OWL API binding for JPL's Ontological Modeling Framework (OMF)

Home Page: https://jpl-imce.github.io/gov.nasa.jpl.omf.scala.binding.owlapi/

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gov.nasa.jpl.omf.scala.binding.owlapi's Issues

Add missing rules for creating DescriptionBox representations in OWL

Incorrect parsing & serialization of unreified object properties characteristics

Some ReifiedRelationship specializations are lost

The cause is a typo in using the wrong variable for all available reified relationships.

Alignment with OMF/Schema

Support for named OMF ChainRules

See JPL-IMCE/gov.nasa.jpl.omf.scala.core#18

Re-enable unit tests when the ontologies.public has been properly updated

Due to the development of the OML Conversions among different representations, the unit tests currently fail because the ontologies.public have not yet been updated as a result of running the OML conversions successfully in a roundtrip fashion.

Update for OML Conversions

See JPL-IMCE/gov.nasa.jpl.omf.scala.core#9

Incorrect UUID derivation for rule body segment

Check OWL ontology manager before loading an ontology document

When loading an ontology document (e.g., via a file), the OWL OntologyManager may throw OWLOntologyAlreadyExistsException. This behavior should be avoided; that is, check whether there exists an ontology for a given ontology document before trying to load that document. This way, normal processing should not trigger any OWLOntologyAlreadyExistsException errors.

Cleanup and repair unit tests

Remove the 'NoMetadata' vs. 'WithMetadata' distinction since there is no longer any OMF metadata
Re-enable unit tests since JPL-IMCE/gov.nasa.jpl.imce.ontologies.public#31 is fixed

Import OWL implicitly, not explicitly.

With the OWLAPI v5.0.5 and Protege 5.2.0, this causes some bizarre parsing problems
(see: JPL-IMCE/gov.nasa.jpl.imce.ontologies.public#15)

Incomplete OWL representation of OML DescriptionBox

Missing OWL OntologyImports for OML ModuleEdges involving an OML DescriptionBox.

MutableDescriptionBox needs to create OWL DataPropertyAssertionAxioms with typed literals

This is the root cause of this issue:
JPL-IMCE/gov.nasa.jpl.imce.oml.converters#10

POM is missing dependencies on *.zip artifacts

Somehow, in the move from sbt 0.13.13 => 0.13.15 and sbt coursier resulted in loosing the *.zip dependencies in the published POM.

BUG: MutableTerminologyBox allows creating multiple rules with the same name

Tolerate duplicate SWRL rules for the reified relationship pattern.

See JPL-IMCE/gov.nasa.jpl.imce.ontologies.public#35

Implement chain rule lookup for rule body segment

Parse OWL2 DataOneOf => OML ScalarOneOfLiteralAxioms

OWL2 DataOneOf is parsed; however, the constructed OML ScalarOneOfLiteralAxioms needs to be added to the signature.

Some OWL Axioms are lost

There is a subtle problem with the interaction between Scala & Java8 Streams used in the OWLAPI.

def resolveConceptSubClassAxioms
  (conceptCMs: Map[OWLClass, Concept],
   allConceptsIncludingImported: Map[OWLClass, Concept])
  (implicit reasoner: OWLReasoner, backbone: OMFBackbone)
  : Set[java.lang.Throwable] \/ Unit
  = {

    val sub_sup = for {
      (subC, subM) <- conceptCMs
      supC <- reasoner.getSuperClasses(subC, true).entities().toScala[Set]
      supM <- findEntityConcept(supC.getIRI, allConceptsIncludingImported)
    } yield (subM, supM)

    ( ().right[Set[java.lang.Throwable]] /: sub_sup ) { ... }
}

The problem is in this line: supC <- reasoner.getSuperClasses(subC, true).entities().toScala[Set]

reasoner.getSuperClasses(subC, true) produces an OWLAPI NodeSet
reasoner.getSuperClasses(subC, true).entities() produces a Java8 Stream of OWLAPI Entities.
reasoner.getSuperClasses(subC, true).entities().toScala[Set] converts that Java8 Stream to a Scala Set collection.
supC <- reasoner.getSuperClasses(subC, true).entities().toScala[Set] should iterate over all elements in the converted Scala Set collection.

Unfortunately, only the first element of the stream is iterated over.

The following iterates properly over all elements in the stream:

val sub_sup = for {
      (subC, subM) <- conceptCMs
      supE = reasoner.getSuperClasses(subC, true).entities()
      supS = supE.toScala[Set]
      supC <- supS
      supM <- findEntityConcept(supC.getIRI, allConceptsIncludingImported)
    } yield (subM, supM)

Inconsistencies in UUID generation for UnreifiedRelationshipPropertyPredicate

OWL representation of SWRL rules is incorrect.

OML => OWL results in incorrect representation of reified relationships.

	reifiedRelationship Supplies {
		inverseFunctional
		asymmetric
		irreflexive
		unreified = supplies
		inverse = isSuppliedBy
		source = Authority
		target = SuppliedElement }

produced:


    <rdf:Description>
        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#Imp"/>
        <swrl:body>
            <rdf:Description>
                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                <rdf:first>
                    <rdf:Description>
                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
                        <swrl:propertyPredicate rdf:resource="http://imce.jpl.nasa.gov/foundation/project/project#hasSuppliesSource"/>
                        <swrl:argument1 rdf:resource="urn:swrl#r"/>
                        <swrl:argument2 rdf:resource="urn:swrl#s"/>
                    </rdf:Description>
                </rdf:first>
                <rdf:rest>
                    <rdf:Description>
                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                        <rdf:first>
                            <rdf:Description>
                                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
                                <swrl:propertyPredicate rdf:resource="http://imce.jpl.nasa.gov/foundation/project/project#hasSuppliesTarget"/>
                                <swrl:argument1 rdf:resource="urn:swrl#r"/>
                                <swrl:argument2 rdf:resource="urn:swrl#t"/>
                            </rdf:Description>
                        </rdf:first>
                        <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
                    </rdf:Description>
                </rdf:rest>
            </rdf:Description>
        </swrl:body>
        <swrl:head>
            <rdf:Description>
                <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#AtomList"/>
                <rdf:first>
                    <rdf:Description>
                        <rdf:type rdf:resource="http://www.w3.org/2003/11/swrl#IndividualPropertyAtom"/>
                        <swrl:propertyPredicate rdf:resource="http://imce.jpl.nasa.gov/foundation/project/project#Supplies"/>
                        <swrl:argument1 rdf:resource="urn:swrl#s"/>
                        <swrl:argument2 rdf:resource="urn:swrl#t"/>
                    </rdf:Description>
                </rdf:first>
                <rdf:rest rdf:resource="http://www.w3.org/1999/02/22-rdf-syntax-ns#nil"/>
            </rdf:Description>
        </swrl:head>
    </rdf:Description>

The swrl:head should refer to project#supplies instead of project#Supplies

MutableModule is missing addAnnotation and addAnnotationProperty methods.

Add support for EntityStructuredDataPropertyParticularRestrictionAxiom

See JPL-IMCE/gov.nasa.jpl.omf.scala.core#13

Align built-in OML annotation property IRI: oml#isOMLTerminologyBoxOpen

Currently, the built-in IRI for this annotation property is oml#isTerminologyBoxOpen

Handle dc:description for OML ReifiedRelationship

In OWL:

dc:description annotates the object property of an OML ReifiedRelationship.

In OML:

dc:description annotates the OML ReifiedRelationship itself

Missing entityStructuredDataPropertyParticularRestrictionAxioms in foldAxiom

See JPL-IMCE/gov.nasa.jpl.omf.scala.core#19

Basic conversion of OML ChainRules to/from OWL

Remove the verbose output: `# Searching for OML catalog in: ...`

This is a problem in OML.Tycho:
JPL-IMCE/gov.nasa.jpl.imce.oml#63

For Closed TerminologyBoxes, map particular restrictions to OWL2-DL key axioms

Map DataRelationshipFromEntity with isIdentityCriteria to functional properties in OWL

Add OML provenance for every OWL2 logical axiom

Provenance = UUID of the corresponding OML element

When parsing SWRL rules, need to reorder the body atoms for OML

In SWRL, a rule may be written like this:

behavior:InteractionBehaviorRegion(?R) ^ 
behavior:InteractionBehaviorAutomaton(?A) ^ 
behavior:hasRegion(?A, ?R) ^
behavior:Interaction(?I) ^ 
behavior:hasInteractionBehaviorClass(?I, ?A) -> 
behavior:hasInteractionBehavior(?I, ?R)

In OML, the corresponding OML ChainRule must be written with the body atoms ordered like this:

behavior:Interaction(?I) ^ 
behavior:hasInteractionBehaviorClass(?I, ?A) ^ 
behavior:InteractionBehaviorAutomaton(?A) ^ 
behavior:hasRegion(?A, ?R) ^ 
behavior:InteractionBehaviorRegion(?R) -> 
behavior:hasInteractionBehavior(?I, ?R)

Improve handling of annotation properties

The OWL API does not reliably produce abbreviated IRIs; especially for dc, rdf and rdfs.
For other ontologies, if the OWLAPI doesn't provide a proper abbreviated IRI, construct one from the last segment of the IRI and of the IRI fragment.

Improve catalog resolution logic for IRIs ending in '/'

When mapping an IRI to an OWL file, strip the trailing '/' before adding '.oml'.

Handle circular imports among ontologies.

Conversions from OWL => OML are currently not possible if the OWL ontologies have circular imports. This happens for RDF & RDFS that import each other but could also happen for other ontologies since circular references are allowed in OML.

ScalarOneOfLiteralAxiom should extend TermAxiom, not Axiom

Use the updated graph-core library instead of the unpublished graph-misc

Replace the dependency on the graph-misc API (see scala-graph/scala-graph#74 (comment)) with equivalent functionality with the updated graph-core (see http://www.scala-graph.org/download/#1.12.0)

Speed up processing large models with hashCode & equals

Exploit the immutable character of many OMF/OWLAPI objects to speed up hashCode operations:

	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ModelScalarDataType.hashCode(ModelScalarDataType.scala:26)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ScalarDataTypeFacetRestrictionAxiom.hashCode(ScalarDataTypeFacetRestrictionAxiom.scala:28)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3$$anonfun$orderedHash$1.apply(MurmurHash3.scala:110)
	at scala.util.hashing.MurmurHash3$$anonfun$orderedHash$1.apply(MurmurHash3.scala:109)
	at scala.collection.Iterator$class.foreach(Iterator.scala:893)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
	at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
	at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
	at scala.util.hashing.MurmurHash3.orderedHash(MurmurHash3.scala:109)
	at scala.util.hashing.MurmurHash3$.seqHash(MurmurHash3.scala:219)
	at scala.collection.IndexedSeqLike$class.hashCode(IndexedSeqLike.scala:44)
	at scala.collection.immutable.Vector.hashCode(Vector.scala:62)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ImmutableModelTerminologyGraph.hashCode(ImmutableModelTerminologyGraph.scala:63)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.TerminologyGraphDirectExtensionAxiom.hashCode(TerminologyGraphDirectExtensionAxiom.scala:25)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3$$anonfun$orderedHash$1.apply(MurmurHash3.scala:110)
	at scala.util.hashing.MurmurHash3$$anonfun$orderedHash$1.apply(MurmurHash3.scala:109)
	at scala.collection.Iterator$class.foreach(Iterator.scala:893)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
	at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
	at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
	at scala.util.hashing.MurmurHash3.orderedHash(MurmurHash3.scala:109)
	at scala.util.hashing.MurmurHash3$.seqHash(MurmurHash3.scala:219)
	at scala.collection.IndexedSeqLike$class.hashCode(IndexedSeqLike.scala:44)
	at scala.collection.immutable.Vector.hashCode(Vector.scala:62)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ImmutableModelTerminologyGraph.hashCode(ImmutableModelTerminologyGraph.scala:63)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.TerminologyGraphDirectExtensionAxiom.hashCode(TerminologyGraphDirectExtensionAxiom.scala:25)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3$$anonfun$orderedHash$1.apply(MurmurHash3.scala:110)
	at scala.util.hashing.MurmurHash3$$anonfun$orderedHash$1.apply(MurmurHash3.scala:109)
	at scala.collection.Iterator$class.foreach(Iterator.scala:893)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
	at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
	at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
	at scala.util.hashing.MurmurHash3.orderedHash(MurmurHash3.scala:109)
	at scala.util.hashing.MurmurHash3$.seqHash(MurmurHash3.scala:219)
	at scala.collection.IndexedSeqLike$class.hashCode(IndexedSeqLike.scala:44)
	at scala.collection.immutable.Vector.hashCode(Vector.scala:62)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ImmutableModelTerminologyGraph.hashCode(ImmutableModelTerminologyGraph.scala:63)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.TerminologyGraphDirectExtensionAxiom.hashCode(TerminologyGraphDirectExtensionAxiom.scala:25)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3$$anonfun$orderedHash$1.apply(MurmurHash3.scala:110)
	at scala.util.hashing.MurmurHash3$$anonfun$orderedHash$1.apply(MurmurHash3.scala:109)
	at scala.collection.Iterator$class.foreach(Iterator.scala:893)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
	at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
	at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
	at scala.util.hashing.MurmurHash3.orderedHash(MurmurHash3.scala:109)
	at scala.util.hashing.MurmurHash3$.seqHash(MurmurHash3.scala:219)
	at scala.collection.IndexedSeqLike$class.hashCode(IndexedSeqLike.scala:44)
	at scala.collection.immutable.Vector.hashCode(Vector.scala:62)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ImmutableModelTerminologyGraph.hashCode(ImmutableModelTerminologyGraph.scala:63)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.TerminologyGraphDirectExtensionAxiom.hashCode(TerminologyGraphDirectExtensionAxiom.scala:25)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3$$anonfun$orderedHash$1.apply(MurmurHash3.scala:110)
	at scala.util.hashing.MurmurHash3$$anonfun$orderedHash$1.apply(MurmurHash3.scala:109)
	at scala.collection.Iterator$class.foreach(Iterator.scala:893)
	at scala.collection.AbstractIterator.foreach(Iterator.scala:1336)
	at scala.collection.IterableLike$class.foreach(IterableLike.scala:72)
	at scala.collection.AbstractIterable.foreach(Iterable.scala:54)
	at scala.util.hashing.MurmurHash3.orderedHash(MurmurHash3.scala:109)
	at scala.util.hashing.MurmurHash3$.seqHash(MurmurHash3.scala:219)
	at scala.collection.IndexedSeqLike$class.hashCode(IndexedSeqLike.scala:44)
	at scala.collection.immutable.Vector.hashCode(Vector.scala:62)
	at scala.runtime.ScalaRunTime$.hash(ScalaRunTime.scala:206)
	at scala.util.hashing.MurmurHash3.productHash(MurmurHash3.scala:64)
	at scala.util.hashing.MurmurHash3$.productHash(MurmurHash3.scala:211)
	at scala.runtime.ScalaRunTime$._hashCode(ScalaRunTime.scala:168)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ImmutableModelTerminologyGraph.hashCode(ImmutableModelTerminologyGraph.scala:63)
	at scala.collection.mutable.FlatHashTable$class.addEntry(FlatHashTable.scala:148)
	at scala.collection.mutable.HashSet.addEntry(HashSet.scala:40)
	at scala.collection.mutable.FlatHashTable$class.growTable(FlatHashTable.scala:225)
	at scala.collection.mutable.FlatHashTable$class.addEntry(FlatHashTable.scala:159)
	at scala.collection.mutable.HashSet.addEntry(HashSet.scala:40)
	at scala.collection.mutable.FlatHashTable$class.addElem(FlatHashTable.scala:139)
	at scala.collection.mutable.HashSet.addElem(HashSet.scala:40)
	at scala.collection.mutable.HashSet.$plus$eq(HashSet.scala:59)
	at scala.collection.mutable.HashSet.$plus$eq(HashSet.scala:40)
	at gov.nasa.jpl.omf.scala.core.OMFOps$$anonfun$closure$1.apply(OMFOps.scala:64)
	at scala.collection.immutable.HashSet$HashSet1.foreach(HashSet.scala:316)
	at scala.collection.immutable.HashSet$HashTrieSet.foreach(HashSet.scala:972)
	at gov.nasa.jpl.omf.scala.core.OMFOps$.closure(OMFOps.scala:63)
	at gov.nasa.jpl.omf.scala.core.package$.terminologyGraphImportClosure(package.scala:123)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ModelTerminologyGraph.isTypeTermDefinedRecursively(ModelTerminologyGraph.scala:93)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.MutableModelTerminologyGraph.addEntityConceptSubClassAxiom(MutableModelTerminologyGraph.scala:1345)
	at gov.nasa.jpl.omf.scala.binding.owlapi.OWLAPIMutableTerminologyGraphOps$class.addEntityConceptSubClassAxiom(OWLAPIOMFOps.scala:1011)
	at gov.nasa.jpl.omf.scala.binding.owlapi.OWLAPIOMFOps.addEntityConceptSubClassAxiom(OWLAPIOMFOps.scala:1257)
	at gov.nasa.jpl.omf.scala.binding.owlapi.OWLAPIOMFOps.addEntityConceptSubClassAxiom(OWLAPIOMFOps.scala:1257)
	at gov.nasa.jpl.omf.scala.core.MutableTerminologyGraphOps$$anonfun$addEntityConceptSubClassAxiom$2.apply(OMFOps.scala:1542)
	at gov.nasa.jpl.omf.scala.core.MutableTerminologyGraphOps$$anonfun$addEntityConceptSubClassAxiom$2.apply(OMFOps.scala:1538)
	at scalaz.$bslash$div.flatMap(Either.scala:135)
	at gov.nasa.jpl.omf.scala.core.MutableTerminologyGraphOps$class.addEntityConceptSubClassAxiom(OMFOps.scala:1538)
	at gov.nasa.jpl.omf.scala.binding.owlapi.OWLAPIOMFOps.addEntityConceptSubClassAxiom(OWLAPIOMFOps.scala:1257)

In this stack trace, there are 4 customizable hashCode methods that have been invoked:


	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ModelScalarDataType.hashCode(ModelScalarDataType.scala:26)
	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ScalarDataTypeFacetRestrictionAxiom.hashCode(ScalarDataTypeFacetRestrictionAxiom.scala:28)
4x	at gov.nasa.jpl.omf.scala.binding.owlapi.types.ImmutableModelTerminologyGraph.hashCode(ImmutableModelTerminologyGraph.scala:63)
4x	at gov.nasa.jpl.omf.scala.binding.owlapi.types.TerminologyGraphDirectExtensionAxiom.hashCode(TerminologyGraphDirectExtensionAxiom.scala:25)

All of these case classes represent immutable objects; which means that it is possible to exploit the optimization trick in Programming in Scala, 3rd Ed, chapter 30, Recipe for hashCode, which defines it as a val computed once at object creation instead of as def method.

Add missing rules for creating OWL representations of OML constructs

[info] - when load xsd *** FAILED ***
[info]   java.util.IllegalFormatConversionException: c != org.semanticweb.owlapi.model.IRI
[info]   at java.util.Formatter$FormatSpecifier.failConversion(Formatter.java:4302)
[info]   at java.util.Formatter$FormatSpecifier.printCharacter(Formatter.java:2869)
[info]   at java.util.Formatter$FormatSpecifier.print(Formatter.java:2757)
[info]   at java.util.Formatter.format(Formatter.java:2520)
[info]   at java.util.Formatter.format(Formatter.java:2455)
[info]   at java.lang.String.format(String.java:2927)
[info]   at scala.collection.immutable.StringLike$class.format(StringLike.scala:318)
[info]   at scalax.collection.connectivity.GraphComponents$$anonfun$scalax$collection$connectivity$GraphComponents$$visit$1$1.apply(GraphComponents.scala:120)

This is a workaround to this issue: scala-graph/scala-graph#75

Improve the OWLAPI parser to handle alternative SWRL formulations

JPL-IMCE/gov.nasa.jpl.imce.ontologies.public#37

For example either of the SWRL rules below should be acceptable:

fault-management:PerformanceConstraint(?P) ^ 
fault-management:ViolationExplanation(?V) ^ 
behavior:ElementBehavior(?B) ^ 
analysis:analyzes(?V, ?P) ^ 
analysis:explains(?V, ?B) -> 
fault-management:violates(?B, ?P)

behavior:ElementBehavior(?B) ^ 
analysis:isExplainedBy(?B, ?V)  ^ 
fault-management:ViolationExplanation(?V) ^ 
analysis:analyzes(?V, ?P) ^ 
fault-management:PerformanceConstraint(?P)-> 
fault-management:violates(?B, ?P)

Either one should result in OML in the following rule:

behavior:ElementBehavior ^ 
analysis:isExplainedBy  ^ 
fault-management:ViolationExplanation ^ 
analysis:analyzes ^ 
fault-management:PerformanceConstraint-> 
fault-management:violates

Update for OML Datatypes and AnnotationPropertyValues

See JPL-IMCE/gov.nasa.jpl.omf.scala.core#7

Update for OML Table annotationPropertyValues

See JPL-IMCE/gov.nasa.jpl.imce.oml.development.generators#4

Remove the OMF Metadata support

The OMF metadata ontology is obsolete, see: JPL-IMCE/gov.nasa.jpl.imce.ontologies.public#42

CatalogIRIMapper.saveResolutionStrategy needs to handle IRI ending in '/'

Support for built-in vocabulary (w3, purl)

For the OWL2API v5.1.2, several vocabularies are effectively "built-in":

purl.org/dc/elements/1.1
www.w3.org/...

These should not be parsed with the OWL2API explicitly.

Incomplete resolution of OWL subclass axioms involving a foreign specific class

When resolving an OWL ontology, specialization axioms are looked up w.r.t. classes defined in that ontology. Instead, the lookup should be extended to classes defined in the transitive import closure of that ontology.

Roundtrip conversions fail because of derived UUID construction differences

This fails because of discrepancies in derived UUID construction:

sbt run-main gov.nasa.jpl.omf.scala.binding.owlapi.converters.ConvertOWL2Tables \
-c \
file:`pwd`/target/extracted/gov.nasa.jpl.imce.ontologies.public/ontologies/imce.local.catalog.xml \
-i \
http://imce.jpl.nasa.gov/foundation/mission/mission \
-o \
file:`pwd`/target/test1/mission.json.zip

See: JPL-IMCE/gov.nasa.jpl.imce.oml.core#1

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