From be328e8b800b8dfb2bc53594faff9e732d88e2d4 Mon Sep 17 00:00:00 2001
From: Richard Eckart de Castilho <richard.eckart@gmail.com>
Date: Mon, 26 Feb 2024 20:00:10 +0100
Subject: [PATCH 1/2] #4562 - Project template for named entity annotation

- Added new entity annotation template
- Still need to add original thumbnail image for this
---
 .../pom.xml                                   |   4 +
 .../EntityAnnotationProjectInitializer.java   | 113 ++++++++++++++++++
 .../EntityLinkingProjectInitializer.java      |   9 +-
 ...dentifierStringRecommenderInitializer.java |  11 +-
 ...uenceClassifierRecommenderInitializer.java |  95 +++++++++++++++
 ...medEntityStringRecommenderInitializer.java |  95 +++++++++++++++
 ...gProjectInitializersAutoConfiguration.java |  31 +++++
 .../wikidatalinking/wicket-package.properties |   1 +
 .../NamedEntityLayerInitializer.java          |   9 +-
 9 files changed, 350 insertions(+), 18 deletions(-)
 create mode 100644 inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.java
 create mode 100644 inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntitySequenceClassifierRecommenderInitializer.java
 create mode 100644 inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntityStringRecommenderInitializer.java

diff --git a/inception/inception-project-initializers-wikidatalinking/pom.xml b/inception/inception-project-initializers-wikidatalinking/pom.xml
index 5295034ae2b..0de82b02346 100644
--- a/inception/inception-project-initializers-wikidatalinking/pom.xml
+++ b/inception/inception-project-initializers-wikidatalinking/pom.xml
@@ -53,6 +53,10 @@
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-imls-stringmatch</artifactId>
     </dependency>
+    <dependency>
+      <groupId>de.tudarmstadt.ukp.inception.app</groupId>
+      <artifactId>inception-imls-opennlp</artifactId>
+    </dependency>
     <dependency>
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-kb</artifactId>
diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.java b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.java
new file mode 100644
index 00000000000..293b659db1d
--- /dev/null
+++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.java
@@ -0,0 +1,113 @@
+/*
+ * 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.initializers.wikidatalinking;
+
+import java.io.IOException;
+import java.lang.invoke.MethodHandles;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
+
+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.model.Project;
+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.project.api.ProjectInitializer;
+import de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking.config.WikiDataLinkingProjectInitializersAutoConfiguration;
+import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
+import de.tudarmstadt.ukp.inception.support.wicket.resource.Strings;
+
+/**
+ * <p>
+ * This class is exposed as a Spring Component via
+ * {@link WikiDataLinkingProjectInitializersAutoConfiguration#entityAnnotationProjectInitializer}.
+ * </p>
+ */
+@Order(5000)
+public class EntityAnnotationProjectInitializer
+    implements QuickProjectInitializer
+{
+    private static final PackageResourceReference THUMBNAIL = new PackageResourceReference(
+            MethodHandles.lookup().lookupClass(), "EntityLinkingProjectInitializer.svg");
+
+    private final AnnotationSchemaService annotationService;
+    private final ApplicationContext context;
+
+    public EntityAnnotationProjectInitializer(ApplicationContext aContext,
+            AnnotationSchemaService aAnnotationService)
+    {
+        context = aContext;
+        annotationService = aAnnotationService;
+    }
+
+    @Override
+    public String getName()
+    {
+        return "Entity annotation";
+    }
+
+    @Override
+    public Optional<String> getDescription()
+    {
+        return Optional.of(Strings.getString("entity-annotation-project.description"));
+    }
+
+    @Override
+    public Optional<ResourceReference> getThumbnail()
+    {
+        return Optional.of(THUMBNAIL);
+    }
+
+    @Override
+    public boolean alreadyApplied(Project aProject)
+    {
+        return false;
+    }
+
+    @Override
+    public List<Class<? extends ProjectInitializer>> getDependencies()
+    {
+        var dependencies = new ArrayList<Class<? extends ProjectInitializer>>();
+        dependencies.add(NamedEntityLayerInitializer.class);
+
+        if (context.getBeanNamesForType(NamedEntityStringRecommenderInitializer.class).length > 0) {
+            dependencies.add(NamedEntityStringRecommenderInitializer.class);
+        }
+
+        if (context.getBeanNamesForType(
+                NamedEntitySequenceClassifierRecommenderInitializer.class).length > 0) {
+            dependencies.add(NamedEntitySequenceClassifierRecommenderInitializer.class);
+        }
+
+        return dependencies;
+    }
+
+    @Override
+    public void configure(Project aProject) throws IOException
+    {
+        var layer = annotationService.findLayer(aProject, NamedEntity.class.getName());
+        var valueFeature = annotationService.getFeature(NamedEntity._FeatName_value, layer);
+        valueFeature.setEnabled(false);
+        annotationService.createFeature(valueFeature);
+    }
+}
diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityLinkingProjectInitializer.java b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityLinkingProjectInitializer.java
index ed11ca995a2..3fd72586f29 100644
--- a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityLinkingProjectInitializer.java
+++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityLinkingProjectInitializer.java
@@ -28,8 +28,6 @@
 import org.springframework.context.ApplicationContext;
 import org.springframework.core.annotation.Order;
 
-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.project.initializers.NamedEntityLayerInitializer;
 import de.tudarmstadt.ukp.clarin.webanno.project.initializers.QuickProjectInitializer;
@@ -90,7 +88,7 @@ public boolean alreadyApplied(Project aProject)
     @Override
     public List<Class<? extends ProjectInitializer>> getDependencies()
     {
-        List<Class<? extends ProjectInitializer>> dependencies = new ArrayList<>();
+        var dependencies = new ArrayList<Class<? extends ProjectInitializer>>();
         dependencies.add(NamedEntityLayerInitializer.class);
         dependencies.add(NamedEntityIdentifierFeatureInitializer.class);
         dependencies.add(WikiDataKnowledgeBaseInitializer.class);
@@ -106,9 +104,8 @@ public List<Class<? extends ProjectInitializer>> getDependencies()
     @Override
     public void configure(Project aProject) throws IOException
     {
-        AnnotationLayer layer = annotationService.findLayer(aProject, NamedEntity.class.getName());
-        AnnotationFeature valueFeature = annotationService.getFeature(NamedEntity._FeatName_value,
-                layer);
+        var layer = annotationService.findLayer(aProject, NamedEntity.class.getName());
+        var valueFeature = annotationService.getFeature(NamedEntity._FeatName_value, layer);
         valueFeature.setEnabled(false);
         annotationService.createFeature(valueFeature);
     }
diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntityIdentifierStringRecommenderInitializer.java b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntityIdentifierStringRecommenderInitializer.java
index c9eb9317185..c3fbbdcf4b8 100644
--- a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntityIdentifierStringRecommenderInitializer.java
+++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntityIdentifierStringRecommenderInitializer.java
@@ -22,8 +22,6 @@
 import java.io.IOException;
 import java.util.List;
 
-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.dkpro.core.api.ner.type.NamedEntity;
 import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer;
@@ -83,12 +81,11 @@ public List<Class<? extends ProjectInitializer>> getDependencies()
     @Override
     public void configure(Project aProject) throws IOException
     {
-        AnnotationLayer spanLayer = annotationService.findLayer(aProject,
-                NamedEntity.class.getName());
-        AnnotationFeature labelFeature = annotationService
-                .getFeature(NamedEntity._FeatName_identifier, spanLayer);
+        var spanLayer = annotationService.findLayer(aProject, NamedEntity.class.getName());
+        var labelFeature = annotationService.getFeature(NamedEntity._FeatName_identifier,
+                spanLayer);
 
-        Recommender recommender = new Recommender(getName(), spanLayer);
+        var recommender = new Recommender(getName(), spanLayer);
         recommender.setFeature(labelFeature);
         recommender.setMaxRecommendations(3);
         recommender.setThreshold(0.0d);
diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntitySequenceClassifierRecommenderInitializer.java b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntitySequenceClassifierRecommenderInitializer.java
new file mode 100644
index 00000000000..c202903e0ab
--- /dev/null
+++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntitySequenceClassifierRecommenderInitializer.java
@@ -0,0 +1,95 @@
+/*
+ * 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.initializers.wikidatalinking;
+
+import static java.util.Arrays.asList;
+
+import java.io.IOException;
+import java.util.List;
+
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity;
+import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer;
+import de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking.config.WikiDataLinkingProjectInitializersAutoConfiguration;
+import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.imls.opennlp.ner.OpenNlpNerRecommenderFactory;
+import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
+import de.tudarmstadt.ukp.inception.ui.kb.initializers.NamedEntityIdentifierFeatureInitializer;
+
+/**
+ * <p>
+ * This class is exposed as a Spring Component via
+ * {@link WikiDataLinkingProjectInitializersAutoConfiguration#namedEntitySequenceClassifierRecommenderInitializer}.
+ * </p>
+ */
+public class NamedEntitySequenceClassifierRecommenderInitializer
+    implements ProjectInitializer
+{
+    private final AnnotationSchemaService annotationService;
+    private final RecommendationService recommendationService;
+    private final OpenNlpNerRecommenderFactory recommenderFactory;
+
+    public NamedEntitySequenceClassifierRecommenderInitializer(
+            RecommendationService aRecommenderService, AnnotationSchemaService aAnnotationService,
+            OpenNlpNerRecommenderFactory aRecommenderFactory)
+    {
+        recommendationService = aRecommenderService;
+        annotationService = aAnnotationService;
+        recommenderFactory = aRecommenderFactory;
+    }
+
+    @Override
+    public String getName()
+    {
+        return "Named entity sequence classifier recommender";
+    }
+
+    @Override
+    public boolean applyByDefault()
+    {
+        return false;
+    }
+
+    @Override
+    public boolean alreadyApplied(Project aProject)
+    {
+        return recommendationService.existsRecommender(aProject, getName());
+    }
+
+    @Override
+    public List<Class<? extends ProjectInitializer>> getDependencies()
+    {
+        return asList(NamedEntityIdentifierFeatureInitializer.class);
+    }
+
+    @Override
+    public void configure(Project aProject) throws IOException
+    {
+        var spanLayer = annotationService.findLayer(aProject, NamedEntity.class.getName());
+        var labelFeature = annotationService.getFeature(NamedEntity._FeatName_value, spanLayer);
+
+        var recommender = new Recommender(getName(), spanLayer);
+        recommender.setFeature(labelFeature);
+        recommender.setMaxRecommendations(3);
+        recommender.setThreshold(0.0d);
+        recommender.setTool(recommenderFactory.getId());
+
+        recommendationService.createOrUpdateRecommender(recommender);
+    }
+}
diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntityStringRecommenderInitializer.java b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntityStringRecommenderInitializer.java
new file mode 100644
index 00000000000..9c042b68027
--- /dev/null
+++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/NamedEntityStringRecommenderInitializer.java
@@ -0,0 +1,95 @@
+/*
+ * 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.initializers.wikidatalinking;
+
+import static java.util.Arrays.asList;
+
+import java.io.IOException;
+import java.util.List;
+
+import de.tudarmstadt.ukp.clarin.webanno.model.Project;
+import de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity;
+import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer;
+import de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking.config.WikiDataLinkingProjectInitializersAutoConfiguration;
+import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
+import de.tudarmstadt.ukp.inception.recommendation.api.model.Recommender;
+import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.span.StringMatchingRecommenderFactory;
+import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
+import de.tudarmstadt.ukp.inception.ui.kb.initializers.NamedEntityIdentifierFeatureInitializer;
+
+/**
+ * <p>
+ * This class is exposed as a Spring Component via
+ * {@link WikiDataLinkingProjectInitializersAutoConfiguration#namedEntityStringRecommenderInitializer}.
+ * </p>
+ */
+public class NamedEntityStringRecommenderInitializer
+    implements ProjectInitializer
+{
+    private final AnnotationSchemaService annotationService;
+    private final RecommendationService recommendationService;
+    private final StringMatchingRecommenderFactory recommenderFactory;
+
+    public NamedEntityStringRecommenderInitializer(RecommendationService aRecommenderService,
+            AnnotationSchemaService aAnnotationService,
+            StringMatchingRecommenderFactory aRecommenderFactory)
+    {
+        recommendationService = aRecommenderService;
+        annotationService = aAnnotationService;
+        recommenderFactory = aRecommenderFactory;
+    }
+
+    @Override
+    public String getName()
+    {
+        return "Named entity string-matching recommender";
+    }
+
+    @Override
+    public boolean applyByDefault()
+    {
+        return false;
+    }
+
+    @Override
+    public boolean alreadyApplied(Project aProject)
+    {
+        return recommendationService.existsRecommender(aProject, getName());
+    }
+
+    @Override
+    public List<Class<? extends ProjectInitializer>> getDependencies()
+    {
+        return asList(NamedEntityIdentifierFeatureInitializer.class);
+    }
+
+    @Override
+    public void configure(Project aProject) throws IOException
+    {
+        var spanLayer = annotationService.findLayer(aProject, NamedEntity.class.getName());
+        var labelFeature = annotationService.getFeature(NamedEntity._FeatName_value, spanLayer);
+
+        var recommender = new Recommender(getName(), spanLayer);
+        recommender.setFeature(labelFeature);
+        recommender.setMaxRecommendations(3);
+        recommender.setThreshold(0.0d);
+        recommender.setTool(recommenderFactory.getId());
+
+        recommendationService.createOrUpdateRecommender(recommender);
+    }
+}
diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/config/WikiDataLinkingProjectInitializersAutoConfiguration.java b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/config/WikiDataLinkingProjectInitializersAutoConfiguration.java
index 6f0387fda1a..0e28888cbda 100644
--- a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/config/WikiDataLinkingProjectInitializersAutoConfiguration.java
+++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/config/WikiDataLinkingProjectInitializersAutoConfiguration.java
@@ -26,11 +26,15 @@
 import de.tudarmstadt.ukp.inception.kb.KnowledgeBaseService;
 import de.tudarmstadt.ukp.inception.kb.config.KnowledgeBaseProperties;
 import de.tudarmstadt.ukp.inception.kb.config.KnowledgeBaseServiceAutoConfiguration;
+import de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking.EntityAnnotationProjectInitializer;
 import de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking.EntityLinkingProjectInitializer;
 import de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking.NamedEntityIdentifierStringRecommenderInitializer;
+import de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking.NamedEntitySequenceClassifierRecommenderInitializer;
+import de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking.NamedEntityStringRecommenderInitializer;
 import de.tudarmstadt.ukp.inception.project.initializers.wikidatalinking.WikiDataKnowledgeBaseInitializer;
 import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
 import de.tudarmstadt.ukp.inception.recommendation.config.RecommenderServiceAutoConfiguration;
+import de.tudarmstadt.ukp.inception.recommendation.imls.opennlp.ner.OpenNlpNerRecommenderFactory;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.config.StringMatchingRecommenderAutoConfiguration;
 import de.tudarmstadt.ukp.inception.recommendation.imls.stringmatch.span.StringMatchingRecommenderFactory;
 import de.tudarmstadt.ukp.inception.schema.api.AnnotationSchemaService;
@@ -67,4 +71,31 @@ public EntityLinkingProjectInitializer entityLinkingProjectInitializer(
     {
         return new EntityLinkingProjectInitializer(aContext, aAnnotationService);
     }
+
+    @Bean
+    public EntityAnnotationProjectInitializer entityAnnotationProjectInitializer(
+            ApplicationContext aContext, AnnotationSchemaService aAnnotationService)
+    {
+        return new EntityAnnotationProjectInitializer(aContext, aAnnotationService);
+    }
+
+    @ConditionalOnBean(RecommendationService.class)
+    @Bean
+    public NamedEntityStringRecommenderInitializer namedEntityStringRecommenderInitializer(
+            RecommendationService aRecommenderService, AnnotationSchemaService aAnnotationService,
+            StringMatchingRecommenderFactory aRecommenderFactory)
+    {
+        return new NamedEntityStringRecommenderInitializer(aRecommenderService, aAnnotationService,
+                aRecommenderFactory);
+    }
+
+    @ConditionalOnBean(RecommendationService.class)
+    @Bean
+    public NamedEntitySequenceClassifierRecommenderInitializer namedEntitySequenceClassifierRecommenderInitializer(
+            RecommendationService aRecommenderService, AnnotationSchemaService aAnnotationService,
+            OpenNlpNerRecommenderFactory aRecommenderFactory)
+    {
+        return new NamedEntitySequenceClassifierRecommenderInitializer(aRecommenderService,
+                aAnnotationService, aRecommenderFactory);
+    }
 }
diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/wicket-package.properties b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/wicket-package.properties
index 68a66a82171..12490e75aa5 100644
--- a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/wicket-package.properties
+++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/wicket-package.properties
@@ -14,3 +14,4 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 entity-linking-project.description=Link entity mentions to WikiData.
+entity-annotation-project.description=Identify and classify named entities.
diff --git a/inception/inception-project-initializers/src/main/java/de/tudarmstadt/ukp/clarin/webanno/project/initializers/NamedEntityLayerInitializer.java b/inception/inception-project-initializers/src/main/java/de/tudarmstadt/ukp/clarin/webanno/project/initializers/NamedEntityLayerInitializer.java
index a9f7464db3a..7a773002f2c 100644
--- a/inception/inception-project-initializers/src/main/java/de/tudarmstadt/ukp/clarin/webanno/project/initializers/NamedEntityLayerInitializer.java
+++ b/inception/inception-project-initializers/src/main/java/de/tudarmstadt/ukp/clarin/webanno/project/initializers/NamedEntityLayerInitializer.java
@@ -35,7 +35,6 @@
 import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
 import de.tudarmstadt.ukp.clarin.webanno.model.OverlapMode;
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
-import de.tudarmstadt.ukp.clarin.webanno.model.TagSet;
 import de.tudarmstadt.ukp.clarin.webanno.project.initializers.config.ProjectInitializersAutoConfiguration;
 import de.tudarmstadt.ukp.dkpro.core.api.ner.type.NamedEntity;
 import de.tudarmstadt.ukp.inception.project.api.ProjectInitializer;
@@ -99,11 +98,11 @@ public boolean alreadyApplied(Project aProject)
     @Override
     public void configure(Project aProject) throws IOException
     {
-        TagSet nerTagSet = annotationSchemaService
-                .getTagSet(NamedEntityTagSetInitializer.TAG_SET_NAME, aProject);
+        var nerTagSet = annotationSchemaService.getTagSet(NamedEntityTagSetInitializer.TAG_SET_NAME,
+                aProject);
 
-        AnnotationLayer neLayer = new AnnotationLayer(NamedEntity.class.getName(), "Named entity",
-                SPAN_TYPE, aProject, true, AnchoringMode.TOKENS, OverlapMode.NO_OVERLAP);
+        var neLayer = new AnnotationLayer(NamedEntity.class.getName(), "Named entity", SPAN_TYPE,
+                aProject, true, AnchoringMode.TOKENS, OverlapMode.NO_OVERLAP);
         annotationSchemaService.createOrUpdateLayer(neLayer);
 
         annotationSchemaService.createFeature(new AnnotationFeature(aProject, neLayer, "value",

From 0dbaf39dc7512bf41fa0cecfd8c4f80993ae0a51 Mon Sep 17 00:00:00 2001
From: Richard Eckart de Castilho <richard.eckart@gmail.com>
Date: Thu, 29 Feb 2024 21:52:24 +0100
Subject: [PATCH 2/2] #4562 - Project template for named entity annotation

- Added thumbnail
---
 .../EntityAnnotationProjectInitializer.java   |    4 +-
 .../EntityAnnotationProjectInitializer.svg    | 1118 +++++++++++++++++
 2 files changed, 1120 insertions(+), 2 deletions(-)
 create mode 100644 inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.svg

diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.java b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.java
index 293b659db1d..3ea7c0004f4 100644
--- a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.java
+++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.java
@@ -43,12 +43,12 @@
  * {@link WikiDataLinkingProjectInitializersAutoConfiguration#entityAnnotationProjectInitializer}.
  * </p>
  */
-@Order(5000)
+@Order(4900)
 public class EntityAnnotationProjectInitializer
     implements QuickProjectInitializer
 {
     private static final PackageResourceReference THUMBNAIL = new PackageResourceReference(
-            MethodHandles.lookup().lookupClass(), "EntityLinkingProjectInitializer.svg");
+            MethodHandles.lookup().lookupClass(), "EntityAnnotationProjectInitializer.svg");
 
     private final AnnotationSchemaService annotationService;
     private final ApplicationContext context;
diff --git a/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.svg b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.svg
new file mode 100644
index 00000000000..bab7e22df4e
--- /dev/null
+++ b/inception/inception-project-initializers-wikidatalinking/src/main/java/de/tudarmstadt/ukp/inception/project/initializers/wikidatalinking/EntityAnnotationProjectInitializer.svg
@@ -0,0 +1,1118 @@
+<?xml version="1.0" encoding="UTF-8" standalone="no"?>
+<!--
+  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.
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