Pipelines no longer build due to ChEBI's .obo form containing unparsable data

geneontology / pipeline

Declarative pipeline for the Gene Ontology.

BSD 3-Clause "New" or "Revised" License

5 stars 5 forks source link

Closed kltm closed 2 years ago

kltm commented 2 years ago

Currently, due to ChEBI containing a bad name the .obo file is no longer parsable with some tooling. https://github.com/ebi-chebi/ChEBI/issues/4273

This brings pretty much all pipelines, except email updates, to a halt. This issue started August 3rd, after 6am our time.

kltm commented 2 years ago

@balhoff Has a workaround in place for the ontology build, switching the .obo file for the parsable .owl file: https://github.com/geneontology/go-ontology/pull/23816

kltm commented 2 years ago

The GOlr/Solr loader should be unaffected by this issue since it has always been loading the .owl file. Now testing on go-ontology-dev.

kltm commented 2 years ago

go-ontology-dev now building again. Clearing workspaces of all other active pipelines.