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EBISPOT / gwasdepo-deposition-service

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When sumstats submissions have a value for "Analysis software", allow sumstats to validate true when p-values are zero #231

Closed jdhayhurst closed 4 months ago

jdhayhurst commented 1 year ago

"Analysis software" is an optional field in the study template. If a value is given, when the POST request is made to the sumstats service to register (and validate) the sumstats files, add the analysis software field per study, analysisSoftware: <sw name>. By analysisSoftware field exists for the study, this tells the sumstats validator to allow p-values of 0, whereas by default these values are invalid.

Slides from discussion are here: https://docs.google.com/presentation/d/1ccWhl1GlU5hKi9yIXwLTdswJtOUsO2gI/edit?usp=sharing&ouid=115921420372247902258&rtpof=true&sd=true

jdhayhurst commented 1 year ago

this is an issue

ljwh2 commented 6 months ago

Discuss and plan in this sprint

karatugo commented 5 months ago

GWAS sumstats service changes tested and merged to sandbox.

sajo-ebi commented 5 months ago

@sajo-ebi to create a ticket for the deposition side

sajo-ebi commented 5 months ago

created ticket https://github.com/EBISPOT/gwasdepo-deposition-service/issues/247 for Deposition side

karatugo commented 5 months ago
karatugo commented 5 months ago

Test okay with the template v1.11

ljwh2 commented 5 months ago

curators to test

earlEBI commented 5 months ago

Tested with 2 sumstats-only submissions. Validation passes as long as something is entered in the analysis software column.

The error message for sumstats files with 0 p-values and nothing entered in the analysis software column is unhelpful: “Errors: test_izzy2.tsv: Summary statistics file validation failed, please run the validator on your file to see the errors (available here: https://pypi.org/project/gwas-sumstats-tools/)”

Would it be possible to give a more helpful error message for this particular scenario, eg. "Error: Analysis software must be provided in the metadata template for summary statistics containing 0 p-values."

karatugo commented 5 months ago

Sure, let me see what I can do.

karatugo commented 5 months ago

Tested here. https://wwwdev.ebi.ac.uk/gwas/deposition/submission/667e92c52b46030001615a5d

karatugo commented 5 months ago

Inserted new error messages for zero p-values to sumstats-error collections of respective Mongo DB instances.

earlEBI commented 4 months ago

Tested with a sumstats-only submission - looks good to me!

karatugo commented 4 months ago

Thanks, deployed to prod

ljwh2 commented 4 months ago

I think users might find the error message confusing:

Analysis software must be provided in the metadata template for summary statistics containing 0 p-values.

would be clearer as

Analysis software must be provided in the metadata template for summary statistics containing p-values equal to zero.

karatugo commented 4 months ago

@karatugo roll back changes until java side is deployed

karatugo commented 4 months ago

Re-deployed v1.4.16.

karatugo commented 4 months ago

Updated the error message. It's ready to deploy when Java side is.