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icgc-argo / argo-data-submission

Workflow to submit genomic data to ARGO RDPC for processing
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Miss to catch the invalid value in schema validation #73

Closed lindaxiang closed 1 year ago

lindaxiang commented 1 year ago

Although the field experiment/platform in submission-song.rdpc-qa sequencing_experiment schema has an enum definition

"platform": {
 "enum": [
  "CAPILLARY",
  "LS454",
  "ILLUMINA",
  "SOLID",
  "HELICOS",
  "IONTORRENT",
  "ONT",
  "PACBIO",
  "Nanopore",
  "BGI"
]

but all the submission payloads pass the schema validation when the field was provided as:

"plzatform": "Illumina",

Plus both submission workflow and the song server validations did not catch the errors.

lindaxiang commented 1 year ago

Thanks to Edmund, the reason was found and there is a typo in the schema which cause the schema validation did not catch the issue. Note that allof, that’s a typo and should be allOf. Two other separate tickets have been created to address the issue with schema and analysis errors: