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Troubleshooting

Issue: Error after updating the repository

When updating the repository (sh run.sh update_repo ), you may encounter an error like the one below:

INFO:root:OUT: UNKNOWN ARG ERROR unknown command or option: odk:import

...

Exception: Failed: robot odk:import -i molsim-edit.owl --exclusive true --add http://purl.obolibrary.org/obo/molsim/imports/uo_import.owl --add http://purl.obolibrary.org/obo/molsim/imports/chebi_import.owl --add http://purl.obolibrary.org/obo/molsim/imports/ncit_import.owl --add http://purl.obolibrary.org/obo/molsim/components/molsim_units_component.owl convert -f ofn -o molsim-edit.owl

Possible Cause

This issue typically occurs when there is a problem with imported ontologies in your configuration.

  1. Identify the ontology import suspected to cause the issue.

  2. Remove or comment it (in this case, ncit) out from the following files:

  3. molsim-odk.yaml

  4. molsim-edit.owl
  5. catalog-v0001.xml

  6. molsim.Makefile

  7. Rebuild the ontology using the usual ODK commands (sh run.sh update_repo or the corresponding step in your workflow).

Reference Example

You can look at commit 1232391bdcb6b41964ce71d7cd73335dfe4ef096 opn the files mentioned above for an example of how these changes were made.