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RFC72 Rebase #10339

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wants to merge 177 commits into from
Closed

RFC72 Rebase #10339

wants to merge 177 commits into from

Commits on Dec 2, 2022

  1. fix #9461 - mutations api endpoint 

    - modified java files to remove unused properties and changes to tests
- db changes, mutationmapper.xml
- Update seed_mini.sql

roll back changes for refseqMrnaId

roll back changes for refseqMrnaId

Update ExtendedMutation.java

Added required property setOncotatorRefseqMrnaId and getOncotatorRefseqMrnaId
    @jagnathan
    jagnathan committed Dec 2, 2022
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  2. Updated more files for removed fields 

    Updated more files for removed fields

Remove unused oncotator fields

Remove unused oncotator fields
ONCOTATOR_DBSNP_RS
ONCOTATOR_UNIPROT_ENTRY_NAME

remove fields from sql file

ONCOTATOR_DBSNP_RS and ONCOTATOR_UNIPROT_ENTRY_NAME removal from sql file
    @jagnathan
    jagnathan committed Dec 2, 2022
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  3. db changes and renaming the column prefixes from oncotator to mutation 

    db changes in sql for renaming columns
renamed the column prefixes from oncotator to mutation on multiple classes and files
    @jagnathan
    jagnathan committed Dec 2, 2022
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  4. Update SQL statements 

    Update testSql.sql

updating testSql for the name change of columns from ONCOTATOR to MUTATION

Update DaoMutation.java

The data files still use the old column prefix of ONCOTATOR instead of MUTATION

Update DaoMutation.java

Update migration.sql

Adding quotes around column names
    @jagnathan
    jagnathan committed Dec 2, 2022
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  5. db changes and renaming the column prefixes from oncotator to mutation 

    db changes in sql for renaming columns
renamed the column prefixes from oncotator to mutation on multiple classes and files
    @jagnathan
    jagnathan committed Dec 2, 2022
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  6. Update migration.sql 

    Update migration.sql

fix syntax errors in mysql change column

Update migration.sql

fix syntax errors in mysql change column

setting db version

setting db version
    @jagnathan
    jagnathan committed Dec 2, 2022
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  7. Removed Link columns 

    Removed Link columns and modified the documentation
    @jagnathan
    jagnathan committed Dec 2, 2022
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Commits on Feb 6, 2023

  1. Update news.md

    @sbabyanusha
    sbabyanusha committed Feb 6, 2023
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Commits on Feb 14, 2023

  1. update news.md

    @sbabyanusha
    sbabyanusha committed Feb 14, 2023
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Commits on Feb 28, 2023

  1. update cosmic importer for new cosmic datafiles

    @MatthijsPon
    MatthijsPon committed Feb 28, 2023
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Commits on Mar 8, 2023

  1. Update DB version and renaming mutation_event fields

    @dippindots
    dippindots committed Mar 8, 2023
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  2. Update Mutation model

    @dippindots
    dippindots committed Mar 8, 2023
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Commits on Mar 14, 2023

  1. Merge pull request #9914 from jagnathan/fix-9461-mutations-api-endpoi… 

    …nt-final

Fix 9461 mutations api endpoint final
    @dippindots
    dippindots authored Mar 14, 2023
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Commits on Mar 15, 2023

  1. Update SQL to fix incompatibility with sqlmode OnlyFullGroupBy and ad… 

    …d support for multiple database impls to support mysql and h2
    @haynescd
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  2. Merge remote-tracking branch 'origin/master' into bugfix/ch/Fix-incom… 

    …patible-with-sqlmodeOnlyFullGroupBy
    @haynescd
    haynescd committed Mar 15, 2023
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  3. Merge pull request #10079 from haynescd/bugfix/ch/Fix-incompatible-wi… 

    …th-sqlmodeOnlyFullGroupBy

Update SQL to fix incompatibility with sqlmode OnlyFullGroupBy
    @haynescd
    haynescd authored Mar 15, 2023
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  4. Allow binning and filtering of custom (numerical and categorical) data

    @pvannierop @dippindots
    pvannierop authored and dippindots committed Mar 15, 2023
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  5. Several small fixes and cleanup after feedback @dippindots

    @dippindots
    Bas Leenknegt authored and dippindots committed Mar 15, 2023
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  6. Remove excess whitespace

    @dippindots
    Bas Leenknegt authored and dippindots committed Mar 15, 2023
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Commits on Mar 17, 2023

  1. Merge pull request #10039 from BasLee/custom_data_binning_endpoint 

    Binning of custom data
    @dippindots
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Commits on Mar 20, 2023

  1. Fix combined Entrez Gene Id and Stuct Var Query in StructuralVariantM… 

    …apper.xml
    @pvannierop
    pvannierop committed Mar 20, 2023
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Commits on Mar 21, 2023

  1. update bilkent members

    @inodb
    inodb authored Mar 21, 2023
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Commits on Mar 22, 2023

  1. Merge pull request #10097 from cBioPortal/master 

    Merge master into v5.3.0
    @dippindots
    dippindots authored Mar 22, 2023
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  2. Frontend v5.3.0

    @dippindots
    dippindots authored Mar 22, 2023
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  3. Update ClinicalEventMyBatisRepositoryTest.java 

    We need to update this test because it's not java 8 compatible.
    @dippindots
    dippindots authored Mar 22, 2023
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  4. Address java8 compatible issues in more tests

    @dippindots
    dippindots committed Mar 22, 2023
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  5. Merge pull request #10098 from cBioPortal/demo-v5.3.0 

    Release v5.3.0
    @dippindots
    dippindots authored Mar 22, 2023
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Commits on Mar 24, 2023

  1. Merge pull request #10054 from thehyve/update-cosmic-importer 

    update cosmic importer for new cosmic datafiles
    @inodb
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  2. Merge pull request #10091 from pvannierop/fix_sv_queries 

    Fix StructuralVariantMapper.xml
    @dippindots
    dippindots authored Mar 24, 2023
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Commits on Mar 28, 2023

  1. Add importer and validator section to release-drafter.yml

    @dippindots
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  2. Fix release-drafter.yml error

    @dippindots
    dippindots authored Mar 28, 2023
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  3. Update news.md

    @sbabyanusha
    sbabyanusha committed Mar 28, 2023
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Commits on Mar 29, 2023

  1. Frontend v5.3.1

    @dippindots
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  2. Update News.md

    @sbabyanusha
    sbabyanusha committed Mar 29, 2023
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  3. Merge branch 'master' into feb-6-2023-newsreleas

    @sbabyanusha
    sbabyanusha authored Mar 29, 2023
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Commits on Apr 3, 2023

  1. Use custom driver annotations in sv counts

    Bas Leenknegt committed Apr 3, 2023
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  2. Test custom driver annotations filter in sv count query

    Bas Leenknegt committed Apr 3, 2023
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  3. Differentiate between test svs by making annotations unique

    Bas Leenknegt committed Apr 3, 2023
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  4. Fix sv whereSite1IsNot2 clause, add es0 sv custom driver data

    Bas Leenknegt committed Apr 3, 2023
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  5. Remove unused DriverManagerDataSource fields from db tests

    Bas Leenknegt committed Apr 3, 2023
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  6. Add comment to mybatis sv whereSite1IsNot2 clause

    Bas Leenknegt committed Apr 3, 2023
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Commits on Apr 4, 2023

  1. Fix validation result_report.html: include new sv

    Bas Leenknegt committed Apr 4, 2023
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Commits on Apr 5, 2023

  1. Frontend v5.3.2

    @dippindots
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  2. Merge pull request #10092 from BasLee/sv-counts-with-custom-driver-an… 

    …notations

Include driver filter in sv count query
    @dippindots
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  3. Update News.md

    @sbabyanusha
    sbabyanusha authored Apr 5, 2023
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  4. Merge branch 'master' into feb-6-2023-newsreleas

    @sbabyanusha
    sbabyanusha authored Apr 5, 2023
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  5. Merge pull request #9994 from cBioPortal/feb-6-2023-newsreleas 

    Update news.md
    @inodb
    inodb authored Apr 5, 2023
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Commits on Apr 6, 2023

  1. fixed swagger page validation errors

    @jfkonecn @inodb
    jfkonecn authored and inodb committed Apr 6, 2023
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Commits on Apr 7, 2023

  1. Merge pull request #10101 from jfkonecn/hotfix 

    fixed swagger page validation errors
    @inodb
    inodb authored Apr 7, 2023
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Commits on Apr 11, 2023

  1. Frontend v5.3.3

    @dippindots
    dippindots authored Apr 11, 2023
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Commits on Apr 12, 2023

  1. Add MSK database migration documentation (#10115) 

    Co-authored-by: Ino de Bruijn <[email protected]>
    @dippindots @inodb
    dippindots and inodb authored Apr 12, 2023
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Commits on Apr 13, 2023

  1. Do not call next study view filter when no samples left (#10124)

    @pvannierop
    pvannierop authored Apr 13, 2023
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Commits on Apr 17, 2023

  1. Add studyId to CancerStudyTag entity

    Bas Leenknegt committed Apr 17, 2023
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  2. Merge pull request #10116 from BasLee/tags-with-study-id 

    Add studyId to CancerStudyTag entity
    @alisman
    alisman authored Apr 17, 2023
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Commits on Apr 19, 2023

  1. Frontend v5.3.4

    @alisman
    alisman authored Apr 19, 2023
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Commits on Apr 20, 2023

  1. Merge pull request #10130 from cBioPortal/alisman-patch-7 

    Frontend v5.3.4
    @alisman
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Commits on Apr 21, 2023

  1. 🔧 Add Configuration Properties for study view summary limits

    @haynescd
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  2. Merge pull request #10128 from haynescd/feature/10125-Add-Configurati… 

    …on-Property-max-number-of-studies

🔧 Add Configuration Properties for study view summary limits
    @alisman
    alisman authored Apr 21, 2023
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Commits on Apr 22, 2023

  1. add sitemaps for retype 

    adding url should fix this
    @inodb
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Commits on Apr 25, 2023

  1. Frontend v5.3.5

    @dippindots
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  2. Merge pull request #10137 from cBioPortal/frontend-v5.3.5 

    Frontend v5.3.5
    @dippindots
    dippindots authored Apr 25, 2023
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Commits on Apr 26, 2023

  1. Add tutorials from others

    @inodb
    inodb authored Apr 26, 2023
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  2. Add Farhan Haq tutorial video

    @inodb
    inodb authored Apr 26, 2023
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Commits on Apr 27, 2023

  1. Merge pull request #10142 from cBioPortal/add-additional-tutorials 

    Add tutorials from others
    @inodb
    inodb authored Apr 27, 2023
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  2. 🔧 Add StudyDownloadUrl to portal.properties

    @haynescd
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Commits on May 3, 2023

  1. Frontend v5.3.6

    @dippindots
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  2. Merge pull request #10143 from haynescd/feature/10135-Add-Configurati… 

    …on-Property-For-StudyDownloadUrl

🔧 Add StudyDownloadUrl to portal.properties
    @inodb
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Commits on May 4, 2023

  1. Update News-Genie.md

    @ritikakundra
    ritikakundra authored May 4, 2023
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Commits on May 8, 2023

  1. Fix study tag search when no studies present

    Bas Leenknegt committed May 8, 2023
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  2. Merge pull request #10164 from BasLee/fix-study-tags-search-with-no-s… 

    …tudies

Fix study tag search when no studies available
    @inodb
    inodb authored May 8, 2023
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  3. Add dsnparse Python requirement 

    Needed for future PR concerning using db.connection_string to connect to the database
    @pvannierop
    pvannierop authored May 8, 2023
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  4. Merge pull request #10165 from cBioPortal/pvannierop-patch-4 

    Add dsnparse Python requirement
    @dippindots
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  5. add jeremy to about page

    @tmazor
    tmazor authored May 8, 2023
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  6. Merge pull request #10166 from cBioPortal/tmazor-patch-7 

    add jeremy to about page
    @inodb
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Commits on May 19, 2023

  1. Documentation markdown fixes (#10186) 

    * Fix broken hyperlink to retype
* Move development files under development directory
* Fix markdown links for table of contents
    @justinjao
    justinjao authored May 19, 2023
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Commits on May 23, 2023

  1. Frontend v5.3.7

    @dippindots
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  2. Update gene set version and update tests

    @dippindots
    dippindots committed May 23, 2023
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  3. Merge pull request #10168 from cBioPortal/frontend-v5.3.7 

    Frontend v5.3.7
    @dippindots
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Commits on May 24, 2023

  1. Fix integration test

    @dippindots
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  2. Merge pull request #10193 from cBioPortal/fix-integration-test 

    Fix integration test
    @dippindots
    dippindots authored May 24, 2023
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  3. Frontend v5.3.8

    @dippindots
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  4. 📚 Update Priority Documentation

    @haynescd
    haynescd committed May 24, 2023
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  5. ✨ Add ability to set priority to -1 for clinical attr

    @haynescd
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  6. Merge pull request #10156 from haynescd/feature/10133-Exclude-Clinica… 

    …l-Attributes-with-low-priority

Feature/10133 exclude clinical attributes with low priority
    @haynescd
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Commits on May 26, 2023

  1. add statistical tests in FAQ 

    Fixed #10198
    @jjgao
    jjgao authored May 26, 2023
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  2. extend File-Formats.md with mutational signature datatype (#10172)

    @MatthijsPon
    MatthijsPon authored May 26, 2023
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Commits on May 30, 2023

  1. Frontend v5.3.9

    @dippindots
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Commits on May 31, 2023

  1. Merge pull request #10202 from cBioPortal/frontend-v5.3.9 

    Frontend v5.3.9
    @dippindots
    dippindots authored May 31, 2023
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Commits on Jun 2, 2023

  1. change docker compose cmds

    @inodb
    inodb authored Jun 2, 2023
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  2. fix contact email in dev section

    @inodb
    inodb authored Jun 2, 2023
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  3. fix release notes docs link

    @inodb
    inodb authored Jun 2, 2023
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  4. fix release procedure info

    @inodb
    inodb authored Jun 2, 2023
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Commits on Jun 6, 2023

  1. Frontend v5.3.10

    @dippindots
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Commits on Jun 7, 2023

  1. Merge pull request #10210 from cBioPortal/frontend-v5.3.10 

    Frontend v5.3.10
    @dippindots
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  2. Add note about official releases

    @inodb
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Commits on Jun 8, 2023

  1. Add AACR GENIE BPC tutorial videos (#10215)

    @ritikakundra
    ritikakundra authored Jun 8, 2023
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Commits on Jun 9, 2023

  1. Adding new features news (#10149) 

    * Adding new features news from 2022/05 to current

Co-authored-by: Ino de Bruijn <[email protected]>
    @dippindots @inodb
    dippindots and inodb authored Jun 9, 2023
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  2. Update web-API-and-Clients.md (#10209) 

    Add description of cbioportalR in web API section
    @karissawhiting
    karissawhiting authored Jun 9, 2023
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Commits on Jun 12, 2023

  1. Merge pull request #10199 from cBioPortal/jjgao-patch-1 

    add statistical tests in GC in FAQ
    @dippindots
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Commits on Jun 13, 2023

  1. Frontend v5.3.11

    @dippindots
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Commits on Jun 14, 2023

  1. Paginate clinical table response using Page and Pagable spring interf… 

    …aces
    Bas Leenknegt committed Jun 14, 2023
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  2. Use PaginatedClinicalData

    Bas Leenknegt committed Jun 14, 2023
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  3. Add query to count items in clinical table

    Bas Leenknegt committed Jun 14, 2023
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  4. Replace spring page with page response headers

    Bas Leenknegt committed Jun 14, 2023
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  5. Fix page size when sorting clinical table

    Bas Leenknegt committed Jun 14, 2023
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  6. Sort clinical table by sample and patient ID

    Bas Leenknegt committed Jun 14, 2023
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  7. Fix distinct in patient attr sorting

    Bas Leenknegt committed Jun 14, 2023
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  8. Fix difference h2 and mysql in sorting nulls last

    Bas Leenknegt committed Jun 14, 2023
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  9. Rename *SampleClinicalTable* methods

    Bas Leenknegt committed Jun 14, 2023
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  10. update members about us page 

    add calla & bryan, move several people to alumni
    @inodb
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Commits on Jun 15, 2023

  1. Revert controler rename to keep backward compatible

    Bas Leenknegt committed Jun 15, 2023
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Commits on Jun 16, 2023

  1. Merge pull request #10211 from BasLee/poc-paginated-clinical-table 

    Paginated clinical table
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Commits on Jun 20, 2023

  1. Impl. Struct Var count endpoint for Study View

    @pvannierop
    pvannierop authored and Bas Leenknegt committed Jun 20, 2023
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  2. Remove unused imports 

    PR feedback Gaofei
    @pvannierop
    pvannierop authored and Bas Leenknegt committed Jun 20, 2023
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  3. Correct variable name 

    PR feedback Gaofei
    @pvannierop
    pvannierop authored and Bas Leenknegt committed Jun 20, 2023
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  4. Change HashMap to Set 

    PR feedback Gaofei
    @pvannierop
    pvannierop authored and Bas Leenknegt committed Jun 20, 2023
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  5. Return counts when gene 1 or gene2 is null

    @pvannierop
    pvannierop authored and Bas Leenknegt committed Jun 20, 2023
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  6. Change missing site1 or site2 gene for SV to INFO log level 

    Was WARN before.
    @pvannierop
    pvannierop authored and Bas Leenknegt committed Jun 20, 2023
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  7. Update result report

    @pvannierop
    pvannierop authored and Bas Leenknegt committed Jun 20, 2023
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  8. Create property to show reference genome in study list

    @oplantalech
    oplantalech committed Jun 20, 2023
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  9. Frontend v5.3.12

    @alisman
    alisman committed Jun 20, 2023
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  10. Merge pull request #10234 from alisman/v5.3.12 

    Frontend v5.3.12
    @alisman
    alisman authored Jun 20, 2023
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Commits on Jun 21, 2023

  1. Merge pull request #10233 from oplantalech/reference_genome_badge 

    Create property to show reference genome in study list
    @alisman
    alisman authored Jun 21, 2023
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Commits on Jun 22, 2023

  1. fix contributor last name

    @onursumer
    onursumer committed Jun 22, 2023
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Commits on Jun 26, 2023

  1. Merge pull request #10239 from onursumer/about-us-name-correction 

    Fix contributor last name
    @alisman
    alisman authored Jun 26, 2023
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  2. Merge pull request #10119 from pvannierop/sv_counts_endpoint 

    RFC68: Impl. Struct Var count endpoint for Study View
    @alisman
    alisman authored Jun 26, 2023
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Commits on Jun 28, 2023

  1. Frontend v5.3.13

    @dippindots
    dippindots authored Jun 28, 2023
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  2. Merge pull request #10243 from cBioPortal/frontend-v5.3.13 

    Frontend v5.3.13
    @dippindots
    dippindots authored Jun 28, 2023
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Commits on Jul 5, 2023

  1. Impl. Struct Var filter queries for /filtered-samples/fetch endpoint

    @pvannierop
    pvannierop authored and Bas Leenknegt committed Jul 5, 2023
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  2. Add unit tests for resolveEntrezGeneIds

    @pvannierop
    pvannierop authored and Bas Leenknegt committed Jul 5, 2023
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  3. Changes after PR reviews 

    - Rename StructVar* to StructuralVariant*
- Revert JsonInclude Always to NON_NULL
-
    Bas Leenknegt committed Jul 5, 2023
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Commits on Jul 7, 2023

  1. Merge pull request #10214 from pvannierop/studyview_sv_queryfilter 

    RFC68: Impl. structural variant filtering in Study View filter
    @dippindots
    dippindots authored Jul 7, 2023
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  2. Add Java 11 as requirement

    @inodb
    inodb authored Jul 7, 2023
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  3. modify documentation for skin.hide_download_controls

    @qlu-cls
    qlu-cls committed Jul 7, 2023
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Commits on Jul 10, 2023

  1. Merge pull request #10258 from h164654156465/data-download-control 

    modify documentation for skin.hide_download_controls
    @alisman
    alisman authored Jul 10, 2023
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  2. Improve treatment data api performance

    @kalletlak
    kalletlak committed Jul 10, 2023
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Commits on Jul 12, 2023

  1. Improve study view treatment api performance

    @kalletlak
    kalletlak committed Jul 12, 2023
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  2. Update download control options (#10264)

    @kalletlak
    kalletlak authored Jul 12, 2023
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  3. Merge remote-tracking branch 'cbio/master' into timeline-performance

    @kalletlak
    kalletlak committed Jul 12, 2023
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  4. Add more tests and comments

    @kalletlak
    kalletlak committed Jul 12, 2023
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Commits on Jul 13, 2023

  1. Merge pull request #10261 from kalletlak/timeline-performance 

    Improve study-view treatment api's performance
    @kalletlak
    kalletlak authored Jul 13, 2023
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Commits on Jul 17, 2023

  1. fix 10221 - 403 issue 

    fix 10221 - 403 issue; swagger annotations cause issue in authentication object. If user authorization is enabled, authentication object is obtained from SecurityContextHolder
    @jagnathan @dippindots
    jagnathan authored and dippindots committed Jul 17, 2023
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Commits on Jul 18, 2023

  1. Merge pull request #10267 from jagnathan/fix10221-403-authorized-stud… 

    …ies-2

fix 10221 - 403 issue; authentication object is obtained from Security Context.
    @dippindots
    dippindots authored Jul 18, 2023
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  2. Update Pyyaml package 

    See yaml/pyyaml#724 for details of this update
    @dippindots
    dippindots authored Jul 18, 2023
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  3. Merge pull request #10283 from cBioPortal/update-pyyaml 

    Update Pyyaml package
    @dippindots
    dippindots authored Jul 18, 2023
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  4. Frontend v5.3.14

    @dippindots
    dippindots committed Jul 18, 2023
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  5. Merge pull request #10281 from cBioPortal/frontend-v5.3.14 

    Frontend v5.3.14
    @dippindots
    dippindots authored Jul 18, 2023
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Commits on Jul 19, 2023

  1. Changes related to download group

    @kalletlak
    kalletlak committed Jul 19, 2023
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  2. Merge pull request #10254 from kalletlak/feature/10248 

    Set download button visibility in UI based on user role/group
    @kalletlak
    kalletlak authored Jul 19, 2023
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Commits on Jul 20, 2023

  1. Allow ProfiledCasesCounter to add counts to empty alteration count li… 

    …st (#10255)
    BasLee authored Jul 20, 2023
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  2. Update about us page

    @dippindots
    dippindots authored Jul 20, 2023
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Commits on Jul 25, 2023

  1. Frontend v5.3.15

    @dippindots
    dippindots authored Jul 25, 2023
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  2. Merge pull request #10297 from cBioPortal/frontend-v5.3.15 

    Frontend v5.3.15
    @dippindots
    dippindots authored Jul 25, 2023
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Commits on Jul 26, 2023

  1. Cache treatment endpoints (#10282)

    @kalletlak
    kalletlak authored Jul 26, 2023
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Commits on Aug 1, 2023

  1. update one-sided fisher test to two-sided

    @dippindots
    Bryan Lai authored and dippindots committed Aug 1, 2023
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  2. Merge pull request #10288 from gblaih/two-sided-fisher-test 

    Two sided fishers test
    @dippindots
    dippindots authored Aug 1, 2023
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  3. Allow redis service unavailable when Redis is enabled

    @dippindots
    dippindots committed Aug 1, 2023
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  4. Merge pull request #10305 from dippindots/catch-redis-error 

    Allow Redis service unavailable when Redis is enabled
    @dippindots
    dippindots authored Aug 1, 2023
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  5. Frontend v5.3.16

    @dippindots
    dippindots authored Aug 1, 2023
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  6. Merge pull request #10306 from cBioPortal/frontend-v5.3.16 

    Frontend v5.3.16
    @dippindots
    dippindots authored Aug 1, 2023
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Commits on Aug 3, 2023

  1. Update two-sided fisher tests news (#10312) 

    * Add two-sided fisher tests news

---------

Co-authored-by: Ino de Bruijn <[email protected]>
    @dippindots @inodb
    dippindots and inodb authored Aug 3, 2023
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Commits on Aug 8, 2023

  1. Genomic data counts study-view endpoint (#10300) 

    * implement getting CNA types for a gene specific

* add tests for genomic-data-counts endpoint

* change CopyNumberDataCounterFilter to StudyViewFilter and GenomicDataCountFilter

* change to molecularDataService to fetch data

* add filter logic for DISCRETE molecular profiles

* Refactor

* count NA and clean up codes

* Updates

* Update StudyViewServiceImplTest.java

---------

Co-authored-by: Qi-Xuan Lu <[email protected]>
Co-authored-by: Karthik <[email protected]>
    @7xuanlu @qlu-cls @kalletlak
    3 people authored Aug 8, 2023
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  2. Frontend v5.3.17

    @dippindots
    dippindots authored Aug 8, 2023
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  3. Merge pull request #10292 from cBioPortal/dippindots-patch-1 

    Update about us page
    @dippindots
    dippindots authored Aug 8, 2023
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  4. Merge pull request #10318 from cBioPortal/frontend-v5.3.17 

    Frontend v5.3.17
    @dippindots
    dippindots authored Aug 8, 2023
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Commits on Aug 10, 2023

  1. Add defaults for genomic evolution tab in patient view (#10309) 

    * Add defaults for mutation heatmap and line chart checkboxes

* Update text

---------

Co-authored-by: Gaofei Zhao <[email protected]>
    @dippindots
    BasLee and dippindots authored Aug 10, 2023
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Commits on Aug 14, 2023

  1. Add data access token user role filter feature (#10315) 

    * Add data access token user role filter feature
* Update and more tests
* Update failing test

---------

Co-authored-by: Jeremy R. Easton-Marks <[email protected]>
    @kalletlak @JREastonMarks
    kalletlak and JREastonMarks authored Aug 14, 2023
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  2. Update About-Us.md (#10196) 

    Update About-Us.md
    @ritikakundra
    ritikakundra authored Aug 14, 2023
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Commits on Aug 15, 2023

  1. Add label check test for pull request

    @dippindots
    dippindots authored Aug 15, 2023
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  2. Merge pull request #10329 from cBioPortal/label-check 

    Add label check test for pull request
    @dippindots
    dippindots authored Aug 15, 2023
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  3. Frontend v5.3.18

    @dippindots
    dippindots authored Aug 15, 2023
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  4. Merge pull request #10331 from cBioPortal/frontend-v5.3.18 

    Frontend v5.3.18
    @dippindots
    dippindots authored Aug 15, 2023
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Commits on Aug 16, 2023

  1. add info about adding labels

    @inodb
    inodb authored Aug 16, 2023
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Commits on Aug 17, 2023

  1. add property show_web_tours (#10333)

    @Beking0912
    Beking0912 authored Aug 17, 2023
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Commits on Aug 18, 2023

  1. (GSoC) Generic Assay Categorical/Binary data implementation Backend (#… 

    …10303)

* update backend

* finish tests

* modify controller file structure

* modify import

* update backend

* finish tests

* modify controller file structure

* refactor some variables

* modify enrichment compare and validate issue

* refactor the controllers and services

* refactor test

* Update GenericAssayEnrichmentServiceImpl.java

* fixed simplification issues

* add inline comments

* modify import

* solve core test issue

* test check

* modify expressionenrichment

* modify imports

* update backend

* finish tests

* modify controller file structure

* modify import

* update backend

* finish tests

* modify controller file structure

* refactor some variables

* modify enrichment compare and validate issue

* refactor the controllers and services

* refactor test

* Update GenericAssayEnrichmentServiceImpl.java

* fixed simplification issues

* add inline comments

* modify import

* solve core test issue

* test check

* modify expressionenrichment

* modify imports

* update imports

* Update GenericAssayEnrichment.java
    @Djokovic0311
    Djokovic0311 authored Aug 18, 2023
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Commits on Aug 22, 2023

  1. Merge branch 'rfc72'

    @JREastonMarks
    JREastonMarks committed Aug 22, 2023
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  2. Revert "Merge branch 'rfc72'" 

    This reverts commit 4f28eac, reversing
changes made to 901406f.
    @JREastonMarks
    JREastonMarks committed Aug 22, 2023
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