Clickbase #5

alisman · 2024-03-08T14:17:07Z

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Is this PR adding logic based on one or more clinical attributes? If yes, please make sure validation for this attribute is also present in the data validation / data loading layers (in backend repo) and documented in File-Formats Clinical data section!

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- 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

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

db changes in sql for renaming columns renamed the column prefixes from oncotator to mutation on multiple classes and files

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

db changes in sql for renaming columns renamed the column prefixes from oncotator to mutation on multiple classes and files

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

Removed Link columns and modified the documentation

…api-endpoint-final Fix 9461 mutations api endpoint final

…d support for multiple database impls to support mysql and h2

…patible-with-sqlmodeOnlyFullGroupBy

…patible-with-sqlmodeOnlyFullGroupBy Update SQL to fix incompatibility with sqlmode OnlyFullGroupBy

…ndpoint Binning of custom data

…apper.xml

Merge master into v5.3.0

We need to update this test because it's not java 8 compatible.

Release v5.3.0

update cosmic importer for new cosmic datafiles

Fix StructuralVariantMapper.xml

See yaml/pyyaml#724 for details of this update

Update Pyyaml package

Frontend v5.3.14

Set download button visibility in UI based on user role/group

…st (cBioPortal#10255)

Frontend v5.3.15

Two sided fishers test

Allow Redis service unavailable when Redis is enabled

Frontend v5.3.16

* Add two-sided fisher tests news --------- Co-authored-by: Ino de Bruijn <ino@ino.bio>

* 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 <qlu@carisls.com> Co-authored-by: Karthik <kalletlakarthik@gmail.com>

Update about us page

Frontend v5.3.17

) * Add defaults for mutation heatmap and line chart checkboxes * Update text --------- Co-authored-by: Gaofei Zhao <15748980+dippindots@users.noreply.github.com>

* Add data access token user role filter feature * Update and more tests * Update failing test --------- Co-authored-by: Jeremy R. Easton-Marks <j.r.eastonmarks@gmail.com>

Update About-Us.md

Add label check test for pull request

Frontend v5.3.18

jagnathan and others added 30 commits December 2, 2022 12:23

db changes and renaming the column prefixes from oncotator to mutation

3b2f8bb

db changes in sql for renaming columns renamed the column prefixes from oncotator to mutation on multiple classes and files

db changes and renaming the column prefixes from oncotator to mutation

871eccd

db changes in sql for renaming columns renamed the column prefixes from oncotator to mutation on multiple classes and files

Update migration.sql

98c892f

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

Removed Link columns

dec3627

Removed Link columns and modified the documentation

Update news.md

1c56e26

update news.md

f8e3350

update cosmic importer for new cosmic datafiles

d7be358

Update DB version and renaming mutation_event fields

89bde61

Update Mutation model

9ca0563

Merge pull request cBioPortal#9914 from jagnathan/fix-9461-mutations-…

ec2236f

…api-endpoint-final Fix 9461 mutations api endpoint final

Update SQL to fix incompatibility with sqlmode OnlyFullGroupBy and ad…

30578f4

…d support for multiple database impls to support mysql and h2

Merge remote-tracking branch 'origin/master' into bugfix/ch/Fix-incom…

c1a38a8

…patible-with-sqlmodeOnlyFullGroupBy

Merge pull request cBioPortal#10079 from haynescd/bugfix/ch/Fix-incom…

f375e62

…patible-with-sqlmodeOnlyFullGroupBy Update SQL to fix incompatibility with sqlmode OnlyFullGroupBy

Allow binning and filtering of custom (numerical and categorical) data

5ec8632

Several small fixes and cleanup after feedback @dippindots

b4f3097

Remove excess whitespace

bae8b2b

Merge pull request cBioPortal#10039 from BasLee/custom_data_binning_e…

ca13827

…ndpoint Binning of custom data

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

05bfd35

…apper.xml

update bilkent members

0d6ca0e

Merge pull request cBioPortal#10097 from cBioPortal/master

327a4eb

Merge master into v5.3.0

Frontend v5.3.0

4c46c8d

Update ClinicalEventMyBatisRepositoryTest.java

b1308d5

We need to update this test because it's not java 8 compatible.

Address java8 compatible issues in more tests

945cd5a

Merge pull request cBioPortal#10098 from cBioPortal/demo-v5.3.0

0b2dfa6

Release v5.3.0

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

1656299

update cosmic importer for new cosmic datafiles

Merge pull request cBioPortal#10091 from pvannierop/fix_sv_queries

2f3653a

Fix StructuralVariantMapper.xml

Add importer and validator section to release-drafter.yml

3711cf7

dippindots and others added 30 commits July 18, 2023 15:25

Update Pyyaml package

b7de8f3

See yaml/pyyaml#724 for details of this update

Merge pull request cBioPortal#10283 from cBioPortal/update-pyyaml

78dbe9e

Update Pyyaml package

Frontend v5.3.14

1a115f6

Merge pull request cBioPortal#10281 from cBioPortal/frontend-v5.3.14

a3794f7

Frontend v5.3.14

Changes related to download group

16acfa7

Merge pull request cBioPortal#10254 from kalletlak/feature/10248

8f6534e

Set download button visibility in UI based on user role/group

Allow ProfiledCasesCounter to add counts to empty alteration count li…

7339191

…st (cBioPortal#10255)

Update about us page

173cb57

Frontend v5.3.15

8412f5e

Merge pull request cBioPortal#10297 from cBioPortal/frontend-v5.3.15

4ac327b

Frontend v5.3.15

Cache treatment endpoints (cBioPortal#10282)

0ed4759

update one-sided fisher test to two-sided

0425e7b

Merge pull request cBioPortal#10288 from gblaih/two-sided-fisher-test

70f4597

Two sided fishers test

Allow redis service unavailable when Redis is enabled

dbee06e

Merge pull request cBioPortal#10305 from dippindots/catch-redis-error

731bd62

Allow Redis service unavailable when Redis is enabled

Frontend v5.3.16

4b76f51

Merge pull request cBioPortal#10306 from cBioPortal/frontend-v5.3.16

58a9cbe

Frontend v5.3.16

Update two-sided fisher tests news (cBioPortal#10312)

d035bb1

* Add two-sided fisher tests news --------- Co-authored-by: Ino de Bruijn <ino@ino.bio>

Frontend v5.3.17

1b9b31c

Merge pull request cBioPortal#10292 from cBioPortal/dippindots-patch-1

1acb7a1

Update about us page

Merge pull request cBioPortal#10318 from cBioPortal/frontend-v5.3.17

4956dcb

Frontend v5.3.17

Add defaults for genomic evolution tab in patient view (cBioPortal#10309

7b2bbe2

) * Add defaults for mutation heatmap and line chart checkboxes * Update text --------- Co-authored-by: Gaofei Zhao <15748980+dippindots@users.noreply.github.com>

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

7f523c8

* Add data access token user role filter feature * Update and more tests * Update failing test --------- Co-authored-by: Jeremy R. Easton-Marks <j.r.eastonmarks@gmail.com>

Update About-Us.md (cBioPortal#10196)

63d2c6a

Update About-Us.md

Add label check test for pull request

ca96047

Merge pull request cBioPortal#10329 from cBioPortal/label-check

dc7b0ea

Add label check test for pull request

Frontend v5.3.18

92d79bf

Merge pull request cBioPortal#10331 from cBioPortal/frontend-v5.3.18

e9cbd82

Frontend v5.3.18

add info about adding labels

643cfcd

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Clickbase #5

Clickbase #5

alisman commented Mar 8, 2024

Clickbase #5

Are you sure you want to change the base?

Clickbase #5

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alisman commented Mar 8, 2024

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