Added obsoletion menu.

README.md

@@ -1,3 +1,3 @@
 # OBO annotations editor #
 
-A plug-in for Protege that provides entry fields for standard OBO annotation properties.
+A plug-in for Protege that provides entry fields for standard OBO annotation properties, as well as menu actions such as term obsoletion.

pom.xml

@@ -4,7 +4,7 @@
 
 	<groupId>org.geneontology</groupId>
 	<artifactId>obo-annotations-plugin</artifactId>
-	<version>0.3.0</version>
+	<version>0.4.0</version>
 	<packaging>bundle</packaging>
 
 	<name>OBO Annotations Editor</name>
@@ -33,7 +33,7 @@
 		<developer>
 			<id>balhoff</id>
 			<name>Jim Balhoff</name>
-			<email>jim@balhoff.org</email>
+			<email>balhoff@renci.org</email>
 		</developer>
 	</developers>
 

src/main/java/org/protege/oboeditor/menu/ObsoleteEntityMenuAction.java

@@ -0,0 +1,94 @@
+package org.protege.oboeditor.menu;
+
+import java.util.Set;
+
+import org.protege.editor.owl.ui.action.SelectedOWLEntityAction;
+import org.semanticweb.owlapi.model.OWLAnnotation;
+import org.semanticweb.owlapi.model.OWLAnnotationAssertionAxiom;
+import org.semanticweb.owlapi.model.OWLAnnotationProperty;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLClassExpression;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLDisjointClassesAxiom;
+import org.semanticweb.owlapi.model.OWLEntity;
+import org.semanticweb.owlapi.model.OWLEquivalentClassesAxiom;
+import org.semanticweb.owlapi.model.OWLHasKeyAxiom;
+import org.semanticweb.owlapi.model.OWLLiteral;
+import org.semanticweb.owlapi.model.OWLOntology;
+import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+import org.semanticweb.owlapi.vocab.OWLRDFVocabulary;
+
+public class ObsoleteEntityMenuAction extends SelectedOWLEntityAction {
+
+	private static final long serialVersionUID = -1431847694761565949L;
+
+	@Override
+	protected void actionPerformed(OWLEntity entity) {
+		final OWLOntologyManager manager = this.getOWLModelManager().getOWLOntologyManager();
+		final OWLDataFactory factory = this.getOWLDataFactory();
+		final OWLOntology ontology = this.getOWLModelManager().getActiveOntology();
+		this.relabel(entity);
+		manager.addAxiom(ontology, factory.getDeprecatedOWLAnnotationAssertionAxiom(entity.getIRI()));
+		if (entity.isOWLClass()) {
+			final OWLClass ontClass = entity.asOWLClass();
+			for (OWLEquivalentClassesAxiom axiom : ontology.getEquivalentClassesAxioms(ontClass)) {
+				manager.removeAxiom(ontology, axiom);
+				final Set<OWLClassExpression> otherClasses = axiom.getClassExpressionsMinus(ontClass);
+				final Set<OWLAnnotation> annotations = axiom.getAnnotations();
+				if (otherClasses.size() > 1) {
+					final OWLEquivalentClassesAxiom newAxiom = factory.getOWLEquivalentClassesAxiom(otherClasses, annotations);
+					manager.addAxiom(ontology, newAxiom);
+				}
+			}
+			for (OWLSubClassOfAxiom axiom : ontology.getSubClassAxiomsForSubClass(ontClass)) {
+				manager.removeAxiom(ontology, axiom);
+			}
+			for (OWLSubClassOfAxiom axiom : ontology.getSubClassAxiomsForSuperClass(ontClass)) {
+				manager.removeAxiom(ontology, axiom);
+			}
+			for (OWLHasKeyAxiom axiom : ontology.getHasKeyAxioms(ontClass)) {
+				manager.removeAxiom(ontology, axiom);
+			}
+			for (OWLDisjointClassesAxiom axiom : ontology.getDisjointClassesAxioms(ontClass)) {
+				manager.removeAxiom(ontology, axiom);
+				final Set<OWLClassExpression> otherClasses = axiom.getClassExpressionsMinus(ontClass);
+				final Set<OWLAnnotation> annotations = axiom.getAnnotations();
+				if (otherClasses.size() > 1) {
+					final OWLDisjointClassesAxiom newAxiom = factory.getOWLDisjointClassesAxiom(otherClasses, annotations);
+					manager.addAxiom(ontology, newAxiom);
+				}
+			}
+		}
+		if (entity.isOWLNamedIndividual()) {
+			//TODO
+		}
+		if (entity.isOWLObjectProperty()) {
+			//TODO
+		}
+	}
+
+	@Override
+	protected void disposeAction() throws Exception {}
+
+	private void relabel(OWLEntity entity) {
+		final OWLOntologyManager manager = this.getOWLModelManager().getOWLOntologyManager();
+		final OWLDataFactory factory = this.getOWLDataFactory();
+		final OWLAnnotationProperty rdfsLabel = factory.getOWLAnnotationProperty(OWLRDFVocabulary.RDFS_LABEL.getIRI());
+		final OWLOntology ontology = this.getOWLModelManager().getActiveOntology();
+		for (OWLAnnotationAssertionAxiom annotation : ontology.getAnnotationAssertionAxioms(entity.getIRI())) {
+			if (annotation.getProperty().equals(rdfsLabel)) {
+				if (annotation.getValue() instanceof OWLLiteral) {
+					final Set<OWLAnnotation> annotationAnnotations = annotation.getAnnotations();
+					final OWLLiteral literal = (OWLLiteral)(annotation.getValue());
+					final String newLabel = "obsolete " + literal.getLiteral();
+					final OWLLiteral newLiteral = factory.getOWLLiteral(newLabel);
+					final OWLAnnotationAssertionAxiom newAxiom = factory.getOWLAnnotationAssertionAxiom(rdfsLabel, entity.getIRI(), newLiteral, annotationAnnotations);
+					manager.removeAxiom(ontology, annotation);
+					manager.addAxiom(ontology, newAxiom);
+				}
+			}
+		}
+	}
+
+}

src/main/resources/plugin.xml

@@ -8,5 +8,13 @@
         <headerColor value="B1CAF6"/>
         <category value="OBO"/>
     </extension>
+
+    <extension id="menu.ObsoleteEntity" name="Make entity obsolete" point="org.protege.editor.core.application.EditorKitMenuAction">
+        <class value="org.protege.oboeditor.menu.ObsoleteEntityMenuAction"/>
+        <name value="Make entity obsolete"/>
+        <toolTip value="Deprecates the selected entity and removes its defining axioms."/>
+       <path value="org.protege.editor.core.application.menu.EditMenu/SlotOBO-Z"/>
+       <editorKitId value="OWLEditorKit"/>
+    </extension>
 
 </plugin>

update.properties

@@ -1,6 +1,6 @@
 id=org.protege.oboeditor
-version=0.3.0
-download=https://github.com/owlcollab/protege-obo-plugin/releases/download/v0.3.0/obo-annotations-plugin-0.3.0.jar
+version=0.4.0
+download=https://github.com/owlcollab/protege-obo-plugin/releases/download/v0.4.0/obo-annotations-plugin-0.4.0.jar
 name=OBO Annotations Editor
 readme=https://raw.githubusercontent.com/owlcollab/protege-obo-plugin/master/README.md
 license=https://opensource.org/licenses/BSD-3-Clause