Properly handle nonexistent input relations; add documentation on default relations (#157)

* Don’t fail when processing a requested but undeclared property.

* Add documentation about default properties.

* Add test file to git.

Author: balhoff

cli/src/main/scala/org/renci/relationgraph/Config.scala

@@ -18,10 +18,10 @@ final case class Config(
                          @HelpMessage("Configure style of triples to be output. RDF mode is the default; each existential relation is collapsed to a single direct triple.")
                          @ValueDescription("RDF|OWL")
                          mode: OutputMode = RDFMode,
-                         @HelpMessage("Property to restrict output relations to. Provide option multiple times for multiple properties.")
+                         @HelpMessage("Property to restrict output relations to. Provide option multiple times for multiple properties. If no properties are provided (via CLI or file), then all properties found in the ontology will be used.")
                          @ValueDescription("IRI")
                          property: List[String] = Nil,
-                         @HelpMessage("File containing line-separated property IRIs to restrict output relations to.")
+                         @HelpMessage("File containing line-separated property IRIs to restrict output relations to. If no properties are provided (via CLI or file), then all properties found in the ontology will be used.")
                          @ValueDescription("filename")
                          propertiesFile: Option[String],
                          @HelpMessage("Include entailed rdfs:subClassOf or owl:equivalentClass relations in output (default false)")

core/src/main/scala/org/renci/relationgraph/RelationGraph.scala

@@ -58,7 +58,7 @@ object RelationGraph extends StrictLogging {
     val indexedWhelk = IndexedReasonerState(whelk)
     logger.info("Done running reasoner")
     val classes = classHierarchy(indexedWhelk.state)
-    val properties = propertyHierarchy(ontology)
+    val properties = propertyHierarchy(ontology, specifiedProperties)
     val allProperties = properties.subclasses.keySet.map(c => Role(c.id))
     val ontologyDeclarationStream = ZStream.succeed(ZIO.succeed(TriplesGroup(Set(Triple.create(NodeFactory.createBlankNode("redundant"), RDFType, OWLOntology)))))
       .when(outputConfig.mode == OWLMode)
@@ -181,7 +181,7 @@ object RelationGraph extends StrictLogging {
     Hierarchy(equivMap, subclassTaxonomy)
   }
 
-  def propertyHierarchy(ont: OWLOntology): Hierarchy = {
+  def propertyHierarchy(ont: OWLOntology, requestedProperties: Set[AtomicConcept]): Hierarchy = {
     val subPropAxioms = ont.getAxioms(AxiomType.SUB_OBJECT_PROPERTY).asScala.to(Set).collect {
       case ax if ax.getSubProperty.isNamed && ax.getSuperProperty.isNamed && !ax.getSuperProperty.isOWLTopObjectProperty => ConceptInclusion(
         AtomicConcept(ax.getSubProperty.asOWLObjectProperty.getIRI.toString),
@@ -191,7 +191,10 @@ object RelationGraph extends StrictLogging {
       .filterNot(_.isOWLTopObjectProperty)
       .map(prop =>
         ConceptInclusion(AtomicConcept(prop.getIRI.toString), AtomicConcept(prop.getIRI.toString)))
-    val allAxioms = (subPropAxioms ++ allProps).toSet[Axiom]
+    val requestedProps = requestedProperties
+      .filterNot(_ == BuiltIn.Top)
+      .map(prop => ConceptInclusion(prop, prop))
+    val allAxioms = (subPropAxioms ++ allProps ++ requestedProps).toSet[Axiom]
     val whelk = Reasoner.assert(allAxioms)
     classHierarchy(whelk)
   }