Problem with InvalidReferenceViolations on all axioms with deprecated subjects

[jamesaoverton]

With the 1.4.2 release we're seeing new InvalidReferenceViolation errors on all axioms on deprecated subjects. This includes the deprecated annotation itself:

ERROR org.obolibrary.robot.ReasonOperation - Reference violation: InvalidReferenceViolation [axiom=AnnotationAssertion(owl:deprecated <http:
  //purl.obolibrary.org/obo/OBI_0000898> "true"^^xsd:boolean), referencedObject=<http://purl.obolibrary.org/obo/OBI_0000898>, category=DEPRECATED]

I didn't notice when I checked the release because there's already way too much noise from InvalidReferenceViolations in the ontologies I care about (#259, #374). But now there are so many errors that DO's Travis is failing because the log file is too large.

I think the new behaviour comes from this line:

https://github.com/ontodev/robot/blame/master/robot-core/src/main/java/org/obolibrary/robot/checks/InvalidReferenceChecker.java#L91

which was introduced in #510. It goes away when I revert to axiom.getSignature().

@balhoff Is that line critical to the functionality of #510, or can we revert it?

[jamesaoverton]

Answering my own question: yes reverting that would break the functionality of #510.

Now I'm thinking of just suppressing the error logging for certain violations, around https://github.com/ontodev/robot/blob/master/robot-core/src/main/java/org/obolibrary/robot/ReasonOperation.java#L508

[balhoff]

Aargh, sorry about this!

[jamesaoverton]

Mitigated by #568, released in 1.4.3.