add GE MRI

[allaway]

For NFOSI-810

[github-actions]

PR Preview Action v1.4.7
🚀 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]

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

[github-actions]

Test Suite Report 24.4.1

Template Generation

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

Manifest Validation

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

Manifest Submission

manifest	pass
GenomicsAssayTemplate_control.csv	😄

[allaway]

OK, this is actually ready for review now 😓

[anngvu]

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.

[allaway]

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]

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

[anngvu]

@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]

Superseded by #457