update refinement of axioms

sansa-owl-spark/src/main/scala/net/sansa_stack/owl/spark/rdd/RefineOWLAxioms.scala

@@ -1,5 +1,173 @@
 package net.sansa_stack.owl.spark.rdd
 
-class RefineOWLAxioms {
+import org.apache.spark.broadcast.Broadcast
+import org.semanticweb.owlapi.apibinding.OWLManager
+import org.semanticweb.owlapi.model._
+import org.semanticweb.owlapi.util.OWLAPIStreamUtils.asList
 
+ object RefineOWLAxioms extends Serializable {
+
+  private def manager = OWLManager.createOWLOntologyManager()
+
+  private def dataFactory = manager.getOWLDataFactory
+
+  val parallelism = 240
+
+  def refineOWLAxiom (axiom: OWLAxiom,
+                       dataPropertiesBC: Broadcast[Array[IRI]],
+                       objPropertiesBC: Broadcast[Array[IRI]],
+                       annPropertiesBC: Broadcast[Array[IRI]]): OWLAxiom = {
+
+     val T = axiom.getAxiomType
+
+     val correctAxiom: OWLAxiom = T match {
+        case AxiomType.ANNOTATION_PROPERTY_DOMAIN =>
+          val correctPropertyDomainAxioms = fixWrongPropertyDomainAxioms(axiom, dataPropertiesBC, objPropertiesBC)
+          correctPropertyDomainAxioms
+
+        case AxiomType.SUB_ANNOTATION_PROPERTY_OF =>
+          val correctSubPropertyAxioms = fixWrongSubPropertyAxioms(axiom, dataPropertiesBC, objPropertiesBC)
+          correctSubPropertyAxioms
+
+        case AxiomType.ANNOTATION_ASSERTION =>
+          val correctAssertionAxioms = fixWrongPropertyAssertionAxioms(axiom,
+                                                                      dataPropertiesBC, objPropertiesBC, annPropertiesBC)
+          correctAssertionAxioms
+
+        case _ => axiom
+      }
+
+    correctAxiom
+  }
+
+  /**
+    * Handler for wrong domain axioms
+    * OWLDataPropertyDomain and OWLObjectPropertyDomain
+    * converted wrongly to OWLAnnotationPropertyDomain
+    */
+  private def fixWrongPropertyDomainAxioms( propertyDomainAxiom: OWLAxiom,
+                                            dataPropertiesBC: Broadcast[Array[IRI]],
+                                            objPropertiesBC: Broadcast[Array[IRI]]): OWLAxiom = {
+
+    val annPropDomAxiom = propertyDomainAxiom.asInstanceOf[OWLAnnotationPropertyDomainAxiom]
+    val prop = annPropDomAxiom.getProperty.getIRI
+    val domain = annPropDomAxiom.getDomain
+
+    // Annotation property domain axiom turned into object property domain after parsing.
+    if (objPropertiesBC.value.contains(prop)) {
+
+      // FIXME: Case of non-atomic class expressions not handled
+      val domainClass = dataFactory.getOWLClass(domain)
+      val objProp = dataFactory.getOWLObjectProperty(prop)
+      val propertyDomainAxiom =
+        dataFactory.getOWLObjectPropertyDomainAxiom(objProp, domainClass, asList(annPropDomAxiom.annotations))
+
+      propertyDomainAxiom.asInstanceOf[OWLAxiom]
+
+    } else if (dataPropertiesBC.value.contains(prop)) {
+
+      // Annotation property domain axiom turned into data property domain after parsing.
+      // FIXME: Case of non-atomic class expressions not handled
+      val domainClass = dataFactory.getOWLClass(domain)
+      val dataProp = dataFactory.getOWLDataProperty(prop.toString)
+      val propertyDomainAxiom =
+        dataFactory.getOWLDataPropertyDomainAxiom(dataProp, domainClass, asList(annPropDomAxiom.annotations))
+
+      propertyDomainAxiom.asInstanceOf[OWLAxiom]
+
+    } else {
+
+      annPropDomAxiom
+  }
 }
+
+  /**
+    * Handler for wrong subPropertyOf axioms
+    * OWLSubPropertyOf converted wrongly to OWLSubAnnotationPropertyOf
+    * instead of OWLSubDataPropertyOf or OWLSubObjectPropertyOf
+    */
+  private def fixWrongSubPropertyAxioms(SubAnnotationPropertyAxiom: OWLAxiom,
+                                        dataPropertiesBC: Broadcast[Array[IRI]],
+                                        objPropertiesBC: Broadcast[Array[IRI]]): OWLAxiom = {
+
+    val subAnnPropAxiom = SubAnnotationPropertyAxiom.asInstanceOf[OWLSubAnnotationPropertyOfAxiom]
+    val subProperty = subAnnPropAxiom.getSubProperty.getIRI
+    val supProperty = subAnnPropAxiom.getSuperProperty.getIRI
+
+    // SubAnnotationPropertyOf axiom turned into SubObjectPropertyOf after parsing.
+    if (objPropertiesBC.value.contains(subProperty)) {
+
+      val subObjProperty = dataFactory.getOWLObjectProperty(subProperty)
+      val superObjProperty = dataFactory.getOWLObjectProperty(supProperty)
+      val subObjPropertyAxiom =
+        dataFactory.getOWLSubObjectPropertyOfAxiom(subObjProperty, superObjProperty, asList(subAnnPropAxiom.annotations))
+
+      subObjPropertyAxiom.asInstanceOf[OWLAxiom]
+
+    } else if (dataPropertiesBC.value.contains(subProperty)) {
+
+      // SubAnnotationPropertyOf axiom turned to SubDataPropertyOf after parsing.
+      val subDataProperty = dataFactory.getOWLDataProperty(subProperty)
+      val superDataProperty = dataFactory.getOWLDataProperty(supProperty)
+      val subDataPropertyAxiom =
+        dataFactory.getOWLSubDataPropertyOfAxiom(subDataProperty, superDataProperty, asList(subAnnPropAxiom.annotations))
+
+      subDataPropertyAxiom.asInstanceOf[OWLAxiom]
+
+    } else {
+
+      subAnnPropAxiom
+    }
+  }
+
+  /**
+    * Handler for wrong Assertion axioms
+    * OWLDataPropertyAssertion and OWLObjectPropertyAssertion
+    * converted wrongly to OWLAnnotationPropertyAssertion
+    */
+
+  private def fixWrongPropertyAssertionAxioms (annotationAssertionAxiom: OWLAxiom,
+                                               dataPropertiesBC: Broadcast[Array[IRI]],
+                                               objPropertiesBC: Broadcast[Array[IRI]],
+                                               annPropertiesBC: Broadcast[Array[IRI]]): OWLAxiom = {
+
+    val annAssertionAxiom = annotationAssertionAxiom.asInstanceOf[OWLAnnotationAssertionAxiom]
+    val annProperty = annAssertionAxiom.getProperty.getIRI
+
+    // ObjectPropertyAssertion axiom turned into AnnotationAssertion after parsing.
+    if (objPropertiesBC.value.contains(annProperty)) {
+      val annSubject: IRI = annAssertionAxiom.getSubject.asIRI().get()
+      val annValue = annAssertionAxiom.getValue.toString
+
+      val objProperty = dataFactory.getOWLObjectProperty(annProperty)
+      val individual1 = dataFactory.getOWLNamedIndividual(annSubject)
+      val individual2 = dataFactory.getOWLNamedIndividual(annValue)
+      val objPropertyAssertionAxiom =
+        dataFactory.getOWLObjectPropertyAssertionAxiom(objProperty, individual1, individual2)
+
+      objPropertyAssertionAxiom.asInstanceOf[OWLAxiom]
+
+    } else if (dataPropertiesBC.value.contains(annProperty)) {
+
+      // dataPropertyAssertion axiom turned into AnnotationAssertion after parsing.
+
+      val annSubject: IRI = annAssertionAxiom.getSubject.asIRI().get()
+      val annValue = annAssertionAxiom.getValue.asLiteral().get()
+
+      val dataProperty = dataFactory.getOWLDataProperty(annProperty)
+      val individual1 = dataFactory.getOWLNamedIndividual(annSubject)
+      val dataPropertyAssertionAxiom =
+        dataFactory.getOWLDataPropertyAssertionAxiom(dataProperty, individual1, annValue)
+
+      dataPropertyAssertionAxiom.asInstanceOf[OWLAxiom]
+
+    } else if (annPropertiesBC.value.contains(annProperty)) {
+
+      annAssertionAxiom
+
+    } else {
+      null
+    }
+  } // map
+
+ }