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add FISH #377

Merged
merged 7 commits into from
Dec 6, 2023
Merged

add FISH #377

merged 7 commits into from
Dec 6, 2023

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allaway
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@allaway allaway commented Dec 6, 2023

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github-actions bot commented Dec 6, 2023

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

@allaway allaway requested a review from anngvu December 6, 2023 17:18
@allaway allaway marked this pull request as ready for review December 6, 2023 17:18
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allaway commented Dec 6, 2023

Hmm looks like I broke the ScRNASeqTemplate 🤔

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allaway commented Dec 6, 2023

Ah, I see, I think this was caused by a previous change where libraryStrand was set to required, so the change should actually be in the test manifest.

 error: For the attribute 'libraryStrand', on row 2, '' is not one of ['Not Applicable', 'FirstStranded', 'SecondStranded', 'Unstranded'].
error: For the attribute 'libraryStrand', on row 3, '' is not one of ['Not Applicable', 'FirstStranded', 'SecondStranded', 'Unstranded'].
error: For the attribute 'libraryStrand', on row 4, '' is not one of ['Not Applicable', 'FirstStranded', 'SecondStranded', 'Unstranded'].
error: For the attribute 'libraryStrand', on row 5, '' is not one of ['Not Applicable', 'FirstStranded', 'SecondStranded', 'Unstranded'].
[['2', 'libraryStrand', "'' is not one of ['Not Applicable', 'FirstStranded', 'SecondStranded', 'Unstranded']", ''], ['3', 'libraryStrand', "'' is not one of ['Not Applicable', 'FirstStranded', 'SecondStranded', 'Unstranded']", ''], ['4', 'libraryStrand', "'' is not one of ['Not Applicable', 'FirstStranded', 'SecondStranded', 'Unstranded']", ''], ['5', 'libraryStrand', "'' is not one of ['Not Applicable', 'FirstStranded', 'SecondStranded', 'Unstranded']", '']]

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allaway commented Dec 6, 2023

Wait, no, that's the wrong error, that's expected...

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allaway commented Dec 6, 2023

Ok, now that I am actually looking in the right place, it looks like the generate sc rnaseq manifest test just failed due to google API limits:

googleapiclient.errors.HttpError: <HttpError 429 when requesting https://sheets.googleapis.com/v4/spreadsheets/1l5mHnes8Rxab-uVMyJst6d0edejnRuegmMbCeQwUDYQ/values/Sheet2%21P2%3AP51?valueInputOption=RAW&alt=json returned "Quota exceeded for quota metric 'Write requests' and limit 'Write requests per minute per user' of service 'sheets.googleapis.com' for consumer 'project_number:495775691787'.". Details: "[{'@type': 'type.googleapis.com/google.rpc.ErrorInfo', 'reason': 'RATE_LIMIT_EXCEEDED', 'domain': 'googleapis.com', 'metadata': {'quota_limit': 'WriteRequestsPerMinutePerUser', 'consumer': 'projects/495775691787', 'quota_location': 'global', 'service': 'sheets.googleapis.com', 'quota_limit_value': '60', 'quota_metric': 'sheets.googleapis.com/write_requests'}}, {'@type': 'type.googleapis.com/google.rpc.Help', 'links': [{'description': 'Request a higher quota limit.', 'url': 'https://cloud.google.com/docs/quota#requesting_higher_quota'}]}]">

So I imagine that means that this PR is OK.

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👍🏼

@anngvu anngvu merged commit 91b3ef5 into main Dec 6, 2023
1 of 2 checks passed
@anngvu anngvu deleted the patch-new-assays branch December 6, 2023 22:44
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3 participants