Add --strict flag

[beckyjackson]

Resolves #785

• docs/ have been added/updated
• tests have been added/updated
• mvn verify says all tests pass
• mvn site says all JavaDocs correct
• CHANGELOG.md has been updated

First pass at adding a --strict global flag that causes ROBOT to fail on unparsed triples. By default, unparsed triples will now be parsed as errors. I also added a hint about RDF reification if rdfs:Statement is found as an object.

The --strict flag also turns on strict parsing with OWLAPI, but I couldn't find any documentation about what that means. If anybody (@ontodev/robot-team) knows where I can find those details (or has a brief summary) that would be great!

Additionally, are there other examples of issues that cause unparsed triples? I'd like to make sure the documentation does a good job of explaining how to fix the issue.

[beckyjackson]

Error message for undeclared predicates:

UNPARSED TRIPLES ERROR input ontology contains 1 triple(s) that could not be parsed:
 - <urn:robot:reificationExample:Bb65616dcX2Dde2dX2D405aX2Da1aaX2Ddfbb25f03995> <urn:robot:reificationExample:propertyOne> :propertyOne.

Hint: you have undeclared predicates - try adding 'rdf:type' declarations to the following:
 - urn:robot:reificationExample:propertyOne

Error message for RDF reification:

UNPARSED TRIPLES ERROR input ontology contains 4 triple(s) that could not be parsed:
 - <urn:robot:reificationExample:Bb65616dcX2Dde2dX2D405aX2Da1aaX2Ddfbb25f03995> <http://www.w3.org/1999/02/22-rdf-syntax-ns#predicate> <urn:robot:reificationExample:indicatedBy>.
 - <urn:robot:reificationExample:Bb65616dcX2Dde2dX2D405aX2Da1aaX2Ddfbb25f03995> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.w3.org/1999/02/22-rdf-syntax-ns#Statement>.
 - <urn:robot:reificationExample:Bb65616dcX2Dde2dX2D405aX2Da1aaX2Ddfbb25f03995> <http://www.w3.org/1999/02/22-rdf-syntax-ns#object> <urn:robot:reificationExample:Bar>.
 - <urn:robot:reificationExample:Bb65616dcX2Dde2dX2D405aX2Da1aaX2Ddfbb25f03995> <http://www.w3.org/1999/02/22-rdf-syntax-ns#subject> <urn:robot:reificationExample:Foo>.

Hint: you may be using RDF reification - try replacing 'rdf:Statement' with 'owl:Axiom'

One other type of error is these gen IDs... These are in our unit tests:

_:genid2147484004 <http://www.w3.org/2002/07/owl#annotatedTarget> test 3 comment.
_:genid2147484004 <http://www.w3.org/2002/07/owl#annotatedSource> _:genid-nodeid-4.
_:genid2147484004 <http://www.w3.org/2002/07/owl#annotatedProperty> <http://www.w3.org/2000/01/rdf-schema#comment>.

These are for third-level nested annotation axioms:

... and the TTL looks like this:

[ rdf:type owl:Annotation ;
   owl:annotatedSource _:genid4 ;
   owl:annotatedProperty rdfs:comment ;
   owl:annotatedTarget "test 3 comment"@en ;
   rdfs:comment "test 3 comment comment"^^xsd:string
 ] .

Even though it says they're unparsed, running robot convert keeps these. I'm not totally sure what to do about these ones. The error is fixed if you change owl:Annotation to owl:Axiom but that's just how OWLAPI renders these. Honestly, I don't think anybody uses annotations this deep though... (hopefully)

[balhoff]

@beckyjackson:

Even though it says they're unparsed, running robot convert keeps these. I'm not totally sure what to do about these ones.

@ignazio1977 made this comment in owlcs/owlapi#988:

Main problem is that the leftover triples are not very reliable - often I see info messages of that sort that seem incorrect, so some investigation might be required first.

Maybe this is a good test case to resolve that! (third-level nested annotation axioms)

[ignazio1977]

Maybe this is a good test case to resolve that! (third-level nested annotation axioms)

Indeed. There are unit tests for those in OWLAPI, I remember seeing plenty of info messages when debugging them.

[jamesaoverton]

I looked through the docs and the code and I'm happy with it, but can we please have some sort of test? (Probably a unit test in this case.)

[jamesaoverton]

Looks great but please add some sort of unit test.

[jamesaoverton]

Thanks! Please merge when you're ready.