owlcollab / owlcollab/owltools
NullPointerException in OboBasicDagCheck
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- Java
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Description
2015-09-24 08:28:53,033 INFO (OboOntologyReleaseRunner:21) Start - Verifying DAG requirement for OBO Basic.
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
cannot handle:ObjectHasSelf(<http://purl.obolibrary.org/obo/RO_0002465>)
2015-09-24 08:28:53,475 ERROR (OboOntologyReleaseRunner:37) Stopped Release process. Reason: null
java.lang.NullPointerException
at owltools.util.MappingTarjan.notEquals(MappingTarjan.java:55)
at owltools.util.AbstractTarjan.tarjan(AbstractTarjan.java:89)
at owltools.util.AbstractTarjan.tarjan(AbstractTarjan.java:77)
at owltools.util.AbstractTarjan.executeTarjan(AbstractTarjan.java:38)
at owltools.ontologyrelease.OboBasicDagCheck.findCycles(OboBasicDagCheck.java:43)
at owltools.ontologyrelease.OboOntologyReleaseRunner.handleSimpleOntology(OboOntologyReleaseRunner.java:1280)
at owltools.ontologyrelease.OboOntologyReleaseRunner.createRelease(OboOntologyReleaseRunner.java:1058)
at owltools.ontologyrelease.OboOntologyReleaseRunner.createRelease(OboOntologyReleaseRunner.java:494)
at owltools.ontologyrelease.OboOntologyReleaseRunner.main(OboOntologyReleaseRunner.java:193)
2015-09-24 08:28:53,478 INFO (OboOntologyReleaseRunner:21) deleting lock file
To recreate:
ontology-release-runner --catalog-xml catalog-v001.xml --skip-format owx --run-obo-basic-dag-check --error-report envo-errors.txt $< --allow-overwrite --asserted --simple
on envo-edit.owl in https://github.com/EnvironmentOntology/envo/tree/master/src/envo
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Reproduce the failure with the supplied ontology-release-runner command on envo-edit.owl. Start at owltools/util/MappingTarjan.java:55 and follow the calls through AbstractTarjan.java and OboBasicDagCheck.java:43. Done means the OBO Basic DAG check no longer terminates with a NullPointerException on this input.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- tooling
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100