Update for individualID

[anngvu]

Related to FDS-1968.

So we should allow a list of IDs anyway, even aside from the above issue where I think schematic gets confused during submission when a field that's not supposed be a list ends up having commas (?).

[github-actions]

PR Preview Action v1.4.7
🚀 Deployed preview to https://nf-osi.github.io/nf-metadata-dictionary/pr-preview/pr-430/
on branch gh-pages at 2024-04-19 17:45 UTC

[github-actions]

Test Suite Report

Template Generation

template	result	link
AnimalIndividualTemplate	😄	template link
BiospecimenTemplate	😄	template link
ClinicalAssayTemplate	😄	template link
EpigeneticsAssayTemplate	😄	template link
FlowCytometryTemplate	😄	template link
GenomicsAssayTemplate	😄	template link
GenomicsAssayTemplateExtended	😄	template link
HumanCohortTemplate	😄	template link
ImagingAssayTemplate	😄	template link
LightScatteringAssayTemplate	😄	template link
MethylationArrayTemplate	😄	template link
MRIAssayTemplate	😄	template link
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	😄	template link
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
ScRNASeqTemplate_0.csv	😄	Single list val works by using ‘list like’ rule
ScRNASeqTemplate_1.csv	😄	Fail because of missing data in required field libraryStrand

[allaway]

LGTM! One comment, we need to update the individualID attribute here to a stringList:
https://www.synapse.org/#!Synapse:syn16858331/tables/

Will we need to update all of the schemas for the project fileviews too?

[anngvu]

@allaway -- thanks, good reminder -- created ticket here; it does appear there needs to be a bit of cleanup for a couple of instances where ids were submitted as single long strings (e.g. "patient1, patient2, ...") before we can convert, because I'm getting warnings about table column sizes.

[cconrad8]

Nice @anngvu ! I'm just curious where do these validation rules come from? are they specific to linkml or jsonld schema? wondering where to find "list like" and other validation rules

[allaway]

@anngvu , thanks for creating the ticket!

I am pretty sure this function will do what you need to handle the cleanup, though I'm not sure if it still works, since it has been a while!

[cconrad8]

nvm! @mialy-defelice sent me to the page https://sagebionetworks.jira.com/wiki/spaces/SCHEM/pages/3302785036/Schematic+Validation