Review signatures, add exceptions as required

[jamesaoverton]

See #344. We want to maintain backwards compatibility as much as possible, but there are some mistakes that we should fix. It would be better to do this all at once for the 1.2.0 release (which will already break backwards compatibility in QueryOperation because of Jena updates #314).

[beckyjackson]

I was looking at DiffOperation.java and it looks like the original implementation was supposed to include labels and short forms of IRIs (the addLabels method), but it doesn't execute properly.

Updating it changes the output of diff to look something like this:

+ AnnotationAssertion(<obo:IAO_0000117>[term editor] <obo:OBI_0000921>[labeled RNA extract] "Group: OBI group"^^xsd:string)
+ AnnotationAssertion(<obo:IAO_0000117>[term editor] <obo:OBI_0000924>[labeled specimen] "OBI group"^^xsd:string)
+ AnnotationAssertion(<obo:IAO_0000117>[term editor] <obo:OBI_0000925>[infectious agent] "IEDB"@en)
+ AnnotationAssertion(<obo:IAO_0000117>[term editor] <obo:OBI_0000930>[calorimeter] "PERSON:Bjoern Peters"^^xsd:string)

As opposed to the original:

+ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OBI_0000921> "Group: OBI group"^^xsd:string)
+ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OBI_0000924> "OBI group"^^xsd:string)
+ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OBI_0000925> "IEDB"@en)
+ AnnotationAssertion(<http://purl.obolibrary.org/obo/IAO_0000117> <http://purl.obolibrary.org/obo/OBI_0000930> "PERSON:Bjoern Peters"^^xsd:string)

Is this something that should be fixed? I can always do it in a separate issue tracker/PR, but it does add exceptions to some of the methods in DiffOperation.java.

[jamesaoverton]

I changed the default to not look up labels, because of performance problems: #47

I'd rather fix the docs than change this (non-label default) behaviour.

[beckyjackson]

That makes sense. The compare method still loads all the labels from both ontologies, though. We could speed up the diff time by removing this if we aren't using labels anyway:

Map<IRI, String> labels = OntologyHelper.getLabels(ontology1);
labels.putAll(OntologyHelper.getLabels(ontology2));

[beckyjackson]

Closed by #351