robot verify does not use the catalog-xml

[cmungall]

example:

~/repos/robot/robot-core/src/test/resources(master) $ robot verify -i import_test.owl --queries test.sparql -O reports/

where test.sparql is SELECT * WHERE { ?x ?r ?y }

fails with:

org.semanticweb.owlapi.model.UnloadableImportException: Could not load imported ontology: <https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl> Cause: https://github.com/ontodev/robot/robot-core/src/test/resources/simple.owl

This works as expected:

robot convert -i import_test.owl -o foo.obo

This is a bit of a blocker and additionally we have no way of passing in an alternate catalog:
#41

[jamesaoverton]

Use CommandLineHelper.getInputOntology, following some of the other commands I’ve written. This should use IOHelper which should use the catalog.

I can do it, but not until next week.

[jamesaoverton]

In #196 I changed VerifyCommand to work like other commands, including catalogs and chaining.

The bad news is that this didn't solve the problem, because QueryOperation only loads the ontology into the graph, not the imports closure. I'm not 100% certain what the right thing to do is.

The good news is that you can now merge then verify, so this should work:

robot merge -i import_test.owl verify --queries test.sparql -O reports/

Is merge-then-verify acceptable, or do we want to change QueryOperation?

[cmungall]

I think this is acceptable just now.

I would like the pre-merge state to be such that each imported ontology is in its own NG, but we can leave this as it's own separate ticket #158