v3.2.4

🧬 Features

• oncoprint - allow adding gaps to string-valued clinical tracks @adamabeshouse (#2926)
• Add filter bookmark UI to study view page when cohort is filtered @alisman (#3038)

🐛 Bug Fixes

• Study view: filter molecular profiles for gene table @kalletlak (#3066)
• Fix study url in study summary header @kalletlak (#3067)
• Enrichments: Fix downloading gene plot @kalletlak (#3069)

🏎 Performance Tweaks

• Use selected sample instead of sending complete filter object @kalletlak (#3054)

⚙️ Changes to handle external APIs

• Use OncoKB basic endpoints for annotation service @zhx828 (#3055)

📘 Documentation

• remove cirlceci badges @inodb (#3061)

🧰 Maintenance

• update to latest oncokb client @zhx828 (#3071)

📐 Prototype

• On timeline generalize sample label replacement @inodb (#3076)

🕵️‍♀️ Full commit logs

• Backend: cBioPortal/cbioportal@v3.2.3...v3.2.4
• Frontend: v3.2.3...v3.2.4

🏷 Notes on versioning and release procedure

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

v3.2.3

✨ Enhancements

• don't clear selected study list when clicking query tab on homepage @dippindots (#3057)
• survival - use only 2 digit precision for median months @adamabeshouse (#3047)
• Fix samples briefly showing up as unprofiled on patient view tab @onursumer (#3036)

🐛 Bug Fixes

• Hot fix to properly await samples in gene panel calls @alisman (#3051)

📘 Documentation

• Add Software acknowledgment page @ecerami (#3058)
• Improve frontend README (how to run & e2e tests) @ecerami (#3048)

👷‍♀️ Testing, Configuration & Deployment

• Increase timeout to fix flakey unit test @alisman (#3060)
• Updated failing study view screenshots @ecerami (#3049)

🧰 Maintenance

• Set licenses to SPDX Identifier of AGPL-3.0-or-later @ecerami (#3044)

🕵️‍♀️ Full commit logs

• Backend: cBioPortal/cbioportal@v3.2.2...v3.2.3
• Frontend: v3.2.2...v3.2.3

🏷 Notes on versioning and release procedure

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

v3.2.2

🧬 Features

• Add comparison tab to results view, including enrichments and survival tabs @adamabeshouse (#2989)

✨ Enhancements

• Handle 403 errors properly in global fashion @alisman (#3028)

🐛 Bug Fixes

• exclude mutation uncalled profile and fusion profile @dippindots (#3040)
• Fix error while calculating profiled samples count @kalletlak (#3041)
• Study view: fix default group name while creating new group @kalletlak (#3039)
• Disable a track if the corresponding annotation is disabled @onursumer (#3031)
• Study view: fix virtual study description @kalletlak (#3027)

📘 Documentation

• Add windows dev info to README @inodb (#3043)
• remove references to API URL and .env in README @ecerami (#3042)
• Add links to nvm and yvm in README @ecerami (#3029)

👷‍♀️ Testing, Configuration & Deployment

• Expand unit test coverage to cover all functions in MutationUtils.ts @ecerami (#3034)
• Add missing screenshot for oncoprint e2e @alisman (#3035)
• Fix flakey e2e test @adamabeshouse (#3033)

🕵️‍♀️ Full commit logs

• Backend: cBioPortal/cbioportal@v3.2.1...v3.2.2
• Frontend: v3.2.1...v3.2.2

🏷 Notes on versioning and release procedure

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

v3.2.1

🧬 Features

• add hgvsg column and link out to genome nexus @leexgh (#2971)
• Add quick oql edit feature to results view page next to current gene list @alisman (#2994)

✨ Enhancements

• Add separate genome nexus cache for mutation assessor @alisman (#3024)
• Study view: reset filters when custom cases are selected @kalletlak (#2973)
• Let results view oncoprint fill page, instead of imposing a maximum height @adamabeshouse (#2985)
• Study View: Always show selected genes on top and alternate selected rows color @kalletlak (#2980)
• Show gnomad in number @leexgh (#2987)

🐛 Bug Fixes

• Study view: support old chart Ids when retrieving user preference settings @kalletlak (#3010)
• Filter fusion and structural varinat profiles while getting non mutation profiles @kalletlak (#3000)
• Loading tracks after initializing the igv browser @onursumer (#3003)
• oncoprint - fix occasional bug with removing tracks @adamabeshouse (#2930)

🎨 Style Tweaks

• In default search example configuration, change "provisional" to "leg… @alisman (#3026)
• Tweak wording of quick gene edit submit button @alisman (#3011)
• Tweaks to ng-chm button (Fixes #6973) @ChrisWakefield (#2988)
• Change footer version logic @inodb (#2998)

⚙️ Changes to handle external APIs

• Oncokb auth @zhx828 (#2889)
• MatchMiner increase column width for clinical criteria @victoria34 (#2978)

📘 Documentation

• Mention pinned yarn version @Luke-Sikina (#3018)

👷‍♀️ Testing, Configuration & Deployment

• SV: Fix failing test @kalletlak (#2999)
• In localdb e2e tests, don't unnecessarily restart database @alisman (#3004)

🧰 Maintenance

• Prettier @adamabeshouse (#3002)
• Reformat files with prettier @inodb (#3017)
• On Netlify, optimize build times by running ts transpileOnly (except prod build) @alisman (#3006)
• Update circleci build cache key to take packages folder into account @alisman (#3001)

🕵️‍♀️ Full commit logs

• Backend: cBioPortal/cbioportal@v3.2.0...v3.2.1
• Frontend: v3.2.0...v3.2.1

🏷 Notes on versioning and release procedure

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

v3.2.0

v3.2.0

There are three major changes in v3.2.0. All are backend only changes (frontend of these features is under development):

• Importer, backend & REST API support for both old and new style structural variant data. In the old format one would put fusion's in the mutations table. In the new format there's a specific structural variant table and a separate case list for structural variants. As a deployer for cBioPortal one currently does not have to make any changes to the data files. The old format will continue to be supported. The frontend for the new fusion format is still in development (for more info see RFC31_b).
• Importer, backend & REST API support for Generic Assay data. This is for matrix style data where a sample has a value for some "entity". Generic Assays allow one to support all kinds of data, e.g. a drug with a particular response value for a sample, or a mutational signature and the exposure rate in that sample. For more info see RFC51. The current implementation only supports the backend side. There is no generic frontend layer yet. Treatment data has been converted to Generic Assay data and corresponding frontend changes have been made.
• Importer, backend & Rest API support for allele specific copy number data, cancer cell fraction estimates as well as additional free text annotation in JSON format. This is to support data from e.g. Facets. See cBioPortal/cbioportal#6540 for more information.

Many thanks to @khzhu @dippindots @kalletlak @ao508 @averyniceday @sheridancbio @mandawilson @pvannierop @alisman @n1zea144 @onursumer @jjgao @ckandoth @lemccarthy @SRodenburg !

🗄 Database Migration

• Add Generic Assay related tables
• Convert Treatment Response Data to Generic Assay
• Add fusion profiles for studies that have mutations of type FUSION in the mutation table
• Add support for allele specific copy number data, cancer cell fraction estimates as well as additional free text annotation in JSON format for mutations (see: cBioPortal/cbioportal#6540).

⬆️ How to Upgrade

• We recommend to wait for the v3.2.1 release. But if you'd like to upgrade one would need to run the database migration script (https://docs.cbioportal.org/2.1.1-deploy-with-docker-recommended/docker#step-4-migrate-database-to-latest-version) and use the new 3.2.0 docker image (https://hub.docker.com/repository/docker/cbioportal/cbioportal/tags?page=1).

🕵️‍♀️ Full commit logs

• Backend: cBioPortal/cbioportal@v3.1.11...v3.2.0
• Frontend: v3.1.11...v3.2.0

🏷 Notes on versioning and release procedure

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

v3.1.11

✨ Enhancements

• Study View: ignore case while applying filters on pie chart @kalletlak (#2995)
• [react-mutation-mapper] display error message when no transcript available @onursumer (#2993)
• use new oncoprint version, which uses numbers for shape specification @adamabeshouse (#2975)

🐛 Bug Fixes

• Remove empty param from URL in e2e test @adamabeshouse (#2997)
• Fix error while fetching referenceGenomeSize @kalletlak (#2991)
• Fix cursor issue with oql editor and improve styling and behavior @alisman (#2976)

🏎 Performance Tweaks

• Update oncoprint version for performance improvements @adamabeshouse (#2986)

👷‍♀️ Testing, Configuration & Deployment

• Fixed flaky local e2e tests @ngocnn1104 (#2990)

🧰 Maintenance

• Remove empty param from URL in e2e test @adamabeshouse (#2997)

📐 Prototype

• Use SAMPLE_ACQUISITION track for sample order @inodb (#2984)
• Add new timeline styling for GENIE @inodb (#2974)

🕵️‍♀️ Full commit logs

• Backend: cBioPortal/cbioportal@v3.1.10...v3.1.11
• Frontend: v3.1.10...v3.1.11

🏷 Notes on versioning and release procedure

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

v3.1.10

🧬 Features

• Genomic Evolution tab in Patient View with multiple samples @adamabeshouse (#2573)

✨ Enhancements

• Add _GERMLINE and _DRIVER support to oncoprinter @adamabeshouse (#2904)
• Update to custom tab support @kalletlak (#2972)

📘 Documentation

• improved monorepo docs @onursumer (#2969)

🧹 Cleanup & Refactoring 🔧

• Imported react-mutation-mapper repo @onursumer (#2957)

🧰 Maintenance

• Update oncokb client @zhx828 (#2970)
• Allow RMM and commons to be installed with a higher version of node and yarn @zhx828 (#2967)

🕵️‍♀️ Full commit logs

• Backend: cBioPortal/cbioportal@v3.1.9...v3.1.10
• Frontend: v3.1.9...v3.1.10

🏷 Notes on versioning and release procedure

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

v3.1.9

Changes

🧬 Features

• Give option to list unselected cases in the Custom Selection component @zhx828 (#2936)
• Add "View NG-CHM" button on OncoPrint Heatmap tab @ChrisWakefield (#2872)

✨ Enhancements

• Always showing patient icons when there is an alteration @onursumer (#2963)
• Clinical timeline: Create split heirarchy for Diagnosis subtypes @alisman (#2949)
• Routing Improvements @Luke-Sikina (#2891)
• Bookmark feature should give user fullURL (and shortened version if b… @alisman (#2940)

🐛 Bug Fixes

• update svg2pdf to custom version (fix gradient shows up as solid block) @dippindots (#2911)
• fix issue: x-axis in survival plot shifted in study view @dippindots (#2954)
• Update study links in results page query summary @kalletlak (#2942)
• In patient view timeline, treatment data should be split three levels… @alisman (#2947)
• Alteration Enrichments: fix gene barplot where p-value is 0 @kalletlak (#2946)

🎨 Style Tweaks

• Restore loading animation for study summary fetch on results page @alisman (#2960)
• improve footer version logic @inodb (#2945)

⚙️ Changes to handle external APIs

• Change the order and put "Matched Samples" above ARM @victoria34 (#2944)

📘 Documentation

• added monorepo section to readme, fixed publishModules script @onursumer (#2955)

🧹 Cleanup & Refactoring 🔧

• Monorepo with yarn workspaces and lerna @onursumer (#2892)

🧰 Maintenance

• Added a netlify redirect rule to make routing work @onursumer (#2965)
• Fixed a netlify deploy issue for non PR branches @onursumer (#2964)

🕵️‍♀️ Full commit logs

• Backend: cBioPortal/cbioportal@v3.1.8...v3.1.9
• Frontend: v3.1.8...v3.1.9

🏷 Notes on versioning and release procedure

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

v3.1.8

✨ Enhancements

• Frontend should support queries submitted using POST method @alisman #2933

🐛 Bug Fixes

• Study view: Fix scatter plot reset selected filter @kalletlak #2939
• Fix alteration enrichment tables when p-value is 0 @kalletlak #2934
• Fix overwriting of empty parameters on modify query (and all other updateURL calls) @alisman #2925

🧰 Maintenance

• Updated internal API client @onursumer #2932
• Upgraded to react-mutation-mapper 0.3.6 @onursumer #2931

🕵️‍♀️ Full commit logs

• Backend: cBioPortal/cbioportal@v3.1.7...v3.1.8
• Frontend: v3.1.7...v3.1.8

v3.1.7

🧬 Features

• Add Count Bubbles to Oncoprint Toolbar @Luke-Sikina (#2914)
• Gene Panel Modal in Patient View @ngocnn1104 (#2782)
• Gene panel column data in patient view download @ngocnn1104 (#2741)

✨ Enhancements

• Display genes in one column on copy/download @ngocnn1104 (#2920)

🐛 Bug Fixes

• Gene query limit supports case sets @Luke-Sikina (#2924)
• Fix handling of data_priority = profileFilter on submission/modificat… @alisman (#2921)
• Fixed the applyLazyMobXTableFilter function @onursumer (#2917)
• plots tab - make quickplots buttons choose same gene for vertical axis @adamabeshouse (#2905)
• add missing columns in mutation mapper table @leexgh (#2906)

🎨 Style Tweaks

• patient view genomic overview tracks - restyle gene panel icon @adamabeshouse (#2915)
• Fixed Oncoprint controls button alignment @ngocnn1104 (#2927)
• added an option to change the behavior of selection when all values selected @onursumer (#2913)
• Update clinical timeline version to v0.0.19 @inodb (#2908)

⚙️ Changes to handle external APIs

• List matched sample icons under arm description @victoria34 (#2910)

🧹 Cleanup & Refactoring 🔧

• URLWrapper: mediate all read/write interaction between app and url @alisman (#2726)

🧰 Maintenance

• Update OncoKB Client & Update cbioportal-frontend-commons version @zhx828 (#2928)
• improve typescript checking for URLWrapper @adamabeshouse (#2922)
• Update oncokb client && Update react-mutation-mapper to 0.3.4 @zhx828 (#2923)

🕵️‍♀️ Full commit logs

• Backend: cBioPortal/cbioportal@v3.1.6...v3.1.7
• Frontend: v3.1.6...v3.1.7