpack github workflow @zainasir (cbioportal-frontend#5056)
• fix release-management workflow @zainasir (cbioportal-frontend#5054)
• add trigger for modified labels @zainasir (cbioportal-frontend#5053)

📘 Documentation

• Fix seed database commands in docs @VenkateshVishwas (#11279)
• Add property for donate button configuration @alisman (#11284)
• add donate page to docs @inodb (#11282)
• Update news about GDC Target studies @sbabyanusha (#11269)
• Adds documentation for managing keycloak instance via API @hweej (#11264)
• Improve data loading docs @pieterlukasse (#11251)
• Fix typo in feature-development-guide.md @vaibhavlachhwani (#11242)
• Fix broken links in cBioPortal-ER-Diagram.md @vaibhavlachhwani (#11243)

🕵️‍♀️ Full commit logs

• Backend: v6.0.21...v6.0.22
• Frontend: cBioPortal/cbioportal-frontend@v6.0.21...v6.0.22

🏷Notes on versioning and release procedure

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

🧬 Features

• Rfc85 dynamic virtual study @forus (#11040)
• Implement RFC85 Dynamic Virtual Study @forus (cbioportal-frontend#5016)
• Add alphaMissense in functional impact column @leexgh (cbioportal-frontend#5042)

✨ Enhancements

• Add description to top of resource tab on patient view @Nelliney (cbioportal-frontend#4964)

🐛 Bug Fixes

• Fix sample/study counter in VS description @forus (cbioportal-frontend#5028)
• Fix Sift and Polyphen blank in NRAS @leexgh (cbioportal-frontend#5039)

👷‍♀️ Testing, Configuration & Deployment

• add retry logic for 404 errors @zainasir (cbioportal-frontend#5040)
• Update localdb test @dippindots (cbioportal-frontend#5048)

📘 Documentation

• Add setup guide for Kubernetes deployment @zainasir (#11232)
• Add gget CLI client to docs @inodb (#11035)
• Add instructions for accessing frontend on localhost with a self-signed certificate @yashhash2 (#11075)
• Add AlphaMissense news @leexgh (#11202)
• Add Mutation Assessor v4 news @leexgh (#11148)
• Add ICI note to chromoscope news @inodb (#11164)

🧹 Cleanup & Refactoring 🔧

• Remove unused noauthsessionservice property @nbentoneves (#11169)

🕵️‍♀️ Full commit logs

• Backend: v6.0.20...v6.0.21
• Frontend: cBioPortal/cbioportal-frontend@v6.0.20...v6.0.21

🏷Notes on versioning and release procedure

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