translateShorthandIdToExpandedId in conversion to obo

[cmungall]

Example:

<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/phipo.owl#"
     xml:base="http://purl.obolibrary.org/obo/phipo.owl"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace">

    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/phipo.owl">
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/ro/core.owl"/>
    </owl:Ontology>
    

    <!-- http://purl.obolibrary.org/obo/PHIPO_0000304 -->

    <owl:ObjectProperty rdf:about="http://purl.obolibrary.org/obo/FOO_1">
      <oboInOwl:shorthand rdf:datatype="http://www.w3.org/2001/XMLSchema#string">foo</oboInOwl:shorthand>
    </owl:ObjectProperty>

</rdf:RDF>

Exception in thread "main" java.lang.NullPointerException
        at org.obolibrary.obo2owl.OWLAPIObo2Owl.translateShorthandIdToExpandedId(OWLAPIObo2Owl.java:1739)
        at org.obolibrary.obo2owl.OWLAPIObo2Owl.oboIdToIRI_load(OWLAPIObo2Owl.java:1679)
        at org.obolibrary.obo2owl.OWLAPIObo2Owl.oboIdToIRI(OWLAPIObo2Owl.java:1643)
        at org.obolibrary.oboformat.writer.OBOFormatWriter$OWLOntologyNameProvider.getName(OBOFormatWriter.java:992)
        at org.semanticweb.owlapi.oboformat.OBOFormatRenderer$1.getName(OBOFormatRenderer.java:74)
        at org.obolibrary.oboformat.writer.OBOFormatWriter.write(OBOFormatWriter.java:312)
        at org.obolibrary.oboformat.writer.OBOFormatWriter.write(OBOFormatWriter.java:200)
        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.storeOntology(AbstractOWLStorer.java:155)
        at org.semanticweb.owlapi.util.AbstractOWLStorer.storeOntology(AbstractOWLStorer.java:119)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1525)
        at uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl.saveOntology(OWLOntologyManagerImpl.java:1502)
        at owltools.io.ParserWrapper.saveOWL(ParserWrapper.java:289)
        at owltools.io.ParserWrapper.saveOWL(ParserWrapper.java:209)
        at owltools.cli.CommandRunner.runSingleIteration(CommandRunner.java:3712)
        at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:76)
        at owltools.cli.CommandRunnerBase.run(CommandRunnerBase.java:68)
        at owltools.cli.CommandLineInterface.main(CommandLineInterface.java:12)

Note that BOTH the import AND the shorthand need to be present.

At the least the reporting should be more informative as it's a pain to debug these

[cmungall]

Another test case:

<?xml version="1.0"?>
<rdf:RDF xmlns="http://purl.obolibrary.org/obo/phipo.owl#"
     xml:base="http://purl.obolibrary.org/obo/phipo.owl"
     xmlns:owl="http://www.w3.org/2002/07/owl#"
     xmlns:oboInOwl="http://www.geneontology.org/formats/oboInOwl#"
     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#"
     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
     xmlns:xml="http://www.w3.org/XML/1998/namespace">
    <owl:Ontology rdf:about="http://purl.obolibrary.org/obo/phipo.owl">
        <owl:imports rdf:resource="http://purl.obolibrary.org/obo/phipo/imports/ro_import.owl"/>
    </owl:Ontology>
    



    <!-- http://www.geneontology.org/formats/oboInOwl#Subset -->

    <rdf:Description rdf:about="http://www.geneontology.org/formats/oboInOwl#Subset">
        <rdfs:subClassOf rdf:resource="http://purl.obolibrary.org/obo/IAO_0000102"/>
    </rdf:Description>
    


</rdf:RDF>

[cthoyt]

Bump on this, I just had the same issue again I reported in ontodev/robot#1055