By default, the OBO writer strictly enforces document structure rules. If an ontology violates these, the convert to OBO operation will fail. These checks can be ignored by including --check false.
This PR enables passing this check flag through functions in bioontologies that wrap the robot convert command.
Unfortunately, this doesn't solve the issue with VO - it appears that ROBOT creates some metadata elements that are unexpectedly none. Additionally, this PR implements some processing for raw graph documents before loading int Pydantic to remove invalid fields that might get introduced when using --check=false, ultimately allowing VO to get loaded.
The documentation for
robot convertsays:This PR enables passing this check flag through functions in
bioontologiesthat wrap therobot convertcommand.Unfortunately, this doesn't solve the issue with VO - it appears that ROBOT creates some metadata elements that are unexpectedly none. Additionally, this PR implements some processing for raw graph documents before loading int Pydantic to remove invalid fields that might get introduced when using
--check=false, ultimately allowing VO to get loaded.