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Knowledge-Graph-Hub / kg-obo

A package to transform all OBO ontologies into KGX TSV format and OBO json, and put the transformed graph in KGhub
https://knowledge-graph-hub.github.io/kg-obo/getting_started.html
GNU General Public License v3.0
28 stars 2 forks source link

Bump robot version to v1.8.3 and address robot errors #206

Closed caufieldjh closed 1 year ago

caufieldjh commented 1 year ago

This isn't the most recent version of robot, but it is the most recent version that works. Something strange happens between v1.8.3 and v1.8.4 causing OWL parsing to fail.

caufieldjh commented 1 year ago

Getting errors in transforming to obograph json from OWL

caufieldjh commented 1 year ago

I think there's an issue with the way the owl is being parsed:

In bfo, used this value for version: versionIRI
Don't have this version of bfo yet - will transform.
Could not parse OWL definitions enough to locate any imports.
No imports found for bfo.
Completed download from <MagicMock name='get_url()' id='140150636974528'> to /tmp/bfohspsfkui.
Moving from /tmp/bfohspsfkui to data/bfo/2019-08-26/bfo.owl.
ROBOT preprocessing: relax bfo
Relaxing /tmp/bfohspsfkui to /tmp/tmpwon_asiu_bfo_relaxed.owl...
Complete.
Before relax: 0 lines. After relax: 15 lines.
caufieldjh commented 1 year ago

This test error does not occur on a local run of pytest. Weird. Or they don't, that is, until I update robot to v1.9.4. With that version, the relaxed bfo produced is empty because the mocked bfo is an empty file.

caufieldjh commented 1 year ago

Works with robot:

Don't think it's the java version - I'm on v17 locally.