add specimenID to bts:ProcessedAlignedReadsTemplate

[allaway]

SpecimenID is useful here as it often contains info about different replicates, treatments, etc, in cell line sequencing

[github-actions]

PR Preview Action v1.4.7
🚀 Deployed preview to https://nf-osi.github.io/nf-metadata-dictionary/pr-preview/pr-415/
on branch gh-pages at 2024-04-02 16:33 UTC

[github-actions]

Test Suite Report

Template Generation

template	result	link
AnimalIndividualTemplate	❌
BiospecimenTemplate	❌
ClinicalAssayTemplate	❌
EpigeneticsAssayTemplate	❌
FlowCytometryTemplate	❌
GenomicsAssayTemplate	❌
GenomicsAssayTemplateExtended	❌
HumanCohortTemplate	❌
ImagingAssayTemplate	❌
LightScatteringAssayTemplate	❌
MethylationArrayTemplate	❌
MRIAssayTemplate	❌
PharmacokineticsAssayTemplate	❌
PlateBasedReporterAssayTemplate	❌
ProcessedAlignedReadsTemplate	❌
ProcessedExpressionTemplate	❌
ProcessedVariantCallsTemplate	❌
ProteomicsAssayTemplate	❌
ProtocolTemplate	❌
RNASeqTemplate	❌
ScRNASeqTemplate	❌
UpdateMilestoneReport	❌
WESTemplate	❌
WGSTemplate	❌

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

[allaway]

Hmm, not sure if I broke something or the tests are broken..

ImportError: cannot import name 'TypeAliasType' from 'typing_extensions' (/opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/typing_extensions.py)

[anngvu]

Thanks -- you can ignore the test results, there's suddenly some dependency issue on GH Actions

[anngvu]

Actually, I just realized there may be another fix needed, since this inherits from BiologicalAssayDataTemplate, which has specimenID -- let me make suggestion

[anngvu]

OK, from my comments I see why it wasn't at that level originally -- all good!

[anngvu]

We haven't changed any test workflow code since our last working tests last week (#412), so I'm suspecting this is an Actions cache issue -- will be looked into separately.

…

On Tue, Apr 2, 2024, 9:51 AM Robert Allaway ***@***.***> wrote: Hmm, not sure if I broke something or the tests are broken.. ImportError: cannot import name 'TypeAliasType' from 'typing_extensions' (/opt/hostedtoolcache/Python/3.10.12/x64/lib/python3.10/site-packages/typing_extensions.py) — Reply to this email directly, view it on GitHub <#415 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AHZ4M6X6VDZZYQYGNPMCBYDY3LOYPAVCNFSM6AAAAABFTXBZCOVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDAMZSGU3DMNRZG4> . You are receiving this because your review was requested.Message ID: ***@***.***>

[allaway]

OK, from my comments I see why it wasn't at that level originally -- all good!

I went thru the exact same thought process! :) I am happy to move it up a level if that makes sense more generally. I can imagine other assays might benefit from specimenID info.

Thanks for the quick review!