Get all classes in ontology

Dockerfile

@@ -4,4 +4,4 @@ MAINTAINER protege.stanford.edu
 EXPOSE 7770
 ARG JAR_FILE
 COPY target/${JAR_FILE} webprotege-backend-service.jar
-ENTRYPOINT ["java","-jar","/webprotege-backend-service.jar"]
+ENTRYPOINT ["sh", "-c", "java $JVM_ENV -jar /webprotege-backend-service.jar"]

src/main/java/edu/stanford/protege/webprotege/ApplicationBeansConfiguration.java

@@ -299,13 +299,6 @@ ProjectDetailsRepository getProjectDetailsRepository(MongoTemplate mongoTemplate
         return new ProjectDetailsRepository(mongoTemplate, objectMapper);
     }
 
-    @Singleton
-    @Bean
-    ProjectBranchRepository getProjectBranchRepository(MongoTemplate mongoTemplate,
-                                                         ObjectMapper objectMapper) {
-        return new ProjectBranchRepository(mongoTemplate, objectMapper);
-    }
-
     @Singleton
     @Bean
     ProjectRevisionRepository projectRevisionRepository(MongoTemplate mongoTemplate, ObjectMapper objectMapper) {
@@ -585,8 +578,8 @@ CommandExecutor<PrepareBackupFilesForUseRequest, PrepareBackupFilesForUseRespons
     }
 
     @Bean
-    CommandExecutor<CreateProjectSmallFilesRequest, CreateProjectSmallFilesResponse> executorForCreateProjectSmallFiles() {
-        return new CommandExecutorImpl<>(CreateProjectSmallFilesResponse.class);
+    CommandExecutor<CreateNewReproducibleProjectRequest, CreateNewReproducibleProjectResponse> executorForCreateProjectSmallFiles() {
+        return new CommandExecutorImpl<>(CreateNewReproducibleProjectResponse.class);
     }
 
     @Bean

src/main/java/edu/stanford/protege/webprotege/ProjectActionHandlerBeansConfiguration.java

@@ -1066,6 +1066,11 @@ GetEntityChildrenActionHandler getEntityChildrenActionHandler(AccessManager p1,
         return new GetEntityChildrenActionHandler(p1,p2,p3,p4);
     }
 
+
+    @Bean
+    GetAllOwlClassesActionHandler getAllOwlClassesActionHandler(AccessManager p1, ProjectAxiomsSignatureIndex p2) {
+        return new GetAllOwlClassesActionHandler(p1, p2);
+    }
     @Bean
     FilterExistingEntitiesActionHandler filterExistingEntitiesActionHandler(AccessManager p1,
                                                                   ClassHierarchyProvider p2) {

src/main/java/edu/stanford/protege/webprotege/forms/EntityFormRepositoryImpl.java

@@ -16,9 +16,7 @@
 
 import javax.annotation.*;
 import javax.inject.Inject;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Optional;
+import java.util.*;
 import java.util.concurrent.locks.Lock;
 import java.util.concurrent.locks.ReadWriteLock;
 import java.util.concurrent.locks.ReentrantReadWriteLock;
@@ -55,6 +53,7 @@ public class EntityFormRepositoryImpl implements EntityFormRepository {
     private final Lock readLock = readWriteLock.readLock();
 
     private final Lock writeLock = readWriteLock.writeLock();
+    Map<FormId, FormDescriptor> formDescriptorCache = new HashMap<>();
 
     private final static Logger LOGGER = LoggerFactory.getLogger(EntityFormRepositoryImpl.class);
 
@@ -70,6 +69,7 @@ public void deleteFormDescriptor(@Nonnull ProjectId projectId, @Nonnull FormId f
             writeLock.lock();
             var query = new Document(PROJECT_ID, projectId.id()).append(FORM__FORM_ID, formId.getId());
             getCollection().findOneAndDelete(query);
+            formDescriptorCache.remove(formId);
         } finally {
             writeLock.unlock();
         }
@@ -99,6 +99,7 @@ var record = FormDescriptorRecord.get(projectId, formDescriptor, ordinal);
                 var filter = getProjectIdFormIdFilter(projectId, formDescriptor.getFormId());
                 getCollection()
                         .findOneAndReplace(filter, document, new FindOneAndReplaceOptions().upsert(true));
+                formDescriptorCache.remove(formDescriptor.getFormId());
             }
         } finally {
             writeLock.unlock();
@@ -143,6 +144,7 @@ public void setProjectFormDescriptors(@Nonnull ProjectId projectId, @Nonnull Lis
                     var record = FormDescriptorRecord.get(projectId, formDescriptor, ordinal);
                     var recordDocument = objectMapper.convertValue(record, Document.class);
                     docs.add(recordDocument);
+                    formDescriptorCache.remove(formDescriptor.getFormId());
                 }
             }
             collection.deleteMany(new Document(PROJECT_ID, projectId.id()));
@@ -162,6 +164,9 @@ public MongoCollection<Document> getCollection() {
 
     @Override
     public Optional<FormDescriptor> findFormDescriptor(@Nonnull ProjectId projectId, @Nonnull FormId formId) {
+        if(formDescriptorCache.get(formId) != null) {
+            return Optional.of(formDescriptorCache.get(formId));
+        }
         try {
             readLock.lock();
             Bson filter = getProjectIdFormIdFilter(projectId, formId);
@@ -173,6 +178,7 @@ public Optional<FormDescriptor> findFormDescriptor(@Nonnull ProjectId projectId,
             }
             else {
                 var formRecord = objectMapper.convertValue(foundFormDocument, FormDescriptorRecord.class);
+                formDescriptorCache.put(formRecord.getFormDescriptor().getFormId(), formRecord.getFormDescriptor());
                 return Optional.of(formRecord.getFormDescriptor());
             }
         } finally {

src/main/java/edu/stanford/protege/webprotege/icd/actions/CreateClassesFromApiActionHandler.java

@@ -113,7 +113,7 @@ protected CreateClassesFromApiResult createActionResult(ChangeApplicationResult<
             return new CreateClassesFromApiResult(
                     action.changeRequestId(),
                     action.projectId(),
-                    newClass.toStringID()
+                    newClass.getIRI().toString()
             );
         }
     }

src/main/java/edu/stanford/protege/webprotege/icd/actions/GetAllOwlClassesAction.java

@@ -0,0 +1,19 @@
+package edu.stanford.protege.webprotege.icd.actions;
+
+import edu.stanford.protege.webprotege.common.ProjectId;
+import edu.stanford.protege.webprotege.common.ProjectRequest;
+
+public record GetAllOwlClassesAction(ProjectId projectId) implements ProjectRequest<GetAllOwlClassesResult> {
+    public final static String CHANNEL = "webprotege.entities.GetAllOwlClasses";
+
+
+    @Override
+    public String getChannel() {
+        return CHANNEL;
+    }
+
+    @Override
+    public ProjectId projectId(){
+        return projectId;
+    }
+}

src/main/java/edu/stanford/protege/webprotege/icd/actions/GetAllOwlClassesActionHandler.java

@@ -0,0 +1,37 @@
+package edu.stanford.protege.webprotege.icd.actions;
+
+import edu.stanford.protege.webprotege.access.AccessManager;
+import edu.stanford.protege.webprotege.dispatch.AbstractProjectActionHandler;
+import edu.stanford.protege.webprotege.index.ProjectAxiomsSignatureIndex;
+import edu.stanford.protege.webprotege.ipc.ExecutionContext;
+import org.jetbrains.annotations.NotNull;
+import org.semanticweb.owlapi.model.EntityType;
+import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLNamedObject;
+
+import javax.inject.Inject;
+import java.util.List;
+
+public class GetAllOwlClassesActionHandler extends AbstractProjectActionHandler<GetAllOwlClassesAction, GetAllOwlClassesResult> {
+
+    private final ProjectAxiomsSignatureIndex projectAxiomsSignatureIndex;
+
+    @Inject
+    public GetAllOwlClassesActionHandler(@NotNull AccessManager accessManager, ProjectAxiomsSignatureIndex projectAxiomsSignatureIndex) {
+        super(accessManager);
+        this.projectAxiomsSignatureIndex = projectAxiomsSignatureIndex;
+    }
+
+    @NotNull
+    @Override
+    public Class<GetAllOwlClassesAction> getActionClass() {
+        return GetAllOwlClassesAction.class;
+    }
+
+    @NotNull
+    @Override
+    public GetAllOwlClassesResult execute(@NotNull GetAllOwlClassesAction action, @NotNull ExecutionContext executionContext) {
+        List<IRI> allClasses = projectAxiomsSignatureIndex.getProjectAxiomsSignature(EntityType.CLASS).map(OWLNamedObject::getIRI).toList();
+        return new GetAllOwlClassesResult(allClasses);
+    }
+}

src/main/java/edu/stanford/protege/webprotege/icd/actions/GetAllOwlClassesCommandHandler.java

@@ -0,0 +1,37 @@
+package edu.stanford.protege.webprotege.icd.actions;
+
+
+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;
+
+@WebProtegeHandler
+public class GetAllOwlClassesCommandHandler implements CommandHandler<GetAllOwlClassesAction, GetAllOwlClassesResult> {
+
+    private final ActionExecutor executor;
+
+    public GetAllOwlClassesCommandHandler(ActionExecutor executor) {
+        this.executor = executor;
+    }
+
+    @Nonnull
+    @Override
+    public String getChannelName() {
+        return GetAllOwlClassesAction.CHANNEL;
+    }
+
+    @Override
+    public Class<GetAllOwlClassesAction> getRequestClass() {
+        return GetAllOwlClassesAction.class;
+    }
+
+    @Override
+    public Mono<GetAllOwlClassesResult> handleRequest(GetAllOwlClassesAction request,
+                                                                ExecutionContext executionContext) {
+        return executor.executeRequest(request, executionContext);
+    }
+}

src/main/java/edu/stanford/protege/webprotege/icd/actions/GetAllOwlClassesResult.java

@@ -0,0 +1,12 @@
+package edu.stanford.protege.webprotege.icd.actions;
+
+
+import com.fasterxml.jackson.annotation.JsonTypeName;
+import edu.stanford.protege.webprotege.dispatch.Result;
+import org.semanticweb.owlapi.model.IRI;
+
+import java.util.List;
+
+@JsonTypeName(GetAllOwlClassesAction.CHANNEL)
+public record GetAllOwlClassesResult(List<IRI> owlClassList) implements Result {
+}

src/main/java/edu/stanford/protege/webprotege/icd/actions/GetClassAncestorsActionHandler.java

@@ -9,12 +9,10 @@
 import edu.stanford.protege.webprotege.ipc.ExecutionContext;
 import edu.stanford.protege.webprotege.renderer.RenderingManager;
 import org.jetbrains.annotations.NotNull;
-import org.semanticweb.owlapi.model.OWLClass;
 import uk.ac.manchester.cs.owl.owlapi.OWLClassImpl;
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.stream.Collectors;
 
 @JsonTypeName("webprotege.entities.GetClassAncestors")
 public class GetClassAncestorsActionHandler extends AbstractProjectActionHandler<GetClassAncestorsAction, GetClassAncestorsResult> {
@@ -38,19 +36,16 @@ public Class<GetClassAncestorsAction> getActionClass() {
     @NotNull
     @Override
     public GetClassAncestorsResult execute(@NotNull GetClassAncestorsAction action, @NotNull ExecutionContext executionContext) {
-        AncestorHierarchyNode<OWLClass> classTree = classHierarchyProvider.getAncestorsTree(new OWLClassImpl(action.classIri()));
-
-        AncestorHierarchyNode<OWLEntityData> entityDataTree = mapToEntityData(classTree);
-        return new GetClassAncestorsResult(entityDataTree);
-    }
-
-    private AncestorHierarchyNode<OWLEntityData> mapToEntityData(AncestorHierarchyNode<OWLClass> ancestorHierarchyNode) {
+        List<AncestorHierarchyNode<OWLEntityData>> ancestors =  classHierarchyProvider.getParents(new OWLClassImpl(action.classIri())).stream().map(owlCLass -> {
+            OWLEntityData entityData = renderingManager.getRendering(owlCLass);
+            AncestorHierarchyNode<OWLEntityData> resp = new AncestorHierarchyNode<>();
+            resp.setNode(entityData);
+            return resp;
+        }).toList();
         AncestorHierarchyNode<OWLEntityData> response = new AncestorHierarchyNode<>();
-        response.setNode(renderingManager.getRendering(ancestorHierarchyNode.getNode()));
-        response.setChildren(new ArrayList<>());
-        for(AncestorHierarchyNode<OWLClass> child: ancestorHierarchyNode.getChildren()) {
-            response.getChildren().add(mapToEntityData(child));
-        }
-        return response;
+        response.setNode(renderingManager.getRendering(new OWLClassImpl(action.classIri())));
+        response.setChildren(ancestors);
+        return new GetClassAncestorsResult(response);
     }
 }
+

src/main/java/edu/stanford/protege/webprotege/icd/projects/CreateProjectSmallFilesRequest.java → src/main/java/edu/stanford/protege/webprotege/icd/projects/CreateNewReproducibleProjectRequest.java

@@ -3,13 +3,14 @@
 import com.fasterxml.jackson.annotation.*;
 import edu.stanford.protege.webprotege.common.*;
 
-import static edu.stanford.protege.webprotege.icd.projects.CreateProjectSmallFilesRequest.CHANNEL;
+import static edu.stanford.protege.webprotege.icd.projects.CreateNewReproducibleProjectRequest.CHANNEL;
 
 @JsonTypeName(CHANNEL)
-public record CreateProjectSmallFilesRequest(
-        @JsonProperty("projectId") ProjectId projectId
-)implements Request<CreateProjectSmallFilesResponse> {
-    public static final String CHANNEL = "icatx.versioning.CreateProjectSmallFiles";
+public record CreateNewReproducibleProjectRequest(
+        @JsonProperty("projectId") ProjectId projectId,
+        @JsonProperty("branch") String branch
+)implements Request<CreateNewReproducibleProjectResponse> {
+    public static final String CHANNEL = "icatx.versioning.CreateNewReproducibleProjectRequest";
 
     @Override
     public String getChannel() {

src/main/java/edu/stanford/protege/webprotege/icd/projects/CreateProjectSmallFilesResponse.java → src/main/java/edu/stanford/protege/webprotege/icd/projects/CreateNewReproducibleProjectResponse.java

@@ -3,8 +3,8 @@
 import com.fasterxml.jackson.annotation.JsonTypeName;
 import edu.stanford.protege.webprotege.dispatch.Result;
 
-import static edu.stanford.protege.webprotege.icd.projects.CreateProjectSmallFilesRequest.CHANNEL;
+import static edu.stanford.protege.webprotege.icd.projects.CreateNewReproducibleProjectRequest.CHANNEL;
 
 @JsonTypeName(CHANNEL)
-public record CreateProjectSmallFilesResponse() implements Result {
+public record CreateNewReproducibleProjectResponse() implements Result {
 }