Patch tests, schematic update with 'typing_extensions' bug workaround, add bmp format

[anngvu]

Fix broken tests (#416) and make sure to use latest version of schematic (#422). Add needed term to trigger tests, assess fix.

• Note: Now that tests are working, found that we need to update test manifests validation because diagnosis was made required in make diagnosis required attribute #417.

[github-actions]

PR Preview Action v1.4.7
🚀 Deployed preview to https://nf-osi.github.io/nf-metadata-dictionary/pr-preview/pr-421/
on branch gh-pages at 2024-04-11 15:11 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