Fixing ROBOT-reported issues

The odk:fix-robot-report command is intended to automatically fix some of the issues reported by ROBOT’s report command.

Given an input ontology and a report file (as generated by said report command), the command will attempt to fix all the issues that are trivial enough not to require the manual intervention of the ontology maintainer/editor.

Use

Use as follows:

robot odk:fix-robot-report --input myont.owl \
                           --robot-report report.tsv \
                           --output myont-fixed.owl

where report.tsv is the file produced by ROBOT’s report command.

Note that, for the command to work properly, the report must refer to entities by their ID rather than by their label, meaning the --labels true option of the report command MUST NOT be used.

Supported issues

Currently, the command will fix the following issues:

missing_obsolete_label,
lowercase_definition.

Fixing dubious issues

By default, the command only fixes an error if it is positive that (1) it is really an error and (2) the possible fix is the correct fix.

To also try to fix errors about which there is an uncertainty, use the --fix-dubious true option.