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[RFC 65] Add custom namespace columns to CNA #9878

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BasLee
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@BasLee BasLee commented Nov 3, 2022

Add custom namespace columns to CNA events

image

Changes

  • Add ANNOTATION_JSON column to sample_cna_event table
  • Add CustomNamespaceParser.java that imports custom columns of both mutations and CNA's
  • Expose the custom columns as namespaceColumns in the DiscreteCopyNumberController (see DiscreteCopyNumberDataMixin)

Tests

  • Cna importer imports custom namespace columns, see: TestImportCnaDiscreteLongData
  • API exposes custom namespace columns, see: DiscreteCopyNumberServiceImplTest and DiscreteCopyNumberControllerTest

Checks

response.filter(e => e.entrezGeneId === 116983 && e.sampleId === 'TCGA-A2-A04U-01').map(e => e.namespaceColumns)
{
   "MyNamespace": {
       "column1": "value1b",
       "column2": "value2b"
   },
   "MyNamespace2": {
       "blarp": "bluirp2"
   }
}

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@Luke-Sikina Luke-Sikina left a comment

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Very small changes. Nice job!

@BasLee BasLee force-pushed the custom-cna-namespace-annotation-json branch 2 times, most recently from 7bccc41 to 60d4cdc Compare November 17, 2022 16:11
@BasLee BasLee changed the base branch from custom-cna-namespace to master November 17, 2022 16:14
@BasLee BasLee force-pushed the custom-cna-namespace-annotation-json branch from 60d4cdc to f5a8ad9 Compare November 23, 2022 08:45
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sonarcloud bot commented Nov 23, 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 4 Code Smells

0.0% 0.0% Coverage
0.0% 0.0% Duplication

@BasLee BasLee changed the title Add custom namespace columns to CNA [RFC 65] Add custom namespace columns to CNA Nov 28, 2022
@dippindots dippindots merged commit bd6285a into cBioPortal:master Nov 30, 2022
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3 participants