core: exporters: owl2: refactor export of items' annotations

Previous to this all project's annotations (except for axiom annotations)
where exported by iterating over all project IRIs at the end of
the export procedure, and generating an annotation assertion for each of them.
This has the drawback that there is no control for filtering
annotations of entities that are part of diagrams excluded from
the exported OWL ontology.

This commit refactors the way annotations associated to items are exported
by moving their generation at the time where an item is exported (similarly
to what happended with the meta system), so that the diagram filtering
is applied. Remaining non-item annotations (such as ontology annotations)
are still dealt with separately.

Closes #155

eddy/core/exporters/owl2.py

@@ -526,6 +526,7 @@ def __init__(self, project, path=None, **kwargs):
         if not self.vm.isRunning():
             self.vm.initialize()
         self.vm.attachThreadToJVM()
+        self.AddOntologyAnnotation = self.vm.getJavaClass('org.semanticweb.owlapi.model.AddOntologyAnnotation')
         self.DefaultPrefixManager = self.vm.getJavaClass('org.semanticweb.owlapi.util.DefaultPrefixManager')
         self.FunctionalSyntaxDocumentFormat = self.vm.getJavaClass('org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat')
         self.HashSet = self.vm.getJavaClass('java.util.HashSet')
@@ -675,6 +676,27 @@ def step(self, num, increase=0):
     #   AUXILIARY METHODS
     #################################
 
+    def getOWLApiAnnotation(self, annotation):
+        """
+        Returns an OWLAnnotation corresponding to the given annotation object.
+        :type annotation: Annotation
+        :rtype: OWLAnnotation
+        """
+        prop = self.df.getOWLAnnotationProperty(self.IRI.create(str(annotation.assertionProperty)))
+        if annotation.isIRIValued():
+            value = self.IRI.create(str(annotation.value))
+        else:
+            lexicalForm = annotation.value.replace('\n', ' ')
+            if annotation.language:
+                value = self.df.getOWLLiteral(lexicalForm, annotation.language)
+            else:
+                if annotation.datatype:
+                    datatype = self.df.getOWLDatatype(self.IRI.create(str(annotation.datatype)))
+                else:
+                    datatype = self.OWL2Datatype.RDF_PLAIN_LITERAL
+                value = self.df.getOWLLiteral(lexicalForm, datatype)
+        return self.df.getOWLAnnotation(prop, value)
+
     def getOWLApiDatatype(self, datatype):
         """
         Returns the OWLDatatype matching the given Datatype.
@@ -807,25 +829,9 @@ def getAxiomAnnotationSet(self, edge):
         :rtype: Set
         """
         collection = self.HashSet()
-        for annotation in edge.annotations:
-            annProp = annotation.assertionProperty
-            owlApiProp = self.df.getOWLAnnotationProperty(self.IRI.create(str(annProp)))
-            if annotation.isIRIValued():
-                obj = annotation.value
-                owlApiObj = self.IRI.create(str(obj))
-            else:
-                obj = annotation.value.replace('\n', ' ')
-                datatype = annotation.datatype
-                lang = annotation.language
-                if lang:
-                    owlApiObj = self.df.getOWLLiteral(obj, lang)
-                else:
-                    if datatype:
-                        owlApiDatatype = self.df.getOWLDatatype(self.IRI.create(str(datatype)))
-                    else:
-                        owlApiDatatype = self.df.getOWLDatatype(self.IRI.create(str(OWL2Datatype.PlainLiteral.value)))
-                    owlApiObj = self.df.getOWLLiteral(obj, owlApiDatatype)
-            collection.add(self.df.getOWLAnnotation(owlApiProp, owlApiObj))
+        if OWLAxiom.Annotation in self.axiomsList:
+            for annotation in edge.annotations:
+                collection.add(self.getOWLApiAnnotation(annotation))
         return collection
 
     def getComplement(self, node):
@@ -1316,6 +1322,17 @@ def getValueDomain(self, node):
     #   AXIOMS GENERATION
     #################################
 
+    def createAnnotationAssertionAxioms(self, node):
+        """
+        Generate a set of OWL 2 annotation assertion axioms for the given node annotations.
+        :type node: AbstractNode
+        """
+        if OWLAxiom.Annotation in self.axiomsList:
+            for annotation in node.iri.annotationAssertions:
+                subject = self.IRI.create(str(annotation.subject))
+                value = self.getOWLApiAnnotation(annotation)
+                self.addAxiom(self.df.getOWLAnnotationAssertionAxiom(subject, value))
+
     def createClassAssertionAxiom(self, edge):
         """
         Generate a OWL 2 ClassAssertion axiom.
@@ -1805,6 +1822,15 @@ def run(self):
             for prefix, ns in self.project.prefixDictItems():
                 self.pm.setPrefix(prefix, ns)
 
+            #############################################
+            # ONTOLOGY ANNOTATIONS
+            #################################
+
+            if OWLAxiom.Annotation in self.axiomsList:
+                for annotation in self.project.ontologyIRI.annotationAssertions:
+                    value = self.getOWLApiAnnotation(annotation)
+                    self.ontology.applyChange(self.AddOntologyAnnotation(self.ontology, value))
+
             LOGGER.debug('Initialized OWL 2 Ontology: %s', ontologyIRI)
 
             #############################################
@@ -1837,6 +1863,10 @@ def run(self):
                         self.createPropertyRangeAxiom(node)
                     elif node.type() is Item.HasKeyNode:
                         self.createHasKeyAxiom(node)
+
+                    if node.isPredicate():
+                        self.createAnnotationAssertionAxioms(node)
+
                     self.step(+1)
 
             LOGGER.debug('Generated OWL 2 axioms from nodes (axioms = %s)', len(self.axioms()))
@@ -1953,35 +1983,6 @@ def run(self):
 
             LOGGER.debug('Generated OWL 2 axioms from edges (axioms = %s)', len(self.axioms()))
 
-            #############################################
-            # ANNOTATION ASSERTIONS
-            #################################
-
-            if OWLAxiom.Annotation in self.axiomsList:
-                for ann in [x for iri in self.project.iris for x in iri.annotationAssertions]:
-                    subj = ann.subject
-                    owlApiSubj = self.IRI.create(str(subj))
-                    annProp = ann.assertionProperty
-                    owlApiProp = self.df.getOWLAnnotationProperty(self.IRI.create(str(annProp)))
-                    if ann.isIRIValued():
-                        obj = ann.value
-                        owlApiObj = self.IRI.create(str(obj))
-                    else:
-                        obj = ann.value.replace('\n', ' ')
-                        datatype = ann.datatype
-                        lang = ann.language
-                        if lang:
-                            owlApiObj = self.df.getOWLLiteral(obj, lang)
-                        else:
-                            if datatype:
-                                owlApiDatatype = self.df.getOWLDatatype(self.IRI.create(str(datatype)))
-                            else:
-                                owlApiDatatype = self.df.getOWLDatatype(self.IRI.create(str(OWL2Datatype.PlainLiteral.value)))
-                            owlApiObj = self.df.getOWLLiteral(obj, owlApiDatatype)
-                    self.addAxiom(self.df.getOWLAnnotationAssertionAxiom(owlApiProp, owlApiSubj, owlApiObj))
-
-            LOGGER.debug('Generated OWL 2 annotation assertion axioms from edges (axioms = %s)', len(self.axioms()))
-
             #############################################
             # APPLY GENERATED AXIOMS
             #################################