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protegeproject · May 16, 2024 · bdc7678 · bdc7678
2 parents 16a1a86 + b61ca3a
commit bdc7678
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diff --git a/.github/workflows/ci.yaml b/.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
diff --git a/.github/workflows/pub-docker-hub.yaml b/.github/workflows/pub-docker-hub.yaml
@@ -0,0 +1,29 @@
+name: Publish Docker image to Docker Hub
+on:
+  release:
+    types:
+      - published
+
+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: Publish package
+        run: mvn --batch-mode clean deploy
+env:
+  DOCKER_USERNAME: ${{secrets.DOCKER_USERNAME}}
+  DOCKER_TOKEN: ${{secrets.DOCKER_PASSWORD}}
diff --git a/pom.xml b/pom.xml
@@ -5,7 +5,7 @@
 
     <groupId>edu.stanford.protege</groupId>
     <artifactId>webprotege-gwt-ui</artifactId>
-    <version>5.0.5-WHO</version>
+    <version>5.0.6-WHO</version>
     <packaging>pom</packaging>
 
     <properties>

diff --git a/readme.md b/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.
diff --git a/webprotege-gwt-ui-client/pom.xml b/webprotege-gwt-ui-client/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>edu.stanford.protege</groupId>
         <artifactId>webprotege-gwt-ui</artifactId>
-        <version>5.0.5-WHO</version>
+        <version>5.0.6-WHO</version>
     </parent>
 
     <artifactId>webprotege-gwt-ui-client</artifactId>

diff --git a/...i-client/src/main/java/edu/stanford/bmir/protege/web/client/project/ProjectPresenter.java b/...i-client/src/main/java/edu/stanford/bmir/protege/web/client/project/ProjectPresenter.java
@@ -11,7 +11,9 @@
 import edu.stanford.bmir.protege.web.client.progress.BusyView;
 import edu.stanford.bmir.protege.web.client.tag.ProjectTagsStyleManager;
 import edu.stanford.bmir.protege.web.client.topbar.TopBarPresenter;
+import edu.stanford.bmir.protege.web.client.user.LoggedInUserProvider;
 import edu.stanford.bmir.protege.web.shared.HasDispose;
+import edu.stanford.bmir.protege.web.shared.dispatch.actions.GetUserInfoAction;
 import edu.stanford.bmir.protege.web.shared.dispatch.actions.TranslateEventListAction;
 import edu.stanford.bmir.protege.web.shared.event.*;
 import edu.stanford.bmir.protege.web.shared.inject.ProjectSingleton;
@@ -59,6 +61,8 @@ public class ProjectPresenter implements HasDispose, HasProjectId {
 
     private final LargeNumberOfChangesManager largeNumberOfChangesHandler;
 
+    private final LoggedInUserProvider loggedInUserProvider;
+
 
     @Inject
     public ProjectPresenter(ProjectId projectId,
@@ -72,7 +76,7 @@ public ProjectPresenter(ProjectId projectId,
                             PermissionScreener permissionScreener,
                             WebProtegeEventBus eventBus,
                             ProjectTagsStyleManager projectTagsStyleManager,
-                            LargeNumberOfChangesManager largeNumberOfChangesHandler) {
+                            LargeNumberOfChangesManager largeNumberOfChangesHandler, LoggedInUserProvider loggedInUserProvider) {
         this.projectId = projectId;
         this.view = view;
         this.busyView = busyView;
@@ -85,6 +89,7 @@ public ProjectPresenter(ProjectId projectId,
         this.eventBus = eventBus;
         this.projectTagsStyleManager = projectTagsStyleManager;
         this.largeNumberOfChangesHandler = largeNumberOfChangesHandler;
+        this.loggedInUserProvider = loggedInUserProvider;
     }
 
     @Nonnull
@@ -109,7 +114,11 @@ private void displayProject(@Nonnull AcceptsOneWidget container,
                                 @Nonnull ProjectViewPlace place) {
         dispatchServiceManager.execute(new LoadProjectAction(projectId),
                                        result -> handleProjectLoaded(container, eventBus, place));
-        subscribeToWebsocket(projectId.getId());
+        dispatchServiceManager.execute(new GetUserInfoAction(), r -> {
+            subscribeToWebsocket(projectId.getId(),  r.getToken(), this.loggedInUserProvider.getCurrentUserId().getUserName());
+
+        });
+
     }
 
     private void handleProjectLoaded(@Nonnull AcceptsOneWidget container, @Nonnull EventBus eventBus, @Nonnull ProjectViewPlace place) {
@@ -122,6 +131,7 @@ private void handleProjectLoaded(@Nonnull AcceptsOneWidget container, @Nonnull E
                                     projectId,
                                     largeNumberOfChangesHandler);
         container.setWidget(view);
+
         dispatchServiceManager.execute(GetProjectTagsAction.create(projectId),
                                        r -> projectTagsStyleManager.setProjectTags(r.getTags(), view));
         dispatchServiceManager.executeCurrentBatch();
@@ -147,7 +157,7 @@ public void dispatchEventsFromWebsocket(String data) {
 
     }
     /*TODO change the hardcoded broker URL and get it from a config class */
-    public native void subscribeToWebsocket(String projectId)/*-{
+    public native void subscribeToWebsocket(String projectId, String token, String userId)/*-{
         try {
             var that = this;
 
@@ -156,17 +166,22 @@ public native void subscribeToWebsocket(String projectId)/*-{
                 debug: function(str) {
                     console.log(str);
                 },
-                reconnectDelay: 5000,
+                reconnectDelay: 30000,
                 heartbeatIncoming: 4000,
                 heartbeatOutgoing: 4000,
             });
 
 
             stompClient.onConnect = function(frame) {
+                 var headers = {
+                    'token': token,
+                    'userId': userId,
+                    'Authorization' : 'Bearer ' + token
+                  };
                 stompClient.subscribe('/topic/project-events/' + projectId, function(message) {
                     that.@edu.stanford.bmir.protege.web.client.project.ProjectPresenter::dispatchEventsFromWebsocket(Ljava/lang/String;)(message.body);
 
-                });
+                }, headers);
             };
             stompClient.onWebSocketError = function(error) {
                 console.error('Error with websocket', error);

diff --git a/.../src/main/java/edu/stanford/bmir/protege/web/client/sharing/SharingSettingsPresenter.java b/.../src/main/java/edu/stanford/bmir/protege/web/client/sharing/SharingSettingsPresenter.java
@@ -13,6 +13,8 @@
 import edu.stanford.bmir.protege.web.client.permissions.PermissionManager;
 import edu.stanford.bmir.protege.web.client.progress.BusyView;
 import edu.stanford.bmir.protege.web.client.settings.SettingsPresenter;
+import edu.stanford.bmir.protege.web.client.uuid.UuidV4Provider;
+import edu.stanford.bmir.protege.web.shared.perspective.ChangeRequestId;
 import edu.stanford.bmir.protege.web.shared.project.ProjectId;
 import edu.stanford.bmir.protege.web.shared.sharing.GetProjectSharingSettingsAction;
 import edu.stanford.bmir.protege.web.shared.sharing.ProjectSharingSettings;
@@ -63,13 +65,17 @@ public class SharingSettingsPresenter implements Presenter {
     @Nonnull
     private final ProgressDisplay progressDisplay;
 
+    @Nonnull
+    private UuidV4Provider uuidV4Provider;
+
     @Inject
     public SharingSettingsPresenter(@Nonnull ProjectId projectId,
                                     @Nonnull SharingSettingsView view,
                                     @Nonnull BusyView busyView,
                                     @Nonnull DispatchServiceManager dispatchServiceManager,
                                     @Nonnull PermissionManager permissionManager,
                                     @Nonnull PermissionScreener permissionScreener,
+                                    @Nonnull UuidV4Provider uuidV4Provider,
                                     @Nonnull SettingsPresenter settingsPresenter,
                                     @Nonnull Messages messages, @Nonnull DispatchErrorMessageDisplay errorDisplay, @Nonnull ProgressDisplay progressDisplay) {
         this.projectId = checkNotNull(projectId);
@@ -81,6 +87,7 @@ public SharingSettingsPresenter(@Nonnull ProjectId projectId,
         this.settingsPresenter = checkNotNull(settingsPresenter);
         this.messages = checkNotNull(messages);
         this.errorDisplay = checkNotNull(errorDisplay);
+        this.uuidV4Provider = uuidV4Provider;
         this.progressDisplay = checkNotNull(progressDisplay);
     }
 
@@ -113,7 +120,7 @@ private void displaySharingSettings(AcceptsOneWidget container) {
     private void applyChangesAndGoToNextPlace() {
         settingsPresenter.goToNextPlace();
         ProjectSharingSettings settings = new ProjectSharingSettings(projectId, view.getLinkSharingPermission(), view.getSharingSettings());
-        dispatchServiceManager.execute(SetProjectSharingSettingsAction.create(settings), new DispatchServiceCallbackWithProgressDisplay<SetProjectSharingSettingsResult>(errorDisplay, progressDisplay) {
+        dispatchServiceManager.execute(SetProjectSharingSettingsAction.create(settings, ChangeRequestId.get(uuidV4Provider.get()), this.projectId), new DispatchServiceCallbackWithProgressDisplay<SetProjectSharingSettingsResult>(errorDisplay, progressDisplay) {
             @Override
             public void handleSuccess(SetProjectSharingSettingsResult result) {
                 permissionManager.firePermissionsChanged();

diff --git a/webprotege-gwt-ui-client/src/main/module-dev.gwt.xml b/webprotege-gwt-ui-client/src/main/module-dev.gwt.xml
@@ -45,6 +45,11 @@
 
     <set-property name="locale" value="en"/>
 
+<!--    <set-property name="webprotege.brokerUrl" value="ws://webprotege-local.edu/wsapps"/>
+    <set-property name="webprotege.reconnectDelay" value="5000"/>
+    <set-property name="webprotege.heartbeatIncoming" value="4000"/>
+    <set-property name="webprotege.heartbeatOutgoing" value="4000"/>-->
+
     <extend-configuration-property name="rpc.blacklist" value="+com.google.web.bindery.event.shared.Event"/>
 
     <entry-point class="edu.stanford.bmir.protege.web.client.WebProtege"/>

diff --git a/webprotege-gwt-ui-client/src/main/module.gwt.xml b/webprotege-gwt-ui-client/src/main/module.gwt.xml
@@ -49,6 +49,11 @@
     <extend-property name="locale" values="sl"/>
     <extend-property name="locale" values="pt"/>
 
+<!--    <set-property name="webprotege.brokerUrl" value="ws://webprotege-local.edu/wsapps"/>
+    <set-property name="webprotege.reconnectDelay" value="5000"/>
+    <set-property name="webprotege.heartbeatIncoming" value="4000"/>
+    <set-property name="webprotege.heartbeatOutgoing" value="4000"/>-->
+
     <extend-configuration-property name="rpc.blacklist" value="+com.google.web.bindery.event.shared.Event"/>
 
 	<entry-point class="edu.stanford.bmir.protege.web.client.WebProtege"/>

diff --git a/webprotege-gwt-ui-server-core/pom.xml b/webprotege-gwt-ui-server-core/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>webprotege-gwt-ui</artifactId>
         <groupId>edu.stanford.protege</groupId>
-        <version>5.0.5-WHO</version>
+        <version>5.0.6-WHO</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/.../java/edu/stanford/bmir/protege/web/server/dispatch/impl/DispatchServiceExecutorImpl.java b/.../java/edu/stanford/bmir/protege/web/server/dispatch/impl/DispatchServiceExecutorImpl.java
@@ -7,6 +7,8 @@
 import edu.stanford.bmir.protege.web.server.rpc.JsonRpcHttpRequestBuilder;
 import edu.stanford.bmir.protege.web.server.rpc.JsonRpcHttpResponseHandler;
 import edu.stanford.bmir.protege.web.shared.dispatch.*;
+import edu.stanford.bmir.protege.web.shared.dispatch.actions.GetUserInfoAction;
+import edu.stanford.bmir.protege.web.shared.dispatch.actions.GetUserInfoResult;
 import edu.stanford.bmir.protege.web.shared.dispatch.actions.TranslateEventListAction;
 import edu.stanford.bmir.protege.web.shared.event.GetProjectEventsResult;
 import edu.stanford.bmir.protege.web.shared.permissions.PermissionDeniedException;
@@ -59,6 +61,10 @@ public <A extends Action<R>, R extends Result> DispatchServiceResultContainer ex
                 GetProjectEventsResult result = objectMapper.readValue(translateEventsAction.getEventList(), GetProjectEventsResult.class);
                 return DispatchServiceResultContainer.create(result);
             }
+            if(action instanceof GetUserInfoAction) {
+                GetUserInfoResult result = GetUserInfoResult.create(executionContext.getToken());
+                return DispatchServiceResultContainer.create(result);
+            }
             var result = sendRequest(action, executionContext);
             return DispatchServiceResultContainer.create(result);
         }

diff --git a/...ord/bmir/protege/web/shared/sharing/SetProjectSharingSettings_Serialization_TestCase.java b/...ord/bmir/protege/web/shared/sharing/SetProjectSharingSettings_Serialization_TestCase.java
@@ -26,7 +26,7 @@ public void shouldSerializeAction() throws IOException {
                 Optional.of(SharingPermission.EDIT), ImmutableList.of(
                         new SharingSetting(PersonId.get("User"), SharingPermission.EDIT)
         )
-        ));
+        ), null, null);
         JsonSerializationTestUtil.testSerialization(action, Action.class);
     }
 

diff --git a/webprotege-gwt-ui-server/pom.xml b/webprotege-gwt-ui-server/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>edu.stanford.protege</groupId>
         <artifactId>webprotege-gwt-ui</artifactId>
-        <version>5.0.5-WHO</version>
+        <version>5.0.6-WHO</version>
     </parent>
 
     <artifactId>webprotege-gwt-ui-server</artifactId>

diff --git a/webprotege-gwt-ui-shared-core/pom.xml b/webprotege-gwt-ui-shared-core/pom.xml
@@ -5,7 +5,7 @@
     <parent>
         <artifactId>webprotege-gwt-ui</artifactId>
         <groupId>edu.stanford.protege</groupId>
-        <version>5.0.5-WHO</version>
+        <version>5.0.6-WHO</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

diff --git a/webprotege-gwt-ui-shared/pom.xml b/webprotege-gwt-ui-shared/pom.xml
@@ -6,7 +6,7 @@
     <parent>
         <groupId>edu.stanford.protege</groupId>
         <artifactId>webprotege-gwt-ui</artifactId>
-        <version>5.0.5-WHO</version>
+        <version>5.0.6-WHO</version>
     </parent>
 
     <artifactId>webprotege-gwt-ui-shared</artifactId>

diff --git a/...ege-gwt-ui-shared/src/main/java/edu/stanford/bmir/protege/web/shared/dispatch/Result.java b/...ege-gwt-ui-shared/src/main/java/edu/stanford/bmir/protege/web/shared/dispatch/Result.java
@@ -205,7 +205,8 @@
         @JsonSubTypes.Type(UpdateObjectPropertyFrameResult.class),
         @JsonSubTypes.Type(UpdateDataPropertyFrameResult.class),
         @JsonSubTypes.Type(UpdateAnnotationPropertyFrameResult.class),
-        @JsonSubTypes.Type(UpdateNamedIndividualFrameResult.class)
+        @JsonSubTypes.Type(UpdateNamedIndividualFrameResult.class),
+        @JsonSubTypes.Type(GetUserInfoResult.class)
 })
 @JsonTypeInfo(use = JsonTypeInfo.Id.NAME)
 public interface Result extends IsSerializable {

diff --git a/...t-ui-shared/src/main/java/edu/stanford/bmir/protege/web/shared/dispatch/RpcWhiteList.java b/...t-ui-shared/src/main/java/edu/stanford/bmir/protege/web/shared/dispatch/RpcWhiteList.java
@@ -978,6 +978,8 @@ public class RpcWhiteList implements IsSerializable, Action, Result {
 
     DropType _DropType;
 
+    GetUserInfoResult _GetUserInfoResult;
+
     public RpcWhiteList() {
     }
 }
diff --git a/...rc/main/java/edu/stanford/bmir/protege/web/shared/dispatch/actions/GetUserInfoAction.java b/...rc/main/java/edu/stanford/bmir/protege/web/shared/dispatch/actions/GetUserInfoAction.java
@@ -0,0 +1,11 @@
+package edu.stanford.bmir.protege.web.shared.dispatch.actions;
+
+import com.fasterxml.jackson.annotation.JsonTypeName;
+import com.google.gwt.user.client.rpc.IsSerializable;
+import edu.stanford.bmir.protege.web.shared.dispatch.Action;
+import java.io.Serializable;
+
+@JsonTypeName("webprotege.users.GetUserInfo")
+public class GetUserInfoAction implements Action<GetUserInfoResult>, Serializable, IsSerializable {
+
+}