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Migrate GO editors to Protege 5.6.1 #25019

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balhoff opened this issue Feb 25, 2023 · 6 comments
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Migrate GO editors to Protege 5.6.1 #25019

balhoff opened this issue Feb 25, 2023 · 6 comments
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balhoff commented Feb 25, 2023

There is a new release of Protege which includes ELK 0.5 as well as dedicated support for ID ranges files. It also uses the latest OWL API, inline with the latest ROBOT and ODK. To avoid inconsistent file serializations, we should migrate to all of these simultaneously (Protege 5.6.1, ODK 1.4): editors' desktops, this repo QC actions, and GO pipeline.

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@balhoff balhoff self-assigned this Feb 25, 2023
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kltm commented Feb 25, 2023

@balhoff Testing failed with https://build.geneontology.org/job/geneontology/job/pipeline/job/master/716/execution/node/230/log/
If you can't see that, let me know and I'll get the permissions straightened.

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kltm commented Feb 25, 2023

@pgaudet Putting this in misc for now.

@kltm kltm moved this to In Progress in Miscellaneous Feb 25, 2023
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balhoff commented Feb 28, 2023 •
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@kltm I think that pipeline failure is due to stricter handling from the new OWL API for bad term IRIs which were in reacto.owl. Fix is here: geneontology/pathways2GO#234

Once I make a release there, need to update biopax2go version here.

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balhoff commented Feb 28, 2023

@pgaudet here's an issue with term IDs to follow: protegeproject/protege#1108

kltm added a commit to geneontology/pipeline that referenced this issue Mar 13, 2023
@kltm
propagate odk for geneontology/go-ontology#25019
d9e1150
kltm added a commit to geneontology/pipeline that referenced this issue Mar 13, 2023
@kltm
propagate odk for geneontology/go-ontology#25019
ef997be
kltm added a commit to geneontology/pipeline that referenced this issue Mar 13, 2023
@kltm
propagate odk for geneontology/go-ontology#25019
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kltm commented Mar 13, 2023

@balhoff I believe I've propagated this change to all producing pipelines.

@balhoff balhoff mentioned this issue Mar 13, 2023
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balhoff commented Mar 28, 2023

Done.

@balhoff balhoff closed this as completed Mar 28, 2023
@github-project-automation github-project-automation bot moved this from In Progress to Done in Miscellaneous Mar 28, 2023
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