Merge branch 'master-who' into Implement_a_widget_for_class_creation_…

…that_checks_for_duplicates_#4

.github/workflows/ci.yaml

@@ -0,0 +1,17 @@
+name: Java CI
+
+on: [push]
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up JDK 17
+        uses: actions/setup-java@v3
+        with:
+          java-version: '17'
+          distribution: 'temurin'
+      - name: Build with Maven
+        run: mvn --batch-mode --update-snapshots package

.github/workflows/pub-docker-hub.yaml

@@ -0,0 +1,33 @@
+name: Publish Docker image to Docker Hub
+on:
+  release:
+    types:
+      - published
+  workflow_dispatch:
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Login to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{secrets.DOCKER_USERNAME}}
+          password: ${{secrets.DOCKER_PASSWORD}}
+      - uses: actions/checkout@v3
+      - name: Set up Maven Central Repository
+        uses: actions/setup-java@v3
+        with:
+          java-version: '17'
+          distribution: 'adopt'
+          server-id: docker.io
+          server-username: DOCKER_USERNAME
+          server-password: DOCKER_PASSWORD
+      - name: Build package
+        run: mvn --batch-mode clean package
+      - name: Build and push image
+        run: mvn --batch-mode -pl webprotege-gwt-ui-server dockerfile:build dockerfile:push
+
+env:
+  DOCKER_USERNAME: ${{secrets.DOCKER_USERNAME}}
+  DOCKER_TOKEN: ${{secrets.DOCKER_PASSWORD}}

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>edu.stanford.protege</groupId>
     <artifactId>webprotege-gwt-ui</artifactId>
-    <version>5.0.4-WHO</version>
+    <version>5.0.6-WHO</version>
     <packaging>pom</packaging>
 
     <properties>

readme.md

@@ -1,56 +1,3 @@
-WebProtégé
-==========
+# webprotege-gwt-ui
 
-What is WebProtégé?
--------------------
-
-WebProtégé is a free, open source collaborative ontology development environment.
-
-It provides the following features:
-- Support for editing OWL 2 ontologies
-- A default simple editing interface, which provides access to commonly used OWL constructs
-- Full change tracking and revision history
-- Collaboration tools such as, sharing and permissions, threaded notes and discussions, watches and email notifications
-- Customizable user interface
-- Support for editing OBO ontologies
-- Multiple file formats for upload and download of ontologies (supported formats: RDF/XML, Turtle, OWL/XML, OBO, and others)
-
-WebProtégé runs as a Web application. End users access it through their Web browsers.
-They do not need to download or install any software. We encourage end-users to use
-
-https://webprotege.stanford.edu
-
-This repository houses the code for the WebProtege GWT User Interface.
-
-Building
---------
-
-To build WebProtégé from source
-
-1) Clone the github repository
-   ```
-   git clone https://github.com/protegeproject/webprotege-gwt-ui.git
-   ```
-2) Open a terminal in the directory where you clone the repository to
-3) Use maven to package WebProtégé
-   ```
-   mvn clean package
-   ```
-5) The WebProtege .war file will be built into the webprotege-server directory
-
-Running from Maven
-------------------
-
-To run WebProtégé in SuperDev Mode using maven
-
-1) Start the GWT code server in one terminal window
-    ```
-    mvn gwt:codeserver
-    ```
-2) In a different terminal window start the tomcat server
-    ```
-    mvn -Denv=dev tomcat7:run
-    ```
-3) Start the WebProtégé Backend
-
-4) Browse to WebProtégé in a Web browser by navigating to [http://localhost:8080](http://localhost:8080)
+This is the UI server for WebProtégé.

webprotege-gwt-ui-client/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>edu.stanford.protege</groupId>
         <artifactId>webprotege-gwt-ui</artifactId>
-        <version>5.0.4-WHO</version>
+        <version>5.0.6-WHO</version>
     </parent>
 
     <artifactId>webprotege-gwt-ui-client</artifactId>

webprotege-gwt-ui-client/src/main/java/edu/stanford/bmir/protege/web/client/Messages.java

@@ -816,6 +816,10 @@ public interface Messages extends com.google.gwt.i18n.client.Messages {
     @Key("search")
     String search();
 
+    @DefaultMessage("Search Icd")
+    @Key("searchIcd")
+    String searchIcd();
+
 
     @DefaultMessage("Search for Class")
     @Key("search.class")

webprotege-gwt-ui-client/src/main/java/edu/stanford/bmir/protege/web/client/hierarchy/ClassHierarchyPortletPresenter.java

@@ -13,6 +13,7 @@
 import edu.stanford.bmir.protege.web.client.portlet.PortletAction;
 import edu.stanford.bmir.protege.web.client.portlet.PortletUi;
 import edu.stanford.bmir.protege.web.client.search.SearchModal;
+import edu.stanford.bmir.protege.web.client.searchIcd.SearchIcdModal;
 import edu.stanford.bmir.protege.web.client.selection.SelectionModel;
 import edu.stanford.bmir.protege.web.client.tag.TagVisibilityPresenter;
 import edu.stanford.bmir.protege.web.shared.entity.EntityNode;
@@ -51,12 +52,17 @@ public class ClassHierarchyPortletPresenter extends AbstractWebProtegePortletPre
     @Nonnull
     private final SearchModal searchModal;
 
+    @Nonnull
+    private final SearchIcdModal searchIcdModal;
+
     private final Messages messages;
 
     private final EntityHierarchyModel hierarchyModel;
     @Nonnull
     private final EntityNodeHtmlRenderer renderer;
 
+    private final UIAction searchActionIcd;
+
     private final UIAction createClassAction;
 
     private final UIAction deleteClassAction;
@@ -100,6 +106,7 @@ public class ClassHierarchyPortletPresenter extends AbstractWebProtegePortletPre
     public ClassHierarchyPortletPresenter(@Nonnull final ProjectId projectId,
                                           @Nonnull SelectionModel selectionModel,
                                           @Nonnull SearchModal searchModal,
+                                          @Nonnull SearchIcdModal searchIcdModal,
                                           @Nonnull Messages messages,
                                           @Nonnull EntityHierarchyModel hierarchyModel,
                                           @Nonnull EntityHierarchyContextMenuPresenterFactory contextMenuPresenterFactory,
@@ -117,6 +124,7 @@ public ClassHierarchyPortletPresenter(@Nonnull final ProjectId projectId,
                                           @Nonnull DispatchServiceManager dispatch) {
         super(selectionModel, projectId, displayNameRenderer, dispatch);
         this.searchModal = searchModal;
+        this.searchIcdModal = searchIcdModal;
         this.messages = checkNotNull(messages);
         this.hierarchyModel = checkNotNull(hierarchyModel);
         this.contextMenuPresenterFactory = checkNotNull(contextMenuPresenterFactory);
@@ -125,16 +133,19 @@ public ClassHierarchyPortletPresenter(@Nonnull final ProjectId projectId,
         this.createEntityPresenter = checkNotNull(createEntityPresenter);
 
         this.createClassAction = new PortletAction(messages.create(),
-                                                   "wp-btn-g--create-class wp-btn-g--create",
-                                                   this::handleCreateSubClasses);
+                "wp-btn-g--create-class wp-btn-g--create",
+                this::handleCreateSubClasses);
 
         this.deleteClassAction = new PortletAction(messages.delete(),
-                                                   "wp-btn-g--delete-class wp-btn-g--delete",
-                                                   this::handleDelete);
+                "wp-btn-g--delete-class wp-btn-g--delete",
+                this::handleDelete);
 
+        this.searchActionIcd = new PortletAction(messages.searchIcd(),
+                "wp-btn-g--searchIcd",
+                this::handleIcdSearch);
         this.searchAction = new PortletAction(messages.search(),
-                                              "wp-btn-g--search",
-                                              this::handleSearch);
+                "wp-btn-g--search",
+                this::handleSearch);
         this.deleteEntitiesPresenter = deleteEntitiesPresenter;
         this.actionStatePresenter = actionStatePresenter;
         this.dropHandler = dropHandler;
@@ -163,6 +174,7 @@ public void startPortlet(@Nonnull PortletUi portletUi,
                              @Nonnull WebProtegeEventBus eventBus) {
         portletUi.addAction(createClassAction);
         portletUi.addAction(deleteClassAction);
+        portletUi.addAction(searchActionIcd);
         portletUi.addAction(searchAction);
         portletUi.setWidget(treeWidget);
         portletUi.setFilterView(filterView);
@@ -178,14 +190,14 @@ public void startPortlet(@Nonnull PortletUi portletUi,
         renderer.setDisplayLanguage(displayNameSettingsManager.getLocalDisplayNameSettings());
         treeWidget.setRenderer(renderer);
         treeWidget.setModel(GraphTreeNodeModel.create(hierarchyModel,
-                                                      node -> node.getEntity()));
+                node -> node.getEntity()));
         treeWidget.setDropHandler(this.dropHandler);
         dropHandler.start(CLASS_HIERARCHY);
         contextMenuPresenterFactory.create(hierarchyModel,
-                                           treeWidget,
-                                           createClassAction,
-                                           deleteClassAction)
-                                   .install();
+                        treeWidget,
+                        createClassAction,
+                        deleteClassAction)
+                .install();
 
         tagVisibilityPresenter.start(filterView, treeWidget);
         setSelectionInTree(getSelectedEntity());
@@ -205,16 +217,16 @@ private void setPreferredDisplayLanguage(@Nonnull DisplayNameSettings lang) {
 
     private Optional<OWLClass> getFirstSelectedClass() {
         return treeWidget.getFirstSelectedKey()
-                         .filter(sel -> sel instanceof OWLClass)
-                         .map(sel -> (OWLClass) sel);
+                .filter(sel -> sel instanceof OWLClass)
+                .map(sel -> (OWLClass) sel);
     }
 
     private void transmitSelectionFromTree(SelectionChangeEvent event) {
         actionStatePresenter.setSelectionPresent(!treeWidget.getSelectedKeys().isEmpty());
-        if(!treeWidget.isAttached()) {
+        if (!treeWidget.isAttached()) {
             return;
         }
-        if(settingSelectionInTree) {
+        if (settingSelectionInTree) {
             return;
         }
         try {
@@ -231,8 +243,8 @@ private void transmitSelectionFromTree(SelectionChangeEvent event) {
 
     private void handleCreateSubClasses() {
         createEntityPresenter.createEntities(CLASS,
-                                             getFirstSelectedClass(),
-                                             CreateEntitiesInHierarchyHandler.get(treeWidget)
+                getFirstSelectedClass(),
+                CreateEntitiesInHierarchyHandler.get(treeWidget)
         );
     }
 
@@ -249,6 +261,12 @@ private void handleSearch() {
         searchModal.showModal();
     }
 
+    private void handleIcdSearch() {
+        searchIcdModal.setEntityTypes(CLASS);
+        searchIcdModal.setHierarchySelectedOptions(treeWidget.getFirstSelectedUserObject());
+        searchIcdModal.showModal();
+    }
+
     private void selectAndExpandPath(Path<OWLEntity> entityPath) {
         treeWidget.setSelected(entityPath, true, () -> treeWidget.setExpanded(entityPath));
     }
@@ -257,7 +275,7 @@ private void setSelectionInTree(Optional<OWLEntity> selection) {
         if (transmittingSelectionFromTree) {
             return;
         }
-        if(treeWidget.getSelectedKeys().contains(selection.orElse(null))) {
+        if (treeWidget.getSelectedKeys().contains(selection.orElse(null))) {
             return;
         }
         try {