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Published 20 hours ago • verified publisher icon EBISPOT

Traits download has not been updated for several months

Open ljwh2 opened this issue 9 months ago • 1 comments

The traits download does not seem to have been update for several months. A download from 1st March is identical to the 5th May one, and several EFOs that have been updated in the UI have the old version in the download file.

Example, https://www.ebi.ac.uk/gwas/efotraits/EFO_0022597 does not appear in the file, but "aging" appears with uri http://purl.obolibrary.org/obo/GO_0007568 which was obsoleted recently.

ljwh2 avatar May 08 '24 12:05 ljwh2

the following terms added in 2024 are also not in the downloaded file: age of onset of diverticulitis: http://purl.obolibrary.org/obo/OBA_2050355 placenta mass: http://purl.obolibrary.org/obo/OBA_VT0004257 level of endocrine disruptor in urine: http://purl.obolibrary.org/obo/OBA_2050419

Santhi1901 avatar May 08 '24 13:05 Santhi1901

  • mail server was causing issues, switched to hx-smtp instead of outgoing
  • no patch for corrupt EFO release, switched to using old version https://github.com/EBISPOT/efo/releases/download/v3.66.0/efo.owl
  • both the above changes are under {data_dir}/prod/config/application.properties
  • jar file was previously SCP'd from an old version causing flyway errors, redeployed

ala-ebi avatar Jun 26 '24 15:06 ala-ebi

should be fixed in next DR

ala-ebi avatar Jun 26 '24 15:06 ala-ebi

Was running on garfield, moved to codon and that resolved the SMTP connectivity issues, changed the URI to Hinxton SMTP, ...

The version on teh cluster was an old one, a new deployment was done to resolve this, ...

sprintell avatar Jun 27 '24 08:06 sprintell

confirmed that the "aging" term is now correct and up to date

eks-ebi avatar Jul 08 '24 12:07 eks-ebi

other recently-added traits are also there in the updated spreadsheet, so I think this is done

eks-ebi avatar Jul 08 '24 12:07 eks-ebi

@Santhi1901 the only trait I still can't find in the spreadsheet is "placenta mass" - but this trait also looks broken in the Search UI: https://wwwdev.ebi.ac.uk/gwas/efotraits/OBA_VT0004257. Any idea what could be going on there?

eks-ebi avatar Jul 08 '24 13:07 eks-ebi

The paper is published with this EFO (http://ves-ebi-e4.ebi.ac.uk:8080/gwas/curation/publication/37798380), but in the UI this term is missing.

I think the term is still not imported to EFO. This is the EFO ticket for this trait: https://github.com/EBISPOT/efo/issues/2116

Santhi1901 avatar Jul 09 '24 09:07 Santhi1901