Logical definition with filtered trees

pom.xml

@@ -12,7 +12,7 @@
 
     <groupId>edu.stanford.protege</groupId>
     <artifactId>webprotege-backend-service</artifactId>
-    <version>1.3.22-WHO</version>
+    <version>2.0.1-WHO</version>
 
     <properties>
         <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
@@ -67,6 +67,11 @@
             <artifactId>webprotege-common</artifactId>
             <version>0.9.8</version>
         </dependency>
+        <dependency>
+            <groupId>edu.stanford.protege</groupId>
+            <artifactId>webprotege-forms</artifactId>
+            <version>1.1.7</version>
+        </dependency>
         <dependency>
             <groupId>edu.stanford.protege</groupId>
             <artifactId>webprotege-criteria</artifactId>
@@ -86,7 +91,7 @@
         <dependency>
             <groupId>edu.stanford.protege</groupId>
             <artifactId>webprotege-backend-api</artifactId>
-            <version>1.0.26-WHO</version>
+            <version>2.0.2-WHO</version>
         </dependency>
         <dependency>
             <groupId>edu.stanford.protege</groupId>
@@ -457,6 +462,21 @@
                 <groupId>org.springframework.boot</groupId>
                 <artifactId>spring-boot-maven-plugin</artifactId>
             </plugin>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>3.0.0</version>
+                <configuration>
+                    <systemPropertyVariables>
+                        <spring.profiles.active>test</spring.profiles.active>
+                    </systemPropertyVariables>
+                    <includes>
+                        <include>**/*TestCase.java</include>
+                        <include>**/*Test.java</include>
+                        <include>**/*IT.java</include>
+                    </includes>
+                </configuration>
+            </plugin>
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>

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

@@ -16,6 +16,9 @@
 import edu.stanford.protege.webprotege.filemanager.FileContents;
 import edu.stanford.protege.webprotege.forms.EntityFormRepositoryImpl;
 import edu.stanford.protege.webprotege.forms.EntityFormSelectorRepositoryImpl;
+import edu.stanford.protege.webprotege.hierarchy.NamedHierarchyManager;
+import edu.stanford.protege.webprotege.hierarchy.NamedHierarchyManagerImpl;
+import edu.stanford.protege.webprotege.hierarchy.NamedHierarchyRepository;
 import edu.stanford.protege.webprotege.index.*;
 import edu.stanford.protege.webprotege.inject.*;
 import edu.stanford.protege.webprotege.inject.project.ProjectDirectoryFactory;
@@ -41,7 +44,6 @@
 import edu.stanford.protege.webprotege.revision.*;
 import edu.stanford.protege.webprotege.search.EntitySearchFilterRepositoryImpl;
 import edu.stanford.protege.webprotege.sharing.ProjectSharingSettingsManagerImpl;
-import edu.stanford.protege.webprotege.storage.MinioFileDownloader;
 import edu.stanford.protege.webprotege.storage.MinioProperties;
 import edu.stanford.protege.webprotege.tag.EntityTagsRepositoryImpl;
 import edu.stanford.protege.webprotege.tag.TagRepositoryImpl;
@@ -575,4 +577,14 @@ MinioClient minioClient(MinioProperties properties) {
                           .build();
     }
 
+    @Bean
+    NamedHierarchyRepository namedHierarchyRepository(ObjectMapper p0, MongoTemplate p1) {
+        return new NamedHierarchyRepository(p0, p1);
+    }
+
+    @Bean
+    NamedHierarchyManager hierarchiesManager(OWLDataFactory dataFactory, NamedHierarchyRepository repository) {
+        return new NamedHierarchyManagerImpl(dataFactory, repository);
+    }
+
 }

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

@@ -363,4 +363,12 @@ public static Optional<String> getFreshEntityLangTag(OWLEntity entity) {
             return Optional.of(langTag);
         }
     }
+
+    public static OWLObjectProperty getOWLTopObjectProperty() {
+        return DataFactory.getOWLObjectProperty(OWLRDFVocabulary.OWL_TOP_OBJECT_PROPERTY.getIRI());
+    }
+
+    public static OWLDataProperty getOWLTopDataProperty() {
+        return DataFactory.getOWLDataProperty(OWLRDFVocabulary.OWL_TOP_DATA_PROPERTY.getIRI());
+    }
 }

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

@@ -20,11 +20,15 @@
 import edu.stanford.protege.webprotege.icd.actions.GetClassAncestorsActionHandler;
 import edu.stanford.protege.webprotege.icd.hierarchy.ClassHierarchyRetiredClassDetector;
 import edu.stanford.protege.webprotege.index.*;
-import edu.stanford.protege.webprotege.individuals.*;
+import edu.stanford.protege.webprotege.individuals.CreateIndividualsChangeListGeneratorFactory;
+import edu.stanford.protege.webprotege.individuals.CreateNamedIndividualsActionHandler;
+import edu.stanford.protege.webprotege.individuals.GetIndividualsActionHandler;
+import edu.stanford.protege.webprotege.individuals.GetIndividualsPageContainingIndividualActionHandler;
 import edu.stanford.protege.webprotege.ipc.EventDispatcher;
 import edu.stanford.protege.webprotege.issues.*;
 import edu.stanford.protege.webprotege.lang.*;
 import edu.stanford.protege.webprotege.linearization.LinearizationManager;
+import edu.stanford.protege.webprotege.logicaldefinitions.*;
 import edu.stanford.protege.webprotege.mansyntax.*;
 import edu.stanford.protege.webprotege.mansyntax.render.*;
 import edu.stanford.protege.webprotege.match.*;
@@ -502,6 +506,14 @@ AddCommentHandler addEntityCommentActionHandler(ProjectId p1,
     }
 
 
+    @Bean
+    SetNamedHierarchyActionHandler addNamedHierarchyActionHandler(AccessManager p0,
+                                                                  NamedHierarchyManager p1) {
+        return new SetNamedHierarchyActionHandler(p0, p1);
+    }
+
+
+
     @Bean
     DeleteEntityCommentHandler deleteEntityCommentActionHandler(EntityDiscussionThreadRepository p1) {
         return new DeleteEntityCommentHandler(p1);
@@ -578,7 +590,7 @@ GetClassFrameActionHandler getClassFrameActionHandler(AccessManager p1,
 
     @Bean
     GetEntityHierarchyChildrenActionHandler getClassHierarchyChildrenActionHandler(AccessManager p1,
-                                                                                   HierarchyProviderMapper p2,
+                                                                                   HierarchyProviderManager p2,
                                                                                    DeprecatedEntityChecker p3,
                                                                                    GraphNodeRenderer p4,
                                                                                    DictionaryManager p5) {
@@ -587,23 +599,23 @@ GetEntityHierarchyChildrenActionHandler getClassHierarchyChildrenActionHandler(A
 
     @Bean
     GetEntityHierarchyParentsActionHandler getClassHierarchyParentsActionHandler(AccessManager p1,
-                                                                                 HierarchyProviderMapper p2,
+                                                                                 HierarchyProviderManager p2,
                                                                                  RenderingManager p3) {
         return new GetEntityHierarchyParentsActionHandler(p1, p2, p3);
     }
 
 
     @Bean
     GetHierarchyPathsToRootActionHandler getHierarchyPathsToRootActionHandler(AccessManager p1,
-                                                                              HierarchyProviderMapper p2,
+                                                                              HierarchyProviderManager p2,
                                                                               GraphNodeRenderer p3) {
         return new GetHierarchyPathsToRootActionHandler(p1, p2, p3);
     }
 
 
     @Bean
     GetHierarchyRootsActionHandler getHierarchyRootsActionHandler(AccessManager p1,
-                                                                  HierarchyProviderMapper p2,
+                                                                  HierarchyProviderManager p2,
                                                                   EntityNodeRenderer p3) {
         return new GetHierarchyRootsActionHandler(p1, p2, p3);
     }
@@ -733,7 +745,7 @@ GetProjectInfoActionHandler getProjectInfoActionHandler(AccessManager p1,
 
     @Bean
     GetHierarchySiblingsActionHandler getHierarchySiblingsActionHandler(AccessManager p1,
-                                                                        HierarchyProviderMapper p2,
+                                                                        HierarchyProviderManager p2,
                                                                         GraphNodeRenderer p3, DictionaryManager p4) {
         return new GetHierarchySiblingsActionHandler(p1, p2, p3, p4);
     }
@@ -991,4 +1003,20 @@ ExistingOntologyMergeAddActionHandler sExistingOntologyMergeAddActionHandler(Acc
                                                                                  HasApplyChanges p5) {
         return new ExistingOntologyMergeAddActionHandler(p1, p2, p3, p4, p5);
     }
+
+    @Bean
+    GetLogicalDefinitionsActionHandler getLogicalDefinitionsActionHandler(AccessManager p1,
+                                                                          LogicalDefinitionExtractor p2,
+                                                                          NecessaryConditionsExtractor p3) {
+        return new GetLogicalDefinitionsActionHandler(p1, p2, p3);
+
+    }
+
+
+    @Bean
+    UpdateLogicalDefinitionsActionHandler getUpdateLogicalDefinitionsActionHandler(AccessManager p1,
+                                                                                   HasApplyChanges p2,
+                                                                                   UpdateLogicalDefinitionsChangeListGeneratorFactory p3) {
+        return new UpdateLogicalDefinitionsActionHandler(p1, p2, p3);
+    }
 }