Fix 9461 mutations api endpoint final #9914

jagnathan · 2022-12-02T17:32:16Z

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

- 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

sonarcloud · 2022-12-02T18:42:39Z

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dippindots

@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:

And the version should be 2.13.0 based on Database-Versioning

dippindots · 2023-02-27T15:00:45Z

db-scripts/src/main/resources/migration.sql

+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";


@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

sonarcloud · 2023-03-08T06:24:35Z

Kudos, SonarCloud Quality Gate passed!

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0.0% Duplication

inodb · 2023-03-08T23:28:04Z

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


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

but if it's easier to keep the current changes, that's fine too

inodb

Great! Thanks so much @dippindots and @jagnathan !

jagnathan added 7 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

jagnathan requested a review from inodb December 20, 2022 17:13

jagnathan changed the base branch from master to demo-v5.3.0 February 22, 2023 22:38

dippindots reviewed Feb 27, 2023

View reviewed changes

dippindots added 2 commits March 8, 2023 00:16

Update DB version and renaming mutation_event fields

89bde61

Update Mutation model

9ca0563

inodb reviewed Mar 8, 2023

View reviewed changes

inodb approved these changes Mar 8, 2023

View reviewed changes

inodb added the cleanup label Mar 8, 2023

dippindots merged commit ec2236f into cBioPortal:demo-v5.3.0 Mar 14, 2023

dippindots mentioned this pull request Mar 22, 2023

Release v5.3.0 #10098

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Fix 9461 mutations api endpoint final #9914

Fix 9461 mutations api endpoint final #9914

jagnathan commented Dec 2, 2022 •

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Fix 9461 mutations api endpoint final #9914

Fix 9461 mutations api endpoint final #9914

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