Sumstats filetype for GCST90432154 is GWAS-SSF v1.0 but should be non-GWAS-SSF

[eks-ebi]

This summary statistics file is missing two mandatory columns: beta and _standarderror, so should not meet the GWAS-SSF format. I also pushed it through validation manually. I would therefore expect the file type to be non-GWAS-SSF, but it is unexpectedly showing as GWAS-SSF v1.0 in the yaml file.

Actions:

• [x] Change file type to non-GWAS-SSF for this submission
• [x] Investigate to make sure that files with validation manually overriden are being annotated as non-GWAS-SSF as expected in future

[karatugo]

fixed the file type in mongo

[karatugo]

expect the new metadata yaml in 2 days

[karatugo]

Discuss tomorrow in the meeting.

/gwas/deposition/api/v1/bypass-ss-validation - this endpoint sends payloads with forceValid=True and skipValidation=False. I wonder how they should affect file type detection. For example, should we set non-gwas-ssf when either is True? (currently only set non-gwas-ssf when skipValidation=True).

[karatugo]

deployed to sandbox

[karatugo]

test okay in sandbox

[karatugo]

deployed to prod