Should unparsed triples be a WARN instead of ERROR?

[beckyjackson]

trafficstars

Every time we load OBI now, we get the following error message:

2021-02-22 18:43:34,590 ERROR org.obolibrary.robot.IOHelper - Input ontology contains 42 triple(s) that could not be parsed:
 - <http://purl.obolibrary.org/obo/OBI_0000958> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494670.
 - <http://purl.obolibrary.org/obo/OBI_0000901> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494669.
 - <http://purl.obolibrary.org/obo/OBI_0000759> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494662.
 - <http://purl.obolibrary.org/obo/OBI_0001355> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494682.
 - <http://purl.obolibrary.org/obo/OBI_0000756> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494659.
 - <http://purl.obolibrary.org/obo/OBI_0000829> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494668.
 - <http://purl.obolibrary.org/obo/OBI_0002903> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494695.
 - <http://purl.obolibrary.org/obo/OBI_0001375> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494684.
 - <http://purl.obolibrary.org/obo/OBI_0001856> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494692.
 - <http://purl.obolibrary.org/obo/OBI_0000769> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494664.
 - <http://purl.obolibrary.org/obo/OBI_0001287> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494675.
 - <http://purl.obolibrary.org/obo/OBI_0000779> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494667.
 - <http://purl.obolibrary.org/obo/OBI_0001320> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494677.
 - <http://purl.obolibrary.org/obo/OBI_0001347> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494681.
 - <http://purl.obolibrary.org/obo/OBI_0000998> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494672.
 - <http://purl.obolibrary.org/obo/OBI_0001434> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494688.
 - <http://purl.obolibrary.org/obo/OBI_0001424> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494685.
 - <http://purl.obolibrary.org/obo/OBI_0000757> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494660.
 - <http://purl.obolibrary.org/obo/OBI_0001213> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494673.
 - <http://purl.obolibrary.org/obo/OBI_0000765> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494663.
 - <http://purl.obolibrary.org/obo/OBI_0001372> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494683.
 - <http://purl.obolibrary.org/obo/OBI_0000462> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494654.
 - <http://purl.obolibrary.org/obo/OBI_0000754> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494658.
 - <http://purl.obolibrary.org/obo/OBI_0001312> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494676.
 - <http://purl.obolibrary.org/obo/OBI_0001340> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494680.
 - <http://purl.obolibrary.org/obo/OBI_0000462> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494655.
 - <http://purl.obolibrary.org/obo/OBI_0000770> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494665.
 - <http://purl.obolibrary.org/obo/OBI_0000752> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494656.
 - <http://purl.obolibrary.org/obo/OBI_0001338> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494679.
 - <http://purl.obolibrary.org/obo/OBI_0001431> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494687.
 - <http://purl.obolibrary.org/obo/OBI_0001321> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494678.
 - <http://purl.obolibrary.org/obo/OBI_0002755> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494694.
 - <http://purl.obolibrary.org/obo/OBI_0000758> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494661.
 - <http://purl.obolibrary.org/obo/OBI_0001855> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494691.
 - <http://purl.obolibrary.org/obo/OBI_0000979> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494671.
 - <http://purl.obolibrary.org/obo/OBI_0001860> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494693.
 - <http://purl.obolibrary.org/obo/OBI_0001458> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494690.
 - <http://purl.obolibrary.org/obo/OBI_0001428> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494686.
 - <http://purl.obolibrary.org/obo/OBI_0001443> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494689.
 - <http://purl.obolibrary.org/obo/OBI_0001224> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494674.
 - <http://purl.obolibrary.org/obo/OBI_0000753> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494657.
 - <http://purl.obolibrary.org/obo/OBI_0000776> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147494666.

This may indicate we need to fix something in OBI (and we have an issue addressing this), but it's not currently breaking anything. Given that, should these unparsed triples be a WARN level log instead of ERROR?

I worry that there may be some unparsed triples that we actually do want to display as errors, though?

[jamesaoverton]

I want to fix this OBI issue before considering downgrading this logging level.

https://github.com/obi-ontology/obi/issues/1289

[jamesaoverton]

The OBI issue I wanted to fix has been fixed. What do people think about downgrading these unparsed triples to WARN?

[balhoff]

Ignazio made some fixes for over eager reporting of these: https://github.com/owlcs/owlapi/issues/1023 It seems like maybe if the output is more accurate, it might make sense to keep as an error.

[jamesaoverton]

Good point, but that raises a bigger question about updating OWLAPI. We've been trying to match Protege, which uses OWLAPI 4.5.9 in release 5.50. ROBOT is a bit behind, with OWLAPI 4.5.6. Both are far behind the current OWLAPI 4.5.20. Maybe we need to revisit that policy.

[balhoff]

Oh yes, that is an issue.

[matentzn]

Matthew Horridge indicated that he could run a new release when the right OWLAPI version is ready for all of us :)

[balhoff]

Matthew Horridge indicated that he could run a new release when the right OWLAPI version is ready for all of us :)

In that case maybe we should get in any updates to the OBO IO that may be needed!

[matentzn]

You mean the OBO format parser? Remind me what needs to be added, sorry :)

[balhoff]

You mean the OBO format parser? Remind me what needs to be added, sorry :)

I don't actually have something specific in mind; but if this will be a rare chance to update Protege I wanted to make sure we thought about it. :-) (sorry to be hijacking this issue)

[matentzn]

Oh.. bad timing for me (bandwidth) but I will raise it in my meeting with Chris next week

[wdduncan]

When I mvn clean package on the repo as of 2021-11-01, the following errors were reported:

Tests run: 16, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.3 sec
Running org.obolibrary.robot.UnmergeOperationTest
Tests run: 1, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 0.03 sec
Running org.obolibrary.robot.ReasonOperationTest
ERROR Input ontology contains 1 triple(s) that could not be parsed:
 - <http://purl.obolibrary.org/obo/IND_03> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147483979.

ERROR Input ontology contains 1 triple(s) that could not be parsed:
 - <http://purl.obolibrary.org/obo/IND_03> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147483985.

ERROR Input ontology contains 1 triple(s) that could not be parsed:
 - <http://purl.obolibrary.org/obo/IND_03> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147483991.

ERROR Input ontology contains 1 triple(s) that could not be parsed:
 - <http://purl.obolibrary.org/obo/IND_03> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> _:genid2147483997.

Tests run: 20, Failures: 0, Errors: 0, Skipped: 0, Time elapsed: 1.473 sec
Running org.obolibrary.robot.TemplateTest
ERROR Input ontology contains 3 triple(s) that could not be parsed:
 - _:genid2147484006 <http://www.w3.org/2002/07/owl#annotatedTarget> test 3 comment.
 - _:genid2147484006 <http://www.w3.org/2002/07/owl#annotatedProperty> <http://www.w3.org/2000/01/rdf-schema#comment>.
 - _:genid2147484006 <http://www.w3.org/2002/07/owl#annotatedSource> _:genid-nodeid-4.

ERROR Input ontology contains 3 triple(s) that could not be parsed:
 - _:genid2147484027 <http://www.w3.org/2002/07/owl#annotatedProperty> <http://www.w3.org/2000/01/rdf-schema#comment>.
 - _:genid2147484027 <http://www.w3.org/2002/07/owl#annotatedSource> _:genid-nodeid-4.
 - _:genid2147484027 <http://www.w3.org/2002/07/owl#annotatedTarget> test 3 comment.

Is this related to this?

[jamesaoverton]

@wdduncan Yes. These messages from the test suite are normal, but it would be nice not to see them.