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Add clinvar-ingest per clinvar release Q/A measures to workflow #134

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toneillbroad opened this issue Apr 4, 2024 · 1 comment
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@toneillbroad
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Add Q/A measures to per ClinVar release ingest. Measures include:

  • count of VCVs, SCVs, RCVs, Genes, Submitters, Submissions, etc. pcregrep'd from XML file
  • compare those to counts from BQ tables

If counts are off, send a slack messga eindicating the issue.
Create the DO_NOT_PROCESS sentinel file in GCP to stop processing of future clinvar releases until the issue is resolved.

@toneillbroad toneillbroad self-assigned this Apr 4, 2024
@toneillbroad
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toneillbroad commented Jun 5, 2024

Plan refinement:

  1. Pre-parse XML, get counts using JSON path: this is count#1
  2. Get counts during parsing from model object creation: this is count#2
  3. Validation Get VariationArchive parsing and output to file working with minimal fields #1 - post parse compare count#1 == count#2
  4. Post creation of external tables, select count(*) from all external tables: this is count#3
  5. Validation Write unit test for simple output created from parsed input, compared to expected output file #2 - compare count#1 == count#3

Add a command line argument to turn validation off for testing purposes.

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