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nf-osi / nf-metadata-dictionary

Versioned releases of the NF metadata dictionary.
https://nf-osi.github.io/nf-metadata-dictionary/
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add GE MRI #443

Closed allaway closed 1 month ago

allaway commented 1 month ago

For NFOSI-810

github-actions[bot] commented 1 month ago

PR Preview Action v1.4.7 :---: :rocket: Deployed preview to https://nf-osi.github.io/nf-metadata-dictionary/pr-preview/pr-443/ on branch gh-pages at 2024-05-10 15:22 UTC

allaway commented 1 month ago

Converting this back to draft b/c I missed some things...

github-actions[bot] commented 1 month ago

Test Suite Report 24.4.1

Template Generation

template result link
ClinicalAssayTemplate :smile: template link
EpigeneticsAssayTemplate :smile: template link
FlowCytometryTemplate :smile: template link
GenomicsAssayTemplate :x:
GenomicsAssayTemplateExtended :smile: template link
HumanCohortTemplate :smile: template link
ImagingAssayTemplate :smile: template link
LightScatteringAssayTemplate :smile: template link
MethylationArrayTemplate :smile: template link
MRIAssayTemplate :x:
PharmacokineticsAssayTemplate :smile: template link
PlateBasedReporterAssayTemplate :smile: template link
ProcessedAlignedReadsTemplate :smile: template link
ProcessedExpressionTemplate :smile: template link
ProcessedVariantCallsTemplate :smile: template link
ProteomicsAssayTemplate :smile: template link
ProtocolTemplate :smile: template link
RNASeqTemplate :smile: template link
ScRNASeqTemplate :x:
UpdateMilestoneReport :smile: template link
WESTemplate :smile: template link
WGSTemplate :smile: template link

Manifest Validation

manifest result expectation
GenomicsAssayTemplate_0.csv :x: Lists can be blank if attr not required using ‘list like’ rule
GenomicsAssayTemplate_1.csv :x: Mixing blanks and regular list values works
GenomicsAssayTemplate_2.csv :x: Conditional validation for attributes is currently not supported
GenomicsAssayTemplate_control.csv :smile: There should be no issue with this template.
ScRNASeqTemplate_0.csv :x: Single list val works by using ‘list like’ rule
ScRNASeqTemplate_1.csv :smile: Fail because of missing data in required field libraryStrand

Manifest Submission

manifest pass
GenomicsAssayTemplate_control.csv :smile:
allaway commented 1 month ago

OK, this is actually ready for review now 😓

allaway commented 1 month ago

Summary of additional discussion: resolution for now is to keep as single value to retain dropdown with a special selection string value like "Disease1,Disease2,Disease3" until we have better UI.

Actually, I was thinking about just pushing the annotations "Disease1,Disease2,Disease3" manually, ie w/o validation. But I could also add it as a value to the schema. I believe these contributors will not be adding more data to their project, which makes me lean towards the skip-validation approach (it's 3 files total). What do you think?

allaway commented 1 month ago

Actually, now that I think about it, if I'm skipping validation, should I just annotate it as a stringList anyway?

anngvu commented 1 month ago

@allaway Yeah, let's just annotate it as stringList for these 3 files then. We can skip adding the unwieldy "Disease1,Disease2,Disease3" since there's already human validation, technically.

anngvu commented 1 month ago

Superseded by #457