Patch/strict model

[anngvu]

• Todo - add new tests.

The theme of this PR is enforcing a stricter model, relevant to #118 and #277.

@cconrad8 main validator bc:

• person who proposed Make annotations required for RNA sequencing  #277
• good to see more LinkML examples
• give @allaway a break

Issues that I've noticed (which I think is due to some unclear schematic logic):

• Making some fields required is actually not working properly. For example it is working with individualID, but not libraryPreparationMethod as seen in validation tests below and if you take a look at an example manifest from the generation test (highlighted columns). I think we can merge this and see if updating to the latest schematic version fixes this issue or it is because of how we're using Depends On to pull in dependent fields.

[github-actions]

Test Suite Report

Template Generation

template	result	link
ClinicalAssayTemplate	😄	template link
EpigeneticsAssayTemplate	😄	template link
FlowCytometryTemplate	😄	template link
GenomicsAssayTemplate	😄	template link
ImagingAssayTemplate	😄	template link
LightScatteringAssayTemplate	😄	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	😄	Single list val works by using ‘list like’ rule
GenomicsAssayTemplate_2.csv	😄	Mixing blanks and regular list values works
GenomicsAssayTemplate_3.csv	😄	Conditional validation for attributes is currently not supported
GenomicsAssayTemplate_4.csv	❌	A (double) value of 1.5 fails with rule int::inRange 1 2
GenomicsAssayTemplate_5.csv	❌	A value of 0 (outside range) fails with rule int::inRange 1 2
RNASeqTemplate_0.csv	😄	Pass as this is the ‘control’ good manifest
RNASeqTemplate_1.csv	😄	Fail because of missing data in required field individualID
RNASeqTemplate_2.csv	❌	Fail because of missing data in required field libraryPreparationMethod

[anngvu]

Update: found an issue that maybe explains why some required columns are not highlighted blue: Sage-Bionetworks/schematic#1018

[cconrad8]

Looks good to me! Thanks for making the changes