Patch/new cbp mapping

[anngvu]

Add supplemental properties that may curated for certain projects, i.e. see https://www.cell.com/stem-cell-reports/fulltext/S2213-6711(19)30002-5?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2213671119300025%3Fshowall%3Dtrue#tbl1

I expect main reviewers to be Robert or Jineta, but Christina for awareness.

[github-actions]

Test Suite Report

Template Generation

template	result	link
ClinicalAssayTemplate	😄	template link
EpigeneticsAssayTemplate	😄	template link
FlowCytometryTemplate	😄	template link
GenomicsAssayTemplate	😄	template link
GenomicsAssayTemplateExtended	😄	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	😄	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

[cconrad8]

makes sense to me - just curious if this is something we're adding to the regular metadata dictionary (not just cbioportal mapping?)

[anngvu]

@cconrad8 Yep, nf1GermlineMutation and nf1SomaticMutation are now attributes in the model, just not part of any template yet. There's still an issue out to develop a real clinical data template, which could make use of these.

[cconrad8]

@anngvu gotcha sounds good!