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phyloref / jphyloref

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Phyloreference status support #9

Closed gaurav closed 6 years ago

gaurav commented 6 years ago

Add support for phyloreference statuses expressed using the Publication Status Ontology (as per phyloref/curation-tool#25), which marks failing phyloreferences whose status is not "pso:submitted" or "pso:published" to be marked as TODO rather than as test failures. In order to test this easily, I added a command-line option (--no-reasoner) which allows the tests to be run without running the reasoner.

gaurav commented 6 years ago

Thanks for the comments, @hlapp! I've made all the changes you suggested. I've made one more minor change since your review: I realized that --no-reasoner mode could be used to test whether phyloreferences in pre-reasoned OWL files resolved correctly, so I modified jphyloref to do just that (9e86f99). I've confirmed it works on an OWL file obtained by reasoning over extracting class assertions, property assertions, annotations and asserted logical axioms from Protege. Let me know if you have any comments on that commit; otherwise, I'll merge them once we're done with #6!

hlapp commented 6 years ago

Looks good to me.