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OWL to OBO conversion error log #1091

Closed hkir-dev closed 1 year ago

hkir-dev commented 1 year ago

Fix for the issue on https://github.com/ontodev/robot/issues/1088

When processing OWL constructs outside the OBO spec, a nasty error is generated which pollutes the Log files. This error does not affect the conversion, it just logs an error and completes the conversion successfully.

Analysis: This error is introduced with this commit: https://github.com/owlcs/owlapi/commit/49eaf8d3e98052e4632b6407b336956c3107ee94

Fix is to use an injector to get a new manager to create the ontology. A manager provider would be a better solution but there are static methods and interface changes involved.

However, while injecting a new OWLOntologyManager, this injector was unable to initialize the OWLOntologyBuilder and log an error. But in the consecutive steps, ontology factories are manually set from the source manager, so execution continues successfully.

This fix introduces a dummy OWLOntologyBuilder to the injector. By this way the OWLOntologyManager is created without error and then the dummy builder is replaced with a proper one as before.

matentzn commented 1 year ago

Excellent @hkir-dev, lets see if @ignazio1977 agrees this is the right way to fix https://github.com/ontodev/robot/issues/1088.

@ignazio1977 don't make a new release yet after merging this, there is another major bug we do not have a a strategy for yet: https://github.com/ontodev/robot/issues/1089