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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

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JREastonMarks
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Fix # (see https://help.github.com/en/articles/closing-issues-using-keywords)

Describe changes proposed in this pull request:

  • a
  • b

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  • Runs on heroku
  • Has tests or has a separate issue that describes the types of test that should be created. If no test is included it should explicitly be mentioned in the PR why there is no test.
  • The commit log is comprehensible. It follows 7 rules of great commit messages. For most PRs a single commit should suffice, in some cases multiple topical commits can be useful. During review it is ok to see tiny commits (e.g. Fix reviewer comments), but right before the code gets merged to master or rc branch, any such commits should be squashed since they are useless to the other developers. Definitely avoid merge commits, use rebase instead.
  • 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!
  • Make sure your PR has one of the labels defined in https://github.com/cBioPortal/cbioportal/blob/master/.github/release-drafter.yml

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jagnathan and others added 30 commits December 2, 2022 12:23
@jagnathan
fix #9461 - mutations api endpoint
967afbe 
- 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
Updated more files for removed fields
eeb8f8a 
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
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
@jagnathan
Update SQL statements
d1a400d 
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
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
@jagnathan
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
@jagnathan
Removed Link columns
dec3627 
Removed Link columns and modified the documentation
@sbabyanusha
Update news.md
1c56e26
@sbabyanusha
update news.md
f8e3350
@MatthijsPon
update cosmic importer for new cosmic datafiles
d7be358
@dippindots
Update DB version and renaming mutation_event fields
89bde61
@dippindots
Update Mutation model
9ca0563
@dippindots
Merge pull request #9914 from jagnathan/fix-9461-mutations-api-endpoi…
ec2236f 
…nt-final

Fix 9461 mutations api endpoint final
@haynescd
Update SQL to fix incompatibility with sqlmode OnlyFullGroupBy and ad…
30578f4 
…d support for multiple database impls to support mysql and h2
@haynescd
Merge remote-tracking branch 'origin/master' into bugfix/ch/Fix-incom…
c1a38a8 
…patible-with-sqlmodeOnlyFullGroupBy
@haynescd
Merge pull request #10079 from haynescd/bugfix/ch/Fix-incompatible-wi…
f375e62 
…th-sqlmodeOnlyFullGroupBy

Update SQL to fix incompatibility with sqlmode OnlyFullGroupBy
@pvannierop @dippindots
Allow binning and filtering of custom (numerical and categorical) data
5ec8632
@dippindots
Several small fixes and cleanup after feedback @dippindots
b4f3097
@dippindots
Remove excess whitespace
bae8b2b
@dippindots
Merge pull request #10039 from BasLee/custom_data_binning_endpoint
ca13827 
Binning of custom data
@pvannierop
Fix combined Entrez Gene Id and Stuct Var Query in StructuralVariantM…
05bfd35 
…apper.xml
@inodb
update bilkent members
0d6ca0e
@dippindots
Merge pull request #10097 from cBioPortal/master
327a4eb 
Merge master into v5.3.0
@dippindots
Frontend v5.3.0
4c46c8d
@dippindots
Update ClinicalEventMyBatisRepositoryTest.java
b1308d5 
We need to update this test because it's not java 8 compatible.
@dippindots
Address java8 compatible issues in more tests
945cd5a
@dippindots
Merge pull request #10098 from cBioPortal/demo-v5.3.0
0b2dfa6 
Release v5.3.0
@inodb
Merge pull request #10054 from thehyve/update-cosmic-importer
1656299 
update cosmic importer for new cosmic datafiles
@dippindots
Merge pull request #10091 from pvannierop/fix_sv_queries
2f3653a 
Fix StructuralVariantMapper.xml
@dippindots
Add importer and validator section to release-drafter.yml
3711cf7
BasLee and others added 28 commits July 20, 2023 09:44
Allow ProfiledCasesCounter to add counts to empty alteration count li…
7339191 
…st (#10255)
@dippindots
Update about us page
173cb57
@dippindots
Frontend v5.3.15
8412f5e
@dippindots
Merge pull request #10297 from cBioPortal/frontend-v5.3.15
4ac327b 
Frontend v5.3.15
@kalletlak
Cache treatment endpoints (#10282)
0ed4759
@dippindots
update one-sided fisher test to two-sided
0425e7b
@dippindots
Merge pull request #10288 from gblaih/two-sided-fisher-test
70f4597 
Two sided fishers test
@dippindots
Allow redis service unavailable when Redis is enabled
dbee06e
@dippindots
Merge pull request #10305 from dippindots/catch-redis-error
731bd62 
Allow Redis service unavailable when Redis is enabled
@dippindots
Frontend v5.3.16
4b76f51
@dippindots
Merge pull request #10306 from cBioPortal/frontend-v5.3.16
58a9cbe 
Frontend v5.3.16
@dippindots @inodb
Update two-sided fisher tests news (#10312)
d035bb1 
* Add two-sided fisher tests news

---------

Co-authored-by: Ino de Bruijn <[email protected]>
@7xuanlu @qlu-cls @kalletlak
Genomic data counts study-view endpoint (#10300)
ca2bdff 
* 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]>
@dippindots
Frontend v5.3.17
1b9b31c
@dippindots
Merge pull request #10292 from cBioPortal/dippindots-patch-1
1acb7a1 
Update about us page
@dippindots
Merge pull request #10318 from cBioPortal/frontend-v5.3.17
4956dcb 
Frontend v5.3.17
@dippindots
Add defaults for genomic evolution tab in patient view (#10309)
7b2bbe2 
* Add defaults for mutation heatmap and line chart checkboxes

* Update text

---------

Co-authored-by: Gaofei Zhao <[email protected]>
@kalletlak @JREastonMarks
Add data access token user role filter feature (#10315)
7f523c8 
* Add data access token user role filter feature
* Update and more tests
* Update failing test

---------

Co-authored-by: Jeremy R. Easton-Marks <[email protected]>
@ritikakundra
Update About-Us.md (#10196)
63d2c6a 
Update About-Us.md
@dippindots
Add label check test for pull request
ca96047
@dippindots
Merge pull request #10329 from cBioPortal/label-check
dc7b0ea 
Add label check test for pull request
@dippindots
Frontend v5.3.18
92d79bf
@dippindots
Merge pull request #10331 from cBioPortal/frontend-v5.3.18
e9cbd82 
Frontend v5.3.18
@inodb
add info about adding labels
643cfcd
@Beking0912
add property show_web_tours (#10333)
fe2c82e
@Djokovic0311
(GSoC) Generic Assay Categorical/Binary data implementation Backend (#…
901406f 
…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
@JREastonMarks
Merge branch 'rfc72'
4f28eac
@JREastonMarks
Revert "Merge branch 'rfc72'"
4a0ba3c 
This reverts commit 4f28eac, reversing
changes made to 901406f.
@JREastonMarks
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git push -u origin rfc72

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