Closed shawntanzk closed 2 years ago
Current issue seems to be Cause: /work/src/ontology/imports/merged_import.owl (No such file or directory)
This error occurs when i try to run sh run.sh make imports/merged_import.owl
or sh run.sh make no-mirror-refresh-imports
not too sure how to fix given that it almost seems cyclical
Issue seems to be merge is trying to bring in edit file and edit file is trying to bring in merge - removed merge import from edit file and ran sh run.sh make imports/merged_import.owl
and worked - now running sh run.sh make no-mirror-refresh-imports
and will check that everything is in place
Currently HEAPS of CHEBI and CARO dangling classes - I think this is the downside to base file imports. We can fix it by importing them in, or deleting the axioms. Downside to importing: they will probably bring in even more dangling classes Downside to deleting: if we programmatically do it, it might result in future users not being able to use that import if they don't know we did that Happy to do either.
Of note: other ontologies remove it
Best import Chebi. You can potentially delete CARO, but try to import it.. just to see wether you run into consistency issues..
Note to self: there are a couple of NBO terms to deal with too. Will try to fix them in this PR too: https://github.com/obophenotype/provisional_cell_ontology/pull/24
dangling classes still present
after refreshing chebi mirror (in case it was an error from before) and rerunning sh run.sh make no-mirror-refresh-imports
dangling classes still present. Not sure if I need to make a release to fix it? will try.
Ask me in slack.. You dont need a release.
2 things left to fix:
after alot of stupid mistakes my me, and heaps of help from @matentzn, branch is finally clean. Just before I merge just wanted to make sure @dosumis is alright with the stuff I exclude:
exclude_iri_patterns:
- <http://www.informatics.jax.org/marker/MGI:*>
- <http://purl.obolibrary.org/obo/OBA_*>
- <http://purl.obolibrary.org/obo/ENVO_*>
- <http://purl.obolibrary.org/obo/OBI_*>
- <http://purl.obolibrary.org/obo/GOCHE_*>
- <http://purl.obolibrary.org/obo/CARO_*>
- <http://purl.obolibrary.org/obo/NCBITaxon_Union_*>
- <http://www.genenames.org/cgi-bin/gene_symbol_report*>
If so, could you help give a thumbs up please?
Switch to base file imports