Merge branch 'master' into master-who

.github/workflows/ci.yaml

@@ -3,7 +3,7 @@ name: Verify
 on:
   push:
     branches-ignore:
-      - main
+      - master
 
 jobs:
   build:

.github/workflows/release.yaml

@@ -3,8 +3,7 @@ name: Release
 on:
   push:
     branches:
-      - master
-      - main*
+      - master*
 
 jobs:
   build:

pom.xml

@@ -5,7 +5,7 @@
 
     <groupId>edu.stanford.protege</groupId>
     <artifactId>webprotege-gwt-ui</artifactId>
-    <version>5.0.9-WHO</version>
+    <version>5.0.13-WHO</version>
     <packaging>pom</packaging>
 
     <properties>

webprotege-gwt-ui-client/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>edu.stanford.protege</groupId>
         <artifactId>webprotege-gwt-ui</artifactId>
-        <version>5.0.9-WHO</version>
+        <version>5.0.13-WHO</version>
     </parent>
 
     <artifactId>webprotege-gwt-ui-client</artifactId>

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

@@ -2,6 +2,7 @@
 
 import com.google.gwt.core.client.GWT;
 import com.google.gwt.i18n.client.LocalizableResource.DefaultLocale;
+import org.checkerframework.checker.units.qual.K;
 
 /**
  * Matthew Horridge
@@ -231,4 +232,12 @@ public interface FormsMessages extends com.google.gwt.i18n.client.Messages {
     @DefaultMessage("Deprecate")
     @Key("deprecate")
     String deprecate();
+
+    @DefaultMessage("Import and replace forms?")
+    @Key("forms.import.confirmation.title")
+    String confirmImportFormsIntoProject_title();
+
+    @DefaultMessage("Do you really want to import and replace all of the forms in this project?  This cannot be undone.")
+    @Key("forms.import.confirmation.message")
+    String confirmImportFormsIntoProject_message();
 }

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

@@ -0,0 +1,41 @@
+package edu.stanford.bmir.protege.web.client.download;
+
+import javax.annotation.Nonnull;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 2024-06-14
+ */
+public class FetchAndOpenInBrowserWindow {
+
+    /**
+     * GET the specified path and open the result as a blob in a new window
+     * @param path The path
+     * @param token The access token to use.  This will be set in the authorization header.
+     */
+    public static native void fetchUrlAndOpenInWindow(@Nonnull String path,
+                                                      @Nonnull String token,
+                                                      @Nonnull FetchAndOpenInBrowserWindowErrorHandler errorHandler)/*-{
+        var xhr = new XMLHttpRequest();
+
+        xhr.open('GET', path);
+        xhr.onreadystatechange = handler;
+        xhr.responseType = 'blob';
+        xhr.setRequestHeader('Authorization', 'Bearer ' + token);
+        xhr.send();
+
+        function handler() {
+            if (this.readyState === this.DONE) {
+                if (this.status === 200) {
+                    // this.response is a Blob, because we set responseType above
+                    var data_url = URL.createObjectURL(this.response);
+                    $wnd.open(data_url, '_blank');
+                } else {
+                    console.error('Error');
+                    errorHandler.@edu.stanford.bmir.protege.web.client.download.FetchAndOpenInBrowserWindowErrorHandler::handleError(*)();
+                }
+            }
+        }
+    }-*/;
+}

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

@@ -0,0 +1,11 @@
+package edu.stanford.bmir.protege.web.client.download;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 2024-06-14
+ */
+public interface FetchAndOpenInBrowserWindowErrorHandler {
+
+    void handleError();
+}

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

@@ -1,7 +1,9 @@
 package edu.stanford.bmir.protege.web.client.form;
 
 import com.google.gwt.core.client.GWT;
-import com.google.gwt.user.client.Window;
+import edu.stanford.bmir.protege.web.client.dispatch.*;
+import edu.stanford.bmir.protege.web.client.download.FetchAndOpenInBrowserWindow;
+import edu.stanford.bmir.protege.web.shared.dispatch.actions.GetUserInfoAction;
 import edu.stanford.bmir.protege.web.shared.project.ProjectId;
 
 import javax.annotation.Nonnull;
@@ -19,14 +21,27 @@ public class FormsDownloader {
     @Nonnull
     private final ProjectId projectId;
 
+    private final DispatchServiceManager dispatch;
+
+    private final MessageBoxErrorDisplay errorDisplay;
+
     @Inject
-    public FormsDownloader(@Nonnull ProjectId projectId) {
+    public FormsDownloader(@Nonnull ProjectId projectId, DispatchServiceManager dispatch, MessageBoxErrorDisplay errorDisplay) {
         this.projectId = checkNotNull(projectId);
+        this.dispatch = checkNotNull(dispatch);
+        this.errorDisplay = checkNotNull(errorDisplay);
     }
 
     public void download() {
-        String baseURL = GWT.getHostPageBaseURL() + "data/";
-        String downloadURL = baseURL + "projects/" + projectId.getId() + "/forms";
-        Window.open(downloadURL, "Download forms", "");
+        dispatch.execute(new GetUserInfoAction(), result -> {
+            String baseURL = GWT.getHostPageBaseURL() + "data/";
+            String token = result.getToken();
+            FetchAndOpenInBrowserWindow.fetchUrlAndOpenInWindow("/data/projects/" + projectId.getId() + "/forms",
+                                                                token,
+                                                                () -> {
+                                                                    errorDisplay.displayGeneralErrorMessage("Download error",
+                                                                                                            "Could not download project forms");
+                                                                });
+        });
     }
 }

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

@@ -5,6 +5,7 @@
 import com.google.gwt.http.client.*;
 import edu.stanford.bmir.protege.web.client.dispatch.DispatchServiceManager;
 import edu.stanford.bmir.protege.web.client.progress.HasBusy;
+import edu.stanford.bmir.protege.web.shared.dispatch.actions.GetUserInfoAction;
 import edu.stanford.bmir.protege.web.shared.form.*;
 import edu.stanford.bmir.protege.web.shared.project.ProjectId;
 
@@ -67,32 +68,35 @@ public void importForms(@Nonnull String formJsonSerialization,
                             @Nonnull HasBusy busyIndicator,
                             @Nonnull Runnable completeHandler,
                             @Nonnull Runnable errorHandler) {
-        try {
-            String importFormsUrl = "/data/projects/" + projectId.getId() + "/forms";
-            RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.POST,
-                                                               importFormsUrl);
-            requestBuilder.setRequestData(formJsonSerialization);
-            requestBuilder.setCallback(new RequestCallback() {
-                @Override
-                public void onResponseReceived(Request request, Response response) {
-                    busyIndicator.setBusy(false);
-                    completeHandler.run();
-                    if(response.getStatusCode() != Response.SC_CREATED) {
-                        errorHandler.run();
+        dispatch.execute(new GetUserInfoAction(), userInfo -> {
+            try {
+                String importFormsUrl = "/data/projects/" + projectId.getId() + "/forms";
+                RequestBuilder requestBuilder = new RequestBuilder(RequestBuilder.POST,
+                                                                   importFormsUrl);
+                requestBuilder.setRequestData(formJsonSerialization);
+                requestBuilder.setHeader("Authorization", "Bearer " + userInfo.getToken());
+                requestBuilder.setCallback(new RequestCallback() {
+                    @Override
+                    public void onResponseReceived(Request request, Response response) {
+                        busyIndicator.setBusy(false);
+                        completeHandler.run();
+                        if(response.getStatusCode() >= 400) {
+                            errorHandler.run();
+                        }
                     }
-                }
 
-                @Override
-                public void onError(Request request, Throwable exception) {
-                    busyIndicator.setBusy(false);
-                    completeHandler.run();
-                }
-            });
-            requestBuilder.setHeader("Content-Type", "application/json");
-            busyIndicator.setBusy(true);
-            requestBuilder.send();
-        } catch (RequestException e) {
-            GWT.log(e.getMessage());
-        }
+                    @Override
+                    public void onError(Request request, Throwable exception) {
+                        busyIndicator.setBusy(false);
+                        completeHandler.run();
+                    }
+                });
+                requestBuilder.setHeader("Content-Type", "application/json");
+                busyIndicator.setBusy(true);
+                requestBuilder.send();
+            } catch (RequestException e) {
+                GWT.log(e.getMessage());
+            }
+        });
     }
 }

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

@@ -6,8 +6,8 @@
 import com.google.gwt.uibinder.client.UiField;
 import com.google.gwt.user.client.ui.*;
 import edu.stanford.bmir.protege.web.client.FormsMessages;
-import edu.stanford.bmir.protege.web.client.library.msgbox.InputBox;
-import edu.stanford.bmir.protege.web.client.library.msgbox.MessageBox;
+import edu.stanford.bmir.protege.web.client.library.dlg.DialogButton;
+import edu.stanford.bmir.protege.web.client.library.msgbox.*;
 
 import javax.annotation.Nonnull;
 import javax.inject.Inject;
@@ -81,6 +81,17 @@ public void clear() {
 
     @Override
     public void displayImportFormsInputBox(Consumer<String> importFormsJson) {
+        messageBox.showConfirmBox(MessageStyle.ALERT,
+                                  formsMessages.confirmImportFormsIntoProject_title(),
+                                  formsMessages.confirmImportFormsIntoProject_message(),
+                                  DialogButton.NO,
+                                  () -> {},
+                                  DialogButton.YES,
+                                  () -> displayInputBox(importFormsJson),
+                                  DialogButton.NO);
+    }
+
+    private void displayInputBox(Consumer<String> importFormsJson) {
         inputBox.showDialog(formsMessages.importFormsIntoProject_title(),
                             formsMessages.importFormsIntoProject_message(),
                             true, "", importFormsJson::accept);

webprotege-gwt-ui-server-core/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>webprotege-gwt-ui</artifactId>
         <groupId>edu.stanford.protege</groupId>
-        <version>5.0.9-WHO</version>
+        <version>5.0.13-WHO</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

webprotege-gwt-ui-server/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>edu.stanford.protege</groupId>
         <artifactId>webprotege-gwt-ui</artifactId>
-        <version>5.0.9-WHO</version>
+        <version>5.0.13-WHO</version>
     </parent>
 
     <artifactId>webprotege-gwt-ui-server</artifactId>

webprotege-gwt-ui-shared-core/pom.xml

@@ -5,7 +5,7 @@
     <parent>
         <artifactId>webprotege-gwt-ui</artifactId>
         <groupId>edu.stanford.protege</groupId>
-        <version>5.0.9-WHO</version>
+        <version>5.0.13-WHO</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
 

webprotege-gwt-ui-shared/pom.xml

@@ -6,7 +6,7 @@
     <parent>
         <groupId>edu.stanford.protege</groupId>
         <artifactId>webprotege-gwt-ui</artifactId>
-        <version>5.0.9-WHO</version>
+        <version>5.0.13-WHO</version>
     </parent>
 
     <artifactId>webprotege-gwt-ui-shared</artifactId>

webprotege-gwt-ui-shared/src/main/java/edu/stanford/bmir/protege/web/shared/dispatch/Action.java

@@ -209,6 +209,7 @@
         @Type(value = SetOntologyAnnotationsAction.class),
         @Type(value = SetPerspectiveLayoutAction.class),
         @Type(value = SetProjectFormDescriptorsAction.class),
+        @Type(value = SetProjectFormsAction.class),
         @Type(value = SetProjectPrefixDeclarationsAction.class),
         @Type(value = SetProjectSettingsAction.class),
         @Type(value = SetProjectSharingSettingsAction.class),

webprotege-gwt-ui-shared/src/main/java/edu/stanford/bmir/protege/web/shared/dispatch/Result.java

@@ -195,6 +195,7 @@
         @JsonSubTypes.Type(SetOntologyAnnotationsResult.class),
         @JsonSubTypes.Type(SetPerspectiveLayoutResult.class),
         @JsonSubTypes.Type(SetProjectFormDescriptorsResult.class),
+        @JsonSubTypes.Type(SetProjectFormsResult.class),
         @JsonSubTypes.Type(SetProjectPrefixDeclarationsResult.class),
         @JsonSubTypes.Type(SetProjectSettingsResult.class),
         @JsonSubTypes.Type(SetProjectSharingSettingsResult.class),

webprotege-gwt-ui-shared/src/main/java/edu/stanford/bmir/protege/web/shared/form/SetProjectFormsAction.java

@@ -0,0 +1,34 @@
+package edu.stanford.bmir.protege.web.shared.form;
+
+import com.fasterxml.jackson.annotation.JsonTypeName;
+import com.google.auto.value.AutoValue;
+import com.google.common.annotations.GwtCompatible;
+import com.google.common.collect.ImmutableList;
+import edu.stanford.bmir.protege.web.shared.dispatch.*;
+import edu.stanford.bmir.protege.web.shared.project.ProjectId;
+
+import javax.annotation.Nonnull;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 2024-06-15
+ */
+@JsonTypeName("webprotege.forms.SetProjectForms")
+@AutoValue
+@GwtCompatible(serializable = true)
+public abstract class SetProjectFormsAction implements ProjectAction<SetProjectFormsResult> {
+
+    public SetProjectFormsAction get(@Nonnull ProjectId projectId,
+                                     @Nonnull ImmutableList<FormDescriptor> formDescriptors,
+                                     @Nonnull ImmutableList<EntityFormSelector> formSelectors) {
+        return new AutoValue_SetProjectFormsAction(projectId, formDescriptors, formSelectors);
+    }
+
+    @Nonnull
+    public abstract ProjectId getProjectId();
+
+    public abstract ImmutableList<FormDescriptor> getFormDescriptors();
+
+    public abstract ImmutableList<EntityFormSelector> getFormSelectors();
+}

webprotege-gwt-ui-shared/src/main/java/edu/stanford/bmir/protege/web/shared/form/SetProjectFormsResult.java

@@ -0,0 +1,21 @@
+package edu.stanford.bmir.protege.web.shared.form;
+
+import com.fasterxml.jackson.annotation.JsonTypeName;
+import com.google.auto.value.AutoValue;
+import com.google.common.annotations.GwtCompatible;
+import edu.stanford.bmir.protege.web.shared.dispatch.Result;
+
+/**
+ * Matthew Horridge
+ * Stanford Center for Biomedical Informatics Research
+ * 2024-06-15
+ */
+@JsonTypeName("webprotege.forms.SetProjectForms")
+@AutoValue
+@GwtCompatible(serializable = true)
+public abstract class SetProjectFormsResult implements Result {
+
+    public static SetProjectFormsResult get() {
+        return new AutoValue_SetProjectFormsResult();
+    }
+}

webprotege-gwt-ui-shared/src/main/java/edu/stanford/bmir/protege/web/shared/form/data/EntityNameControlDataDto.java

@@ -20,7 +20,7 @@ public abstract class EntityNameControlDataDto implements FormControlDataDto {
 
     @JsonCreator
     public static EntityNameControlDataDto get(@JsonProperty("descriptor") @Nonnull EntityNameControlDescriptor descriptor,
-                                               @JsonProperty("entityData") @Nonnull OWLEntityData entityData,
+                                               @JsonProperty("entity") @Nonnull OWLEntityData entityData,
                                                @JsonProperty("depth") int depth) {
         return new AutoValue_EntityNameControlDataDto(depth, descriptor, entityData);
     }