Patch/schematic 24.5.1

[anngvu]

• Close Update schematic version, add'l conversion, and CLI revision  #449
• Small additional progress on Add deeper submission test to test suite #445 -- analysis code not written yet

I think everything looks good. Currently, you can check the data submitted by downloading logs for https://github.com/nf-osi/nf-metadata-dictionary/actions/runs/9087194193. Please ignore the extra rows with X's for the Submission report, that has been fixed (just didn't want to run the CI again).

The test submissions did take much longer than ~40s per submission, but that's probably the occasional GH Actions slowdown.

[github-actions]

Test Suite Report 24.5.1

Template Generation

template	result	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
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_0-syn59479744_tmp.json	❌
GenomicsAssayTemplate_0-syn59479744.json	❌
GenomicsAssayTemplate_0.csv	😄
GenomicsAssayTemplate_1-syn59479470_tmp.json	❌
GenomicsAssayTemplate_1-syn59479470.json	❌
GenomicsAssayTemplate_1.csv	😄
GenomicsAssayTemplate_2-syn59479824_tmp.json	❌
GenomicsAssayTemplate_2-syn59479824.json	❌
GenomicsAssayTemplate_2.csv	😄
GenomicsAssayTemplate_control-syn59479832_tmp.json	❌
GenomicsAssayTemplate_control-syn59479832.json	❌
GenomicsAssayTemplate_control.csv	😄
ScRNASeqTemplate_0-syn59479689_tmp.json	❌
ScRNASeqTemplate_0-syn59479689.json	❌
ScRNASeqTemplate_0.csv	😄

[allaway]

@anngvu , thanks for doing this! I had a question about the superdataset/dataset assay values disappearing. is that expected?

[anngvu]

@allaway Actually, good catch. The JSON Schema build was trying to select ids that were changed, so just had to make sure that the build ran in the right order. But this reminds me I'll also have to change any other scripts that reference assay and institution values by using their key ids in the model.