#4780 - Optionally include example documents in project templates

- Include example documents with the named entity annotation project template
inception-project · Apr 30, 2024 · 62a8214 · 62a8214
1 parent ac7910a
commit 62a8214
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diff --git a/...sing/src/main/java/de/tudarmstadt/ukp/inception/processing/curation/BulkCurationTask.java b/...sing/src/main/java/de/tudarmstadt/ukp/inception/processing/curation/BulkCurationTask.java
@@ -121,7 +121,7 @@ public void execute() throws IOException, UIMAException
                 // deleting the users annotations!!!), currently fixed by warn message to user
                 // prepare merged CAS
                 curationMergeService.mergeCasses(doc, targetUser, targetCas, annotatorCasses,
-                        mergeStrategy, annotationLayers);
+                        mergeStrategy, annotationLayers, true);
 
                 var targetAnnDoc = documentService.createOrGetAnnotationDocument(doc, targetUser);
                 documentService.writeAnnotationCas(targetCas, targetAnnDoc,

diff --git a/.../src/main/java/de/tudarmstadt/ukp/inception/project/api/ProjectInitializationRequest.java b/.../src/main/java/de/tudarmstadt/ukp/inception/project/api/ProjectInitializationRequest.java
@@ -0,0 +1,78 @@
+/*
+ * Licensed to the Technische Universität Darmstadt under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The Technische Universität Darmstadt 
+ * licenses this file to you under the Apache License, Version 2.0 (the
+ * "License"); you may not use this file except in compliance
+ * with the License.
+ *  
+ * http://www.apache.org/licenses/LICENSE-2.0
+ * 
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package de.tudarmstadt.ukp.inception.project.api;
+
+import java.util.Objects;
+
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+
+public class ProjectInitializationRequest
+{
+    private final Project project;
+    private final boolean includeSampleData;
+
+    private ProjectInitializationRequest(Builder builder)
+    {
+        project = builder.project;
+        includeSampleData = builder.includeSampleData;
+    }
+
+    public static Builder builder()
+    {
+        return new Builder();
+    }
+
+    public Project getProject()
+    {
+        return project;
+    }
+
+    public boolean isIncludeSampleData()
+    {
+        return includeSampleData;
+    }
+
+    public static final class Builder
+    {
+        private Project project;
+        private boolean includeSampleData;
+
+        private Builder()
+        {
+        }
+
+        public Builder withProject(Project aProject)
+        {
+            project = aProject;
+            return this;
+        }
+
+        public Builder withIncludeSampleData(boolean aIncludeSampleData)
+        {
+            includeSampleData = aIncludeSampleData;
+            return this;
+        }
+
+        public ProjectInitializationRequest build()
+        {
+            Objects.requireNonNull(project, "Parameter [project] must be specified.");
+
+            return new ProjectInitializationRequest(this);
+        }
+    }
+}
diff --git a/...roject-api/src/main/java/de/tudarmstadt/ukp/inception/project/api/ProjectInitializer.java b/...roject-api/src/main/java/de/tudarmstadt/ukp/inception/project/api/ProjectInitializer.java
@@ -35,5 +35,21 @@ default boolean applyByDefault()
 
     List<Class<? extends ProjectInitializer>> getDependencies();
 
-    void configure(Project aProject) throws IOException;
+    default void configure(ProjectInitializationRequest aRequest) throws IOException
+    {
+        configure(aRequest.getProject());
+    }
+
+    /**
+     * @param aProject
+     *            the project to initialize.
+     * @throws IOException
+     *             if there is a problem.
+     * @deprecated Implement {@link #configure(ProjectInitializationRequest)} instead.
+     */
+    @Deprecated
+    default void configure(Project aProject) throws IOException
+    {
+        // Do nothing
+    }
 }
diff --git a/...on-project-api/src/main/java/de/tudarmstadt/ukp/inception/project/api/ProjectService.java b/...on-project-api/src/main/java/de/tudarmstadt/ukp/inception/project/api/ProjectService.java
@@ -568,16 +568,30 @@ boolean hasRole(String aUser, Project aProject, PermissionLevel aRole,
      * Initialize the project with default {@link AnnotationLayer}, {@link TagSet}s, and {@link Tag}
      * s. This is done per Project.
      * 
-     * @param aProject
-     *            the project.
+     * @param aRequest
+     *            the project initialization request.
      * @throws IOException
      *             if an I/O error occurs.
      */
-    void initializeProject(Project aProject) throws IOException;
+    void initializeProject(ProjectInitializationRequest aRequest) throws IOException;
 
-    void initializeProject(Project aProject, List<ProjectInitializer> aInitializers)
+    void initializeProject(ProjectInitializationRequest aRequest,
+            List<ProjectInitializer> aInitializers)
         throws IOException;
 
+    default void initializeProject(Project aProject) throws IOException
+    {
+        var request = ProjectInitializationRequest.builder().withProject(aProject).build();
+        initializeProject(request);
+    }
+
+    default void initializeProject(Project aProject, List<ProjectInitializer> aInitializers)
+        throws IOException
+    {
+        var request = ProjectInitializationRequest.builder().withProject(aProject).build();
+        initializeProject(request, aInitializers);
+    }
+
     List<ProjectInitializer> listProjectInitializers();
 
     static MDCContext withProjectLogger(Project aProject)

diff --git a/...java/de/tudarmstadt/ukp/inception/project/initializers/basic/BasicProjectInitializer.java b/...java/de/tudarmstadt/ukp/inception/project/initializers/basic/BasicProjectInitializer.java
@@ -30,6 +30,7 @@
 
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
 import de.tudarmstadt.ukp.clarin.webanno.project.initializers.QuickProjectInitializer;
+import de.tudarmstadt.ukp.inception.project.api.ProjectInitializationRequest;
 import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer;
 import de.tudarmstadt.ukp.inception.project.initializers.basic.config.InceptionBasicProjectInitializersAutoConfiguration;
 
@@ -96,7 +97,7 @@ public List<Class<? extends ProjectInitializer>> getDependencies()
     }
 
     @Override
-    public void configure(Project aProject) throws IOException
+    public void configure(ProjectInitializationRequest aRequest) throws IOException
     {
         // Nothing to do - all initialization is already done by the dependencies
     }

diff --git a/...dt/ukp/inception/project/initializers/doclabeling/BasicDocumentLabelLayerInitializer.java b/...dt/ukp/inception/project/initializers/doclabeling/BasicDocumentLabelLayerInitializer.java
@@ -35,8 +35,8 @@
 import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
 import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
-import de.tudarmstadt.ukp.clarin.webanno.model.TagSet;
 import de.tudarmstadt.ukp.clarin.webanno.project.initializers.LayerInitializer;
+import de.tudarmstadt.ukp.inception.project.api.ProjectInitializationRequest;
 import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer;
 import de.tudarmstadt.ukp.inception.project.initializers.doclabeling.config.InceptionDocumentLabelingProjectInitializersAutoConfiguration;
 import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
@@ -109,21 +109,22 @@ public List<Class<? extends ProjectInitializer>> getDependencies()
     }
 
     @Override
-    public void configure(Project aProject) throws IOException
+    public void configure(ProjectInitializationRequest aRequest) throws IOException
     {
-        AnnotationLayer docTagLayer = new AnnotationLayer(BASIC_DOCUMENT_LABEL_LAYER_NAME,
-                "Document Label", DocumentMetadataLayerSupport.TYPE, aProject, false, TOKENS,
-                ANY_OVERLAP);
+        var project = aRequest.getProject();
+
+        var docTagLayer = new AnnotationLayer(BASIC_DOCUMENT_LABEL_LAYER_NAME, "Document Label",
+                DocumentMetadataLayerSupport.TYPE, project, false, TOKENS, ANY_OVERLAP);
         var traits = docLayerSupport.readTraits(docTagLayer);
         traits.setSingleton(true);
         docLayerSupport.writeTraits(docTagLayer, traits);
         annotationSchemaService.createOrUpdateLayer(docTagLayer);
 
-        TagSet docLabelTagSet = annotationSchemaService.getTagSet(
-                BasicDocumentLabelTagSetInitializer.BASIC_DOCUMENT_LABEL_TAG_SET_NAME, aProject);
+        var docLabelTagSet = annotationSchemaService.getTagSet(
+                BasicDocumentLabelTagSetInitializer.BASIC_DOCUMENT_LABEL_TAG_SET_NAME, project);
 
-        annotationSchemaService.createFeature(new AnnotationFeature(aProject, docTagLayer,
-                BASIC_DOCUMENT_LABEL_LABEL_FEATURE_NAME, "Label", CAS.TYPE_NAME_STRING,
-                "Document label", docLabelTagSet));
+        annotationSchemaService.createFeature(
+                new AnnotationFeature(project, docTagLayer, BASIC_DOCUMENT_LABEL_LABEL_FEATURE_NAME,
+                        "Label", CAS.TYPE_NAME_STRING, "Document label", docLabelTagSet));
     }
 }
diff --git a/...t/ukp/inception/project/initializers/doclabeling/BasicDocumentLabelTagSetInitializer.java b/...t/ukp/inception/project/initializers/doclabeling/BasicDocumentLabelTagSetInitializer.java
@@ -27,6 +27,7 @@
 import de.tudarmstadt.ukp.clarin.webanno.model.Tag;
 import de.tudarmstadt.ukp.clarin.webanno.model.TagSet;
 import de.tudarmstadt.ukp.clarin.webanno.project.initializers.TagSetInitializer;
+import de.tudarmstadt.ukp.inception.project.api.ProjectInitializationRequest;
 import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer;
 import de.tudarmstadt.ukp.inception.project.initializers.doclabeling.config.InceptionDocumentLabelingProjectInitializersAutoConfiguration;
 import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
@@ -75,18 +76,20 @@ public boolean alreadyApplied(Project aProject)
     }
 
     @Override
-    public void configure(Project aProject) throws IOException
+    public void configure(ProjectInitializationRequest aRequest) throws IOException
     {
-        TagSet tagSet = new TagSet();
-        tagSet.setProject(aProject);
+        var project = aRequest.getProject();
+
+        var tagSet = new TagSet();
+        tagSet.setProject(project);
         tagSet.setName(getName());
         tagSet.setDescription("Document labels");
         tagSet.setLanguage("en");
         tagSet.setCreateTag(false);
 
         annotationSchemaService.createTagSet(tagSet);
 
-        Tag[] tags = new Tag[3];
+        var tags = new Tag[3];
         for (int i = 0; i < tags.length; i++) {
             tags[i] = new Tag(tagSet, "Label " + (i + 1));
         }

diff --git a/...p/inception/project/initializers/doclabeling/BasicDocumentLabelingProjectInitializer.java b/...p/inception/project/initializers/doclabeling/BasicDocumentLabelingProjectInitializer.java
@@ -32,16 +32,14 @@
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
 import de.tudarmstadt.ukp.clarin.webanno.project.initializers.QuickProjectInitializer;
 import de.tudarmstadt.ukp.clarin.webanno.project.initializers.TokenLayerInitializer;
-import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.sidebar.AnnotationSidebarState;
 import de.tudarmstadt.ukp.inception.preferences.PreferencesService;
+import de.tudarmstadt.ukp.inception.project.api.ProjectInitializationRequest;
 import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer;
 import de.tudarmstadt.ukp.inception.project.initializers.doclabeling.config.InceptionDocumentLabelingProjectInitializersAutoConfiguration;
 import de.tudarmstadt.ukp.inception.support.wicket.resource.Strings;
 import de.tudarmstadt.ukp.inception.ui.core.docanno.sidebar.DocumentMetadataSidebarFactory;
 import de.tudarmstadt.ukp.inception.workload.matrix.MatrixWorkloadExtension;
-import de.tudarmstadt.ukp.inception.workload.matrix.trait.MatrixWorkloadTraits;
 import de.tudarmstadt.ukp.inception.workload.model.WorkloadManagementService;
-import de.tudarmstadt.ukp.inception.workload.model.WorkloadManager;
 
 /**
  * <p>
@@ -106,9 +104,10 @@ public List<Class<? extends ProjectInitializer>> getDependencies()
     }
 
     @Override
-    public void configure(Project aProject) throws IOException
+    public void configure(ProjectInitializationRequest aRequest) throws IOException
     {
-        aProject.setDescription(String.join("\n",
+        var project = aRequest.getProject();
+        project.setDescription(String.join("\n",
                 // Empty line to avoid the this text showing up in the short description of the
                 // project overview
                 "", //
@@ -124,17 +123,15 @@ public void configure(Project aProject) throws IOException
                 "this projects and annotators may also re-open a document for annotation if they", //
                 "want. You can change this setting in the settings on the **Montoring** page."));
 
-        AnnotationSidebarState sidebarState = prefService
-                .loadDefaultTraitsForProject(KEY_SIDEBAR_STATE, aProject);
+        var sidebarState = prefService.loadDefaultTraitsForProject(KEY_SIDEBAR_STATE, project);
         sidebarState.setExpanded(true);
         sidebarState.setSelectedTab(docMetaSidebar.getBeanName());
-        prefService.saveDefaultTraitsForProject(KEY_SIDEBAR_STATE, aProject, sidebarState);
+        prefService.saveDefaultTraitsForProject(KEY_SIDEBAR_STATE, project, sidebarState);
 
-        WorkloadManager manager = workloadManagementService
-                .loadOrCreateWorkloadManagerConfiguration(aProject);
-        MatrixWorkloadTraits traits = matrixWorkloadExtension.readTraits(manager);
+        var manager = workloadManagementService.loadOrCreateWorkloadManagerConfiguration(project);
+        var traits = matrixWorkloadExtension.readTraits(manager);
         traits.setReopenableByAnnotator(true);
-        matrixWorkloadExtension.writeTraits(traits, aProject);
+        matrixWorkloadExtension.writeTraits(traits, project);
         workloadManagementService.saveConfiguration(manager);
     }
 }
diff --git a/inception/inception-project-initializers-wikidatalinking/pom.xml b/inception/inception-project-initializers-wikidatalinking/pom.xml
@@ -69,6 +69,10 @@
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-recommendation-api</artifactId>
     </dependency>
+    <dependency>
+      <groupId>de.tudarmstadt.ukp.inception.app</groupId>
+      <artifactId>inception-io-json</artifactId>
+    </dependency>
 
     <dependency>
       <groupId>org.apache.wicket</groupId>

diff --git a/...g/EntityAnnotationProjectInitializer.java → ...n/EntityAnnotationProjectInitializer.java b/...g/EntityAnnotationProjectInitializer.java → ...n/EntityAnnotationProjectInitializer.java
@@ -15,23 +15,28 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking;
+package de.tudarmstadt.ukp.inception.project.initializers.neannotation;
 
 import java.io.IOException;
 import java.lang.invoke.MethodHandles;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;
 
+import org.apache.uima.UIMAException;
 import org.apache.wicket.request.resource.PackageResourceReference;
 import org.apache.wicket.request.resource.ResourceReference;
 import org.springframework.context.ApplicationContext;
 import org.springframework.core.annotation.Order;
 
+import de.tudarmstadt.ukp.clarin.webanno.api.export.DocumentImportExportService;
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
 import de.tudarmstadt.ukp.clarin.webanno.project.initializers.NamedEntityLayerInitializer;
 import de.tudarmstadt.ukp.clarin.webanno.project.initializers.QuickProjectInitializer;
 import de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity;
+import de.tudarmstadt.ukp.inception.documents.api.DocumentService;
+import de.tudarmstadt.ukp.inception.io.jsoncas.UimaJsonCasFormatSupport;
 import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer;
 import de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking.config.WikiDataLinkingProjectInitializersAutoConfiguration;
 import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
@@ -52,12 +57,17 @@ public class EntityAnnotationProjectInitializer
 
     private final AnnotationSchemaService annotationService;
     private final ApplicationContext context;
+    private final DocumentImportExportService documentImportExportService;
+    private final DocumentService documentService;
 
     public EntityAnnotationProjectInitializer(ApplicationContext aContext,
-            AnnotationSchemaService aAnnotationService)
+            AnnotationSchemaService aAnnotationService, DocumentService aDocumentService,
+            DocumentImportExportService aDocumentImportExportService)
     {
         context = aContext;
         annotationService = aAnnotationService;
+        documentService = aDocumentService;
+        documentImportExportService = aDocumentImportExportService;
     }
 
     @Override
@@ -106,8 +116,28 @@ public List<Class<? extends ProjectInitializer>> getDependencies()
     public void configure(Project aProject) throws IOException
     {
         var layer = annotationService.findLayer(aProject, NamedEntity.class.getName());
-        var valueFeature = annotationService.getFeature(NamedEntity._FeatName_value, layer);
+        var valueFeature = annotationService.getFeature(NamedEntity._FeatName_identifier, layer);
         valueFeature.setEnabled(false);
         annotationService.createFeature(valueFeature);
+
+        importExampleDocument(aProject,
+                "foodista_blog_2019_08_13_northern-british-columbia_abbreviated.json");
+        importExampleDocument(aProject,
+                "foodista_blog_2019_10_22_lewiston-clarkstons-new-wine-district_abbreviated.json");
+    }
+
+    private void importExampleDocument(Project aProject, String docName) throws IOException
+    {
+        var doc = SourceDocument.builder() //
+                .withProject(aProject) //
+                .withName(docName) //
+                .withFormat(UimaJsonCasFormatSupport.ID) //
+                .build();
+        try (var is = getClass().getResourceAsStream("data/" + docName)) {
+            documentService.uploadSourceDocument(is, doc);
+        }
+        catch (UIMAException e) {
+            throw new IOException(e);
+        }
     }
 }
diff --git a/...ng/EntityAnnotationProjectInitializer.svg → ...on/EntityAnnotationProjectInitializer.svg b/...ng/EntityAnnotationProjectInitializer.svg → ...on/EntityAnnotationProjectInitializer.svg
diff --git a/...enceClassifierRecommenderInitializer.java → ...enceClassifierRecommenderInitializer.java b/...enceClassifierRecommenderInitializer.java → ...enceClassifierRecommenderInitializer.java
@@ -15,7 +15,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking;
+package de.tudarmstadt.ukp.inception.project.initializers.neannotation;
 
 import static java.util.Arrays.asList;
 

diff --git a/...edEntityStringRecommenderInitializer.java → ...edEntityStringRecommenderInitializer.java b/...edEntityStringRecommenderInitializer.java → ...edEntityStringRecommenderInitializer.java
@@ -15,7 +15,7 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking;
+package de.tudarmstadt.ukp.inception.project.initializers.neannotation;
 
 import static java.util.Arrays.asList;