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extend File-Formats.md with mutational signature datatype #10172

Merged
merged 1 commit into from
May 26, 2023
Merged

extend File-Formats.md with mutational signature datatype #10172

merged 1 commit into from
May 26, 2023

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MatthijsPon
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Describe changes proposed in this pull request:

  • extension of file-formats.md with the new mutational signature datatype (a subtype of generic assay)

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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!

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@MatthijsPon MatthijsPon force-pushed the fileformats_mutational_signature_extension branch from 86fd419 to 234b561 Compare May 12, 2023 13:35
@MatthijsPon MatthijsPon self-assigned this May 16, 2023
@MatthijsPon MatthijsPon marked this pull request as ready for review May 16, 2023 15:43
TJMKuijpers
TJMKuijpers reviewed May 17, 2023
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@MatthijsPon MatthijsPon force-pushed the fileformats_mutational_signature_extension branch from 53c68db to f69070e Compare May 17, 2023 10:38
SRodenburg
SRodenburg reviewed May 19, 2023
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@inodb inodb requested a review from dippindots May 22, 2023 14:56
dippindots
dippindots reviewed May 22, 2023
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Looks good to me, just had one question regarding to the datatype, please see my comment below.

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@MatthijsPon MatthijsPon force-pushed the fileformats_mutational_signature_extension branch 2 times, most recently from 1a345ce to 8a78a6e Compare May 23, 2023 13:31
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inodb commented May 25, 2023

@MatthijsPon on standup we discussed that you were making another update to this - is that right?

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MatthijsPon commented May 25, 2023 •
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@inodb

@MatthijsPon on standup we discussed that you were making another update to this - is that right?

Yeah, I've updated the PR with the feedback I got from @dippindots and @SRodenburg. If they approve now. its ready to merge.

@MatthijsPon MatthijsPon force-pushed the fileformats_mutational_signature_extension branch from 8a78a6e to 1943515 Compare May 25, 2023 14:54
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sonarcloud bot commented May 25, 2023

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

dippindots
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Thank @MatthijsPon, this looks good to me now

@inodb inodb merged commit 9af6061 into cBioPortal:master May 26, 2023
@MatthijsPon MatthijsPon deleted the fileformats_mutational_signature_extension branch May 30, 2023 14:02
JREastonMarks added a commit that referenced this pull request Aug 22, 2023
@JREastonMarks @jagnathan
@sbabyanusha @MatthijsPon @dippindots @haynescd @pvannierop @inodb @jfkonecn @alisman @ritikakundra @tmazor @justinjao @jjgao @karissawhiting @oplantalech @onursumer @qlu-cls @kalletlak @7xuanlu @Beking0912 @Djokovic0311
Rebase RFC72 (#10337)
1d97913 
* 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

* 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

* 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

* 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

* 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

* 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

* Removed Link columns

Removed Link columns and modified the documentation

* Update news.md

* update news.md

* update cosmic importer for new cosmic datafiles

* Update DB version and renaming mutation_event fields

* Update Mutation model

* Update SQL to fix incompatibility with sqlmode OnlyFullGroupBy and add support for multiple database impls to support mysql and h2

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

* Several small fixes and cleanup after feedback @dippindots

* Remove excess whitespace

* Fix combined Entrez Gene Id and Stuct Var Query in StructuralVariantMapper.xml

* update bilkent members

* Frontend v5.3.0

* Update ClinicalEventMyBatisRepositoryTest.java

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

* Address java8 compatible issues in more tests

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

* Fix release-drafter.yml error

* Update news.md

* Frontend v5.3.1

* Update News.md

* Use custom driver annotations in sv counts

* Test custom driver annotations filter in sv count query

* Differentiate between test svs by making annotations unique

* Fix sv whereSite1IsNot2 clause, add es0 sv custom driver data

* Remove unused DriverManagerDataSource fields from db tests

* Add comment to mybatis sv whereSite1IsNot2 clause

* Fix validation result_report.html: include new sv

* Frontend v5.3.2

* Update News.md

* fixed swagger page validation errors

* Frontend v5.3.3

* Add MSK database migration documentation (#10115)

Co-authored-by: Ino de Bruijn <ino@ino.bio>

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

* Add studyId to CancerStudyTag entity

* Frontend v5.3.4

* 🔧 Add Configuration Properties for study view summary limits

* add sitemaps for retype

adding url should fix this

* Frontend v5.3.5

* Add tutorials from others

* Add Farhan Haq tutorial video

* 🔧 Add StudyDownloadUrl to portal.properties

* Frontend v5.3.6

* Update News-Genie.md

* Fix study tag search when no studies present

* Add dsnparse Python requirement

Needed for future PR concerning using db.connection_string to connect to the database

* add jeremy to about page

* Documentation markdown fixes (#10186)

* Fix broken hyperlink to retype
* Move development files under development directory
* Fix markdown links for table of contents

* Frontend v5.3.7

* Update gene set version and update tests

* Fix integration test

* Frontend v5.3.8

* 📚 Update Priority Documentation

* ✨ Add ability to set priority to -1 for clinical attr

* add statistical tests in FAQ

Fixed #10198

* extend File-Formats.md with mutational signature datatype (#10172)

* Frontend v5.3.9

* change docker compose cmds

* fix contact email in dev section

* fix release notes docs link

* fix release procedure info

* Frontend v5.3.10

* Add note about official releases

* Add AACR GENIE BPC tutorial videos (#10215)

* Adding new features news (#10149)

* Adding new features news from 2022/05 to current

Co-authored-by: Ino de Bruijn <ino@ino.bio>

* Update web-API-and-Clients.md (#10209)

Add description of cbioportalR in web API section

* Frontend v5.3.11

* Paginate clinical table response using Page and Pagable spring interfaces

* Use PaginatedClinicalData

* Add query to count items in clinical table

* Replace spring page with page response headers

* Fix page size when sorting clinical table

* Sort clinical table by sample and patient ID

* Fix distinct in patient attr sorting

* Fix difference h2 and mysql in sorting nulls last

* Rename *SampleClinicalTable* methods

* update members about us page

add calla & bryan, move several people to alumni

* Revert controler rename to keep backward compatible

* Impl. Struct Var count endpoint for Study View

* Remove unused imports

PR feedback Gaofei

* Correct variable name

PR feedback Gaofei

* Change HashMap to Set

PR feedback Gaofei

* Return counts when gene 1 or gene2 is null

* Change missing site1 or site2 gene for SV to INFO log level

Was WARN before.

* Update result report

* Create property to show reference genome in study list

* Frontend v5.3.12

* fix contributor last name

* Frontend v5.3.13

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

* Add unit tests for resolveEntrezGeneIds

* Changes after PR reviews

- Rename StructVar* to StructuralVariant*
- Revert JsonInclude Always to NON_NULL
-

* Add Java 11 as requirement

* modify documentation for skin.hide_download_controls

* Improve treatment data api performance

* Improve study view treatment api performance

* Update download control options (#10264)

* Add more tests and comments

* 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

* Update Pyyaml package

See yaml/pyyaml#724 for details of this update

* Frontend v5.3.14

* Changes related to download group

* Allow ProfiledCasesCounter to add counts to empty alteration count list (#10255)

* Update about us page

* Frontend v5.3.15

* Cache treatment endpoints (#10282)

* update one-sided fisher test to two-sided

* Allow redis service unavailable when Redis is enabled

* Frontend v5.3.16

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

* Add two-sided fisher tests news

---------

Co-authored-by: Ino de Bruijn <ino@ino.bio>

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

* Frontend v5.3.17

* 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 <15748980+dippindots@users.noreply.github.com>

* 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 <j.r.eastonmarks@gmail.com>

* Update About-Us.md (#10196)

Update About-Us.md

* Add label check test for pull request

* Frontend v5.3.18

* add info about adding labels

* add property show_web_tours (#10333)

* (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

---------

Co-authored-by: Prasanna Kumar Jagannathan <37613906+jagnathan@users.noreply.github.com>
Co-authored-by: sbabyanusha <satravab@mskcc.org>
Co-authored-by: matthijspon <matthijs@thehyve.nl>
Co-authored-by: Gaofei <15748980+dippindots@users.noreply.github.com>
Co-authored-by: haynescd <haynescd@chop.edu>
Co-authored-by: Charles Haynes <33608920+haynescd@users.noreply.github.com>
Co-authored-by: Pim van Nierop <pim@thehyve.nl>
Co-authored-by: Bas Leenknegt <basleenknegt@thehyve.nl>
Co-authored-by: Ino de Bruijn <ino@ino.bio>
Co-authored-by: sbabyanusha <61431648+sbabyanusha@users.noreply.github.com>
Co-authored-by: John Konecny <jfkonecn@gmail.com>
Co-authored-by: alisman <lisman.aaron@gmail.com>
Co-authored-by: ritikakundra <kundrar@mskcc.org>
Co-authored-by: Tali Mazor <tmazor@users.noreply.github.com>
Co-authored-by: Justin Jao <47490085+justinjao@users.noreply.github.com>
Co-authored-by: JJ Gao <jianjiong.gao@gmail.com>
Co-authored-by: Matthijs Pon <63122826+MatthijsPon@users.noreply.github.com>
Co-authored-by: karissawhiting <karissa.whiting@gmail.com>
Co-authored-by: oplantalech <oleguer@thehyve.nl>
Co-authored-by: Onur Sumer <s.onur.sumer@gmail.com>
Co-authored-by: Qi-Xuan Lu <qlu@carisls.com>
Co-authored-by: Karthik <kalletlakarthik@gmail.com>
Co-authored-by: Bryan Lai <laib1@mskcc.org>
Co-authored-by: qi-xuan.lu <h164654156465@outlook.com>
Co-authored-by: Beking0912 <37431792+Beking0912@users.noreply.github.com>
Co-authored-by: Jiahang Li <55948986+Djokovic0311@users.noreply.github.com>
jagnathan pushed a commit to pughlab/cbioportal that referenced this pull request Nov 8, 2023
@MatthijsPon @jagnathan
extend File-Formats.md with mutational signature datatype (cBioPortal…
089fffa 
…#10172)
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