errors when seeding with ECO

[srobb1]

Hello,

I am using the most up-to-date version of ODK (pulled today).

When I try to seed a new repository with ECO I get an error. If I leave off the ECO it runs fine.

I suspect that there are specific issues with ECO that are are not playing well with ODK. Maybe not passing some of the rules. Should I post in ECO repo as well? As a temporary solution Is there another way to include terms from ECO without seeding with it?

Command:

./seed-via-docker.sh  -d ro pato eco -u srobb1 -t "Apple Snail Expression Pattern Ontology" ase

Error:

2018-09-27 19:01:43,945 ERROR org.obolibrary.obo2owl.OWLAPIObo2Owl - error executing obo id to IRI
com.google.common.util.concurrent.UncheckedExecutionException: java.lang.NullPointerException
	at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2203)
	at com.google.common.cache.LocalCache.get(LocalCache.java:3937)
	at com.google.common.cache.LocalCache.getOrLoad(LocalCache.java:3941)
	at com.google.common.cache.LocalCache$LocalLoadingCache.get(LocalCache.java:4824)
	at org.obolibrary.obo2owl.OWLAPIObo2Owl.oboIdToIRI(OWLAPIObo2Owl.java:1664)
	at org.obolibrary.oboformat.writer.OBOFormatWriter$OWLOntologyNameProvider.getName(OBOFormatWriter.java:1182)
	at org.semanticweb.owlapi.oboformat.OBOFormatRenderer$1.getName(OBOFormatRenderer.java:74)
	at org.obolibrary.oboformat.writer.OBOFormatWriter.write(OBOFormatWriter.java:325)
	at org.obolibrary.oboformat.writer.OBOFormatWriter.write(OBOFormatWriter.java:203)
	at org.semanticweb.owlapi.oboformat.OBOFormatRenderer.render(OBOFormatRenderer.java:88)
	at org.semanticweb.owlapi.oboformat.OBOFormatStorer.storeOntology(OBOFormatStorer.java:42)
	at org.semanticweb.owlapi.util.AbstractOWLStorer.store(AbstractOWLStorer.java:99)
	at org.semanticweb.owlapi.util.AbstractOWLStorer.storeOntology(AbstractOWLStorer.java:64)
	at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1302)
	at org.obolibrary.robot.IOHelper.saveOntology(IOHelper.java:559)
	at org.obolibrary.robot.IOHelper.saveOntology(IOHelper.java:500)
	at org.obolibrary.robot.ConvertCommand.execute(ConvertCommand.java:167)
	at org.obolibrary.robot.CommandManager.executeCommand(CommandManager.java:246)
	at org.obolibrary.robot.CommandManager.execute(CommandManager.java:190)
	at org.obolibrary.robot.CommandManager.main(CommandManager.java:139)
	at org.obolibrary.robot.CommandLineInterface.main(CommandLineInterface.java:53)
Caused by: java.lang.NullPointerException
	at org.obolibrary.obo2owl.OWLAPIObo2Owl.translateShorthandIdToExpandedId(OWLAPIObo2Owl.java:1766)
	at org.obolibrary.obo2owl.OWLAPIObo2Owl.oboIdToIRI_load(OWLAPIObo2Owl.java:1705)
	at org.obolibrary.obo2owl.OWLAPIObo2Owl$1.load(OWLAPIObo2Owl.java:81)
	at org.obolibrary.obo2owl.OWLAPIObo2Owl$1.load(OWLAPIObo2Owl.java:77)
	at com.google.common.cache.LocalCache$LoadingValueReference.loadFuture(LocalCache.java:3527)
	at com.google.common.cache.LocalCache$Segment.loadSync(LocalCache.java:2319)
	at com.google.common.cache.LocalCache$Segment.lockedGetOrLoad(LocalCache.java:2282)
	at com.google.common.cache.LocalCache$Segment.get(LocalCache.java:2197)
	... 20 more
Use the -vvv option to show the stack trace.
Use the --help option to see usage information.
Makefile:51: recipe for target 'ase.obo' failed
make: *** [ase.obo] Error 1
rm imports/pato_terms_combined.txt imports/eco_terms_combined.txt imports/ro_terms_combined.txt
ERROR RUNNING: cd src/ontology && make prepare_release
Exiting. Run with '-f' to force execution and ignore errors at ./seed-my-ontology-repo.pl line 330.

Thanks,
Sofia

[beckyjackson]

Hi @srobb1 - this is an issue converting the full eco.owl file to OBO. The converter enforces pretty strict rules for the OBO format and the OWL format violates some of these. We offer an eco-basic.owl file to get around this.

Trying this with -d eco/eco-basic causes an issue because it puts the import file in another folder within the imports folder, when the ODK just expects all the imports to be individual files in that folder. @cmungall - do you think the ODK could support dependencies like this?

[cmungall]

We want everything to starting using the base files for making import modules, where available (#50), e.g.
http://purl.obolibrary.org/obo/eco/eco-base.owl
(should be registered on http://obofoundry.org/ontology/eco.html ...)

Note that this violates the obo format comment cardinality restriction; rather than making the combination of base x basic we should just make odk use the --no-check true option when writing obo

[srobb1]

Thanks! -d eco/eco-basic worked!!

[matentzn]

-> I also added --check false now; so it should work either way (base or otherwise).
#96

Will close this, please re-open if it happens again :)