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Fix 9461 mutations api endpoint final #9914

Merged
merged 9 commits into from
Mar 14, 2023
Merged

Fix 9461 mutations api endpoint final #9914

merged 9 commits into from
Mar 14, 2023

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jagnathan
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@jagnathan jagnathan commented Dec 2, 2022 •
edited by dippindots
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Fix #9461

API Changes:

  • Mutations endpoint has these fields removed:
    • functionalImpactScore
    • fisValue
    • linkXVar
    • linkPdb
    • linkMsa
    • oncotatorDbSnpRs
    • oncotatorUniprotName
  • Mutations endpoint has these fields renamed:
    • oncotatorRefseqMrnaId to refseqMrnaId
    • oncotatorUniprotAccession to uniprotAccession
    • oncotatorCodonChange to codonChange
    • oncotatorProteinPosStart to proteinPosStart
    • oncotatorProteinPosEnd to proteinPosEnd

Schema Changes:

  • mutation_event table removes oncotator fields:
    • ONCOTATOR_DBSNP_RS
    • ONCOTATOR_DBSNP_RS
  • mutation_event table renames oncotator fields:
    • ONCOTATOR_REFSEQ_MRNA_ID to REFSEQ_MRNA_ID
    • ONCOTATOR_CODON_CHANGE to CODON_CHANGE
    • ONCOTATOR_UNIPROT_ACCESSION to UNIPROT_ACCESSION
    • ONCOTATOR_PROTEIN_POS_START to PROTEIN_POS_START
    • ONCOTATOR_PROTEIN_POS_END to PROTEIN_POS_END
  • mutation_event table removes other unnecessary fields:
    • FUNCTIONAL_IMPACT_SCORE
    • FIS_VALUE
    • LINK_XVAR
    • LINK_PDB
    • LINK_MSA

@jagnathan
fix cBioPortal#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
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sonarcloud bot commented Dec 2, 2022

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 7 Code Smells

0.0% 0.0% Coverage
0.0% 0.0% Duplication

@jagnathan jagnathan requested a review from inodb December 20, 2022 17:13
@jagnathan jagnathan changed the base branch from master to demo-v5.3.0 February 22, 2023 22:38
dippindots
dippindots reviewed Feb 27, 2023
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@jagnathan Thanks for making these changes. @inodb could you do a quick final review about changes in this pr?
I just wanted to add a few things about versioning:
We also need to change another two files to make sure DB version is in sync everywhere:

  1. https://github.com/cBioPortal/cbioportal/blob/master/pom.xml#L317
  2. https://github.com/cBioPortal/cbioportal/blob/master/db-scripts/src/main/resources/cgds.sql#L765

And the version should be 2.13.0 based on Database-Versioning

db-scripts/src/main/resources/migration.sql Outdated
ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_UNIPROT_ACCESSION` `MUTATION_UNIPROT_ACCESSION` varchar(64);
ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_START` `MUTATION_PROTEIN_POS_START` int(11);
ALTER TABLE `mutation_event` CHANGE COLUMN `ONCOTATOR_PROTEIN_POS_END` `MUTATION_PROTEIN_POS_END` int(11);
UPDATE `info` SET `DB_SCHEMA_VERSION`="2.12.16";
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@jagnathan Based on the database versioning we discussed, we should update the version to 2.13.0: https://github.com/cBioPortal/cbioportal/blob/master/docs/Database-Versioning.md

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sonarcloud bot commented Mar 8, 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

0.0% 0.0% Coverage
0.0% 0.0% Duplication

inodb
inodb reviewed Mar 8, 2023
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maf/src/main/java/org/mskcc/cbio/maf/MafRecord.java
@@ -103,16 +103,14 @@ public class MafRecord {
private String maLinkMsa;
private String maLinkPdb;

// Oncotator cols
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should we leave this entire MafRecord file as is? Doesn't feel like the oncotator -> maf renaming adds much. Prolly better to leave this for the ticket where we fix the maf parser

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@inodb inodb Mar 8, 2023 •
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but if it's easier to keep the current changes, that's fine too

inodb
inodb approved these changes Mar 8, 2023
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Great! Thanks so much @dippindots and @jagnathan !

@inodb inodb added the cleanup label Mar 8, 2023
@dippindots dippindots merged commit ec2236f into cBioPortal:demo-v5.3.0 Mar 14, 2023
@dippindots dippindots mentioned this pull request Mar 22, 2023
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@inodb inodb inodb approved these changes

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Clean up Mutations end point
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@jagnathan @inodb @dippindots