Obo2Owl can throw a NullPointerException

Copied from  https://github.com/owlcs/owlapi/issues/63

In the class Obo2Owl,  the method 

tr(OWLOntology in) throws OWLOntologyCreationException

throws a NPE at line 324.  It assumes that the ontology has an IRI (i.e. it is 
not anonymous), but this isn't always the case at this point,

if (in != null && in.getOntologyID().getOntologyIRI().equals(ontIRI)) {
     owlOntology = in;
} else {
     owlOntology = manager.createOntology(ontIRI);
}

I'm loading using the following

OWLOntologyManager rootOntologyManager = ...
InputStream inputStream = new BufferedInputStream(new 
FileInputStream(uploadedFile));
StreamDocumentSource streamDocumentSource = new 
StreamDocumentSource(inputStream);
OWLOntologyLoaderConfiguration loaderConfig = new 
OWLOntologyLoaderConfiguration().setMissingImportHandlingStrategy(MissingImportH
andlingStrategy.SILENT);
OWLOntology ontology = 
rootOntologyManager.loadOntologyFromOntologyDocument(streamDocumentSource, 
loaderConfig);
inputStream.close();

The following ontology is enough to cause the problem

format-version: 1.2
date: 27:06:2013 17:08
saved-by: gkoutos
auto-generated-by: OBO-Edit 2.3
subsetdef: abnormal_slim "Abnormal/normal slim"
subsetdef: absent_slim "Absent/present slim"
subsetdef: attribute_slim "Attribute slim"
subsetdef: cell_quality "cell_quality"
subsetdef: disposition_slim "Disposition slim"
subsetdef: mpath_slim "Pathology slim"
subsetdef: prefix_slim "prefix slim"
subsetdef: relational_slim "Relational slim: types of quality that require an 
additional entity in order to exist"
subsetdef: scalar_slim "Scalar slim"
subsetdef: unit_group_slim "unit group slim"
subsetdef: unit_slim "unit slim"
subsetdef: value_slim "Value slim"
default-namespace: quality
namespace-id-rule: * UO:$sequence(7,0,9999999)$
remark: Filtered by Ancestor ID equals "UO:0000000"
ontology: uo
ontology: pato
ontology: pato
ontology: pato

[Term]
id: UO:0000000
name: unit
namespace: unit.ontology
def: "A unit of measurement is a standardized quantity of a physical quality." 
[Wikipedia:Wikipedia]
created_by: george gkoutos

[Term]
id: UO:0000001
name: length unit
namespace: unit.ontology
def: "A unit which is a standard measure of the distance between two points." 
[Wikipedia:Wikipedia]
subset: unit_group_slim
is_a: UO:0000000 ! unit
relationship: is_unit_of PATO:0001708 ! 1-D extent
created_by: george gkoutos
Original issue reported on code.google.com by matthew....@googlemail.com on 26 Nov 2013 at 11:12
owlcollab / oboformat

Obo2Owl can throw a NullPointerException #86
