Patch/issues 486 492

[anngvu]

Issues #486 + #492

@allaway We're going to use libraryKitID to capture library kit, but let me know if it makes sense to use something else.

Update:

• according to test results, need to update test templates.

Update 2:
Logs suggest that

• GenomicsAssayTemplate_1.csv is failing submission because of a timeout error, which is acceptable.
• ScRNASeqTemplate_0.csv is failing submission because there are commas in values for libraryKitID, which is a known issue to be fixed by later releases of schematic.

[github-actions]

PR Preview Action v1.4.7
Preview removed because the pull request was closed.
2024-08-20 18:17 UTC

[github-actions]

Test Suite Report 24.7.2

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.csv	😄
GenomicsAssayTemplate_1.csv	❌
GenomicsAssayTemplate_2.csv	😄
GenomicsAssayTemplate_control.csv	😄
ScRNASeqTemplate_0.csv	❌

[allaway]

This makes sense, we'll just need to port over the annotations currently under libraryID in the portal. Food for thought: if we can dig up some controlled terminology for this, it would be super helpful. The world of probe sets is really painful- lots of versions of the "same" kit and there can be different probeset bed files associated with each of these.

Here;s an example list that UCSC maintains: https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=exomeProbesets