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protegeproject / protege-distribution

Build files for the protege distribution that includes 3rd party plugins
BSD 2-Clause "Simplified" License
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Saving an OBO file fails with #30

Open cbielow opened 2 years ago

cbielow commented 2 years ago 
java.lang.NullPointerException: null
    at org.obolibrary.obo2owl.OWLAPIObo2Owl.translateShorthandIdToExpandedId(OWLAPIObo2Owl.java:1739) ~[na:na]
    at org.obolibrary.obo2owl.OWLAPIObo2Owl.oboIdToIRI_load(OWLAPIObo2Owl.java:1679) ~[na:na]
    at org.obolibrary.obo2owl.OWLAPIObo2Owl.oboIdToIRI(OWLAPIObo2Owl.java:1643) ~[na:na]
    at org.obolibrary.oboformat.writer.OBOFormatWriter$OWLOntologyNameProvider.getName(OBOFormatWriter.java:992) ~[na:na]
    at org.semanticweb.owlapi.oboformat.OBOFormatRenderer$1.getName(OBOFormatRenderer.java:74) ~[na:na]
    at org.obolibrary.oboformat.writer.OBOFormatWriter.write(OBOFormatWriter.java:622) ~[na:na]
    at org.obolibrary.oboformat.writer.OBOFormatWriter.write(OBOFormatWriter.java:351) ~[na:na]
    at org.obolibrary.oboformat.writer.OBOFormatWriter.write(OBOFormatWriter.java:197) ~[na:na]
    at org.semanticweb.owlapi.oboformat.OBOFormatRenderer.render(OBOFormatRenderer.java:88) ~[na:na]
    at org.semanticweb.owlapi.oboformat.OBOFormatStorer.storeOntology(OBOFormatStorer.java:42) ~[na:na]
    at org.semanticweb.owlapi.util.AbstractOWLStorer.store(AbstractOWLStorer.java:99) ~[na:na]
    at org.semanticweb.owlapi.util.AbstractOWLStorer.storeOntology(AbstractOWLStorer.java:64) ~[na:na]
    at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1486) ~[na:na]
    at uk.ac.manchester.cs.owl.owlapi.OWLImmutableOntologyImpl.saveOntology(OWLImmutableOntologyImpl.java:1459) ~[na:na]
    at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.lambda$saveOntology$12(ConcurrentOWLOntologyImpl.java:369) ~[na:na]
    at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.callReadLock(ConcurrentOWLOntologyImpl.java:196) ~[na:na]
    at uk.ac.manchester.cs.owl.owlapi.concurrent.ConcurrentOWLOntologyImpl.saveOntology(ConcurrentOWLOntologyImpl.java:369) ~[na:na]
    at org.protege.editor.owl.model.io.OntologySaver.saveOntologyInternal(OntologySaver.java:96) ~[na:na]
    at org.protege.editor.owl.model.io.OntologySaver.lambda$saveOntologies$0(OntologySaver.java:52) ~[na:na]
    at java.util.concurrent.FutureTask.run(FutureTask.java:266) ~[na:1.8.0_121]
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) ~[na:1.8.0_121]
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) ~[na:1.8.0_121]
    at java.lang.Thread.run(Thread.java:745) ~[na:1.8.0_121]

using Protege 5.5. Loading http://purl.obolibrary.org/obo/ms.owl (attached here as ms.zip) and trying to save in OBO format.