Traits download has not been updated for several months

EBISPOT / goci

GWAS Catalog Ontology and Curation Infrastructure

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Traits download has not been updated for several months #1317

Open ljwh2 opened 1 month ago

ljwh2 commented 1 month ago

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.

Santhi1901 commented 1 month ago

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

ala-ebi commented 2 days ago

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 commented 2 days ago

should be fixed in next DR

sprintell commented 2 days ago

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, ...