wip added edit parents functionality. not tested yet.

src/main/java/edu/stanford/protege/webprotege/bulkop/ChangeEntityParentsActionHandler.java

@@ -0,0 +1,57 @@
+package edu.stanford.protege.webprotege.bulkop;
+
+import com.google.common.collect.ImmutableSet;
+import edu.stanford.protege.webprotege.access.AccessManager;
+import edu.stanford.protege.webprotege.change.ChangeApplicationResult;
+import edu.stanford.protege.webprotege.change.ChangeListGenerator;
+import edu.stanford.protege.webprotege.change.HasApplyChanges;
+import edu.stanford.protege.webprotege.dispatch.AbstractProjectChangeHandler;
+import edu.stanford.protege.webprotege.ipc.ExecutionContext;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLEntity;
+
+import javax.annotation.Nonnull;
+import javax.inject.Inject;
+
+import static com.google.common.collect.ImmutableSet.toImmutableSet;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 25 Sep 2018
+ */
+public class ChangeEntityParentsActionHandler extends AbstractProjectChangeHandler<Boolean, ChangeEntityParentsAction, ChangeEntityParentsResult> {
+
+    @Nonnull
+    private final EditParentsChangeListGeneratorFactory factory;
+
+    @Inject
+    public ChangeEntityParentsActionHandler(@Nonnull AccessManager accessManager,
+                                            @Nonnull HasApplyChanges applyChanges,
+                                            @Nonnull EditParentsChangeListGeneratorFactory factory) {
+        super(accessManager, applyChanges);
+        this.factory = factory;
+    }
+
+    @Nonnull
+    @Override
+    public Class<ChangeEntityParentsAction> getActionClass() {
+        return ChangeEntityParentsAction.class;
+    }
+
+    @Override
+    protected ChangeListGenerator<Boolean> getChangeListGenerator(ChangeEntityParentsAction action, ExecutionContext executionContext) {
+        if(action.entity().isOWLClass()) {
+            ImmutableSet<OWLClass> parents = action.parents().stream().map(OWLEntity::asOWLClass).collect(toImmutableSet());
+            return factory.create(action.changeRequestId(), parents, action.entity().asOWLClass(), action.commitMessage());
+        }
+        return null;
+    }
+
+    @Override
+    protected ChangeEntityParentsResult createActionResult(ChangeApplicationResult<Boolean> changeApplicationResult,
+                                                           ChangeEntityParentsAction action,
+                                                            ExecutionContext executionContext) {
+        return new ChangeEntityParentsResult();
+    }
+}

src/main/java/edu/stanford/protege/webprotege/bulkop/ChangeEntityParentsCommandHandler.java

@@ -0,0 +1,41 @@
+package edu.stanford.protege.webprotege.bulkop;
+
+import edu.stanford.protege.webprotege.api.ActionExecutor;
+import edu.stanford.protege.webprotege.ipc.CommandHandler;
+import edu.stanford.protege.webprotege.ipc.ExecutionContext;
+import edu.stanford.protege.webprotege.ipc.WebProtegeHandler;
+import reactor.core.publisher.Mono;
+
+import javax.annotation.Nonnull;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 2021-08-21
+ */
+@WebProtegeHandler
+public class ChangeEntityParentsCommandHandler implements CommandHandler<ChangeEntityParentsAction, ChangeEntityParentsResult> {
+
+    private final ActionExecutor executor;
+
+    public ChangeEntityParentsCommandHandler(ActionExecutor executor) {
+        this.executor = executor;
+    }
+
+    @Nonnull
+    @Override
+    public String getChannelName() {
+        return ChangeEntityParentsAction.CHANNEL;
+    }
+
+    @Override
+    public Class<ChangeEntityParentsAction> getRequestClass() {
+        return ChangeEntityParentsAction.class;
+    }
+
+    @Override
+    public Mono<ChangeEntityParentsResult> handleRequest(ChangeEntityParentsAction request,
+                                                          ExecutionContext executionContext) {
+        return executor.executeRequest(request, executionContext);
+    }
+}

src/main/java/edu/stanford/protege/webprotege/bulkop/EditParentsChangeListGenerator.java

@@ -0,0 +1,116 @@
+package edu.stanford.protege.webprotege.bulkop;
+
+
+import com.google.common.collect.ImmutableSet;
+import edu.stanford.protege.webprotege.change.AddAxiomChange;
+import edu.stanford.protege.webprotege.change.ChangeApplicationResult;
+import edu.stanford.protege.webprotege.change.ChangeGenerationContext;
+import edu.stanford.protege.webprotege.change.ChangeListGenerator;
+import edu.stanford.protege.webprotege.change.OntologyChangeList;
+import edu.stanford.protege.webprotege.change.RemoveAxiomChange;
+import edu.stanford.protege.webprotege.common.ChangeRequestId;
+import edu.stanford.protege.webprotege.index.ProjectOntologiesIndex;
+import edu.stanford.protege.webprotege.index.SubClassOfAxiomsBySubClassIndex;
+import edu.stanford.protege.webprotege.owlapi.RenameMap;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+import org.semanticweb.owlapi.model.OWLOntologyID;
+import org.semanticweb.owlapi.model.OWLSubClassOfAxiom;
+
+import javax.annotation.Nonnull;
+import javax.inject.Inject;
+
+import static com.google.common.base.Preconditions.checkNotNull;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 25 Sep 2018
+ */
+public class EditParentsChangeListGenerator implements ChangeListGenerator<Boolean> {
+
+    @Nonnull
+    private final ChangeRequestId changeRequestId;
+
+    @Nonnull
+    private final ImmutableSet<OWLClass> parents;
+
+    @Nonnull
+    private final OWLClass entity;
+
+    @Nonnull
+    private final ProjectOntologiesIndex projectOntologies;
+
+    @Nonnull
+    private final SubClassOfAxiomsBySubClassIndex subClassAxiomIndex;
+
+    @Nonnull
+    private final OWLDataFactory dataFactory;
+
+    @Nonnull
+    private final String commitMessage;
+
+    @Inject
+    public EditParentsChangeListGenerator(@Nonnull ChangeRequestId changeRequestId,
+                                          @Nonnull ImmutableSet<OWLClass> parents,
+                                          @Nonnull OWLClass entity,
+                                          @Nonnull String commitMessage,
+                                          @Nonnull ProjectOntologiesIndex projectOntologies,
+                                          @Nonnull SubClassOfAxiomsBySubClassIndex subClassAxiomIndex,
+                                          @Nonnull OWLDataFactory dataFactory) {
+        this.changeRequestId = changeRequestId;
+        this.parents = checkNotNull(parents);
+        this.entity = checkNotNull(entity);
+        this.projectOntologies = checkNotNull(projectOntologies);
+        this.subClassAxiomIndex = checkNotNull(subClassAxiomIndex);
+        this.dataFactory = checkNotNull(dataFactory);
+        this.commitMessage = checkNotNull(commitMessage);
+    }
+
+    @Override
+    public ChangeRequestId getChangeRequestId() {
+        return changeRequestId;
+    }
+
+    @Override
+    public OntologyChangeList<Boolean> generateChanges(ChangeGenerationContext context) {
+        var changeList = new OntologyChangeList.Builder<Boolean>();
+        var ontologyId = projectOntologies.getOntologyIds().filter(owlOntologyID -> owlOntologyID.getOntologyIRI().get()==entity.getIRI()).findAny();
+
+        ontologyId.ifPresent(ontId -> {
+            parents.forEach(parentClass -> {
+                subClassAxiomIndex
+                        .getSubClassOfAxiomsForSubClass(entity, ontId)
+                        .filter(ax -> ax.getSuperClass().isNamed())
+                        .filter(ax -> !ax.getSuperClass().equals(parentClass))
+                        .forEach(ax -> processAxiom(ax, parentClass, ontId, changeList));
+            });
+        });
+
+
+        return changeList.build(true);
+    }
+
+    private void processAxiom(OWLSubClassOfAxiom ax,
+                              OWLClass parent,
+                              OWLOntologyID ontId,
+                              OntologyChangeList.Builder<Boolean> changeList) {
+        var removeAxiom = RemoveAxiomChange.of(ontId, ax);
+        changeList.add(removeAxiom);
+        var replacementAx = dataFactory.getOWLSubClassOfAxiom(entity, parent, ax.getAnnotations());
+        var addAxiom = AddAxiomChange.of(ontId, replacementAx);
+        changeList.add(addAxiom);
+    }
+
+    @Override
+    public Boolean getRenamedResult(Boolean result,
+                                    RenameMap renameMap) {
+        return result;
+    }
+
+    @Nonnull
+    @Override
+    public String getMessage(ChangeApplicationResult<Boolean> result) {
+        return commitMessage;
+    }
+}

src/main/java/edu/stanford/protege/webprotege/bulkop/EditParentsChangeListGeneratorFactory.java

@@ -0,0 +1,42 @@
+package edu.stanford.protege.webprotege.bulkop;
+
+import com.google.common.collect.ImmutableSet;
+import edu.stanford.protege.webprotege.common.ChangeRequestId;
+import edu.stanford.protege.webprotege.index.ProjectOntologiesIndex;
+import edu.stanford.protege.webprotege.index.SubClassOfAxiomsBySubClassIndex;
+import org.semanticweb.owlapi.model.OWLClass;
+import org.semanticweb.owlapi.model.OWLDataFactory;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 2021-07-13
+ */
+public class EditParentsChangeListGeneratorFactory {
+
+    private final ProjectOntologiesIndex projectOntologiesIndex;
+
+    private final SubClassOfAxiomsBySubClassIndex subClassOfAxiomsBySubClassIndex;
+
+    private final OWLDataFactory dataFactory;
+
+    public EditParentsChangeListGeneratorFactory(ProjectOntologiesIndex projectOntologiesIndex,
+                                                 SubClassOfAxiomsBySubClassIndex subClassOfAxiomsBySubClassIndex,
+                                                 OWLDataFactory dataFactory) {
+        this.projectOntologiesIndex = projectOntologiesIndex;
+        this.subClassOfAxiomsBySubClassIndex = subClassOfAxiomsBySubClassIndex;
+        this.dataFactory = dataFactory;
+    }
+
+    public EditParentsChangeListGenerator create(ChangeRequestId changeRequestId,
+                                                 ImmutableSet<OWLClass> parents,
+                                                 OWLClass entity,
+                                                 String commitMessage) {
+        return new EditParentsChangeListGenerator(changeRequestId, parents,
+                                                  entity,
+                                                  commitMessage,
+                                                  projectOntologiesIndex,
+                                                  subClassOfAxiomsBySubClassIndex,
+                                                  dataFactory);
+    }
+}