EVA-3564 - Simplify metadata conversion and validation #55
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apriltuesday
commented
Sep 10, 2024
•
apriltuesday
commented
- Metadata conversion never fails (unless unable to open the excel file) and always generates a JSON to validate
- Scientific name and Biosample name errors correctly parsed and propagated to report
- Added scientific name / taxonomy ID coherence check to semantic validation
- Refactored and updated tests
apriltuesday
changed the title
| /sample/3/bioSampleObject/name | ||
| must have required property 'name' | ||
| must have required property 'name' | ||
| must have required property 'name' |
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not sure what's going on here, but this is the output I get from biovalidator...
| if scientific_name in data: | ||
| data[SPECIES] = data[scientific_name] |
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Is it worth having a mechanism that convert a excel spreadsheet into more than one BioSample field ?
We could then provide this in the spreadsheet2json_conf.yaml as
Sample:
header_row: 3
optional:
Scientific Name: [scientificName, species]There was a problem hiding this comment.
Could do, it would only be used for this case though as far as I know - the name field goes outside of characteristics so has to be handled differently. I probably won't add it to this PR but we should keep it in mind.
| # Sometimes there are multiple (possibly redundant) errors listed under a single property, | ||
| # we only report the first |
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We probably should report that to biovalidator.js
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Good point, I'll make an issue for them.
