Merge branch 'main' into refactoring/Upgrade-to-Spring-Boot-3

* main: (110 commits)
  #4787 - When re-merging a document CASMetadata is not retained
  #4785 - Upgrade dependencies
  [maven-release-plugin] prepare for next development iteration
  [maven-release-plugin] prepare release inception-33.0-beta-1
  #4768 - Bulk curation
  [maven-release-plugin] prepare for next development iteration
  [maven-release-plugin] prepare release inception-33.0-beta-1
  [maven-release-plugin] prepare for next development iteration
  [maven-release-plugin] prepare release inception-32.1
  #4782 - Avoid duplicate key error when importing documents very rapidly
  #4780 - Optionally include example documents in project templates
  #4778 - Links and other active elements in PDFs interfere with annotation and should be disabled
  #4739 - Auto-merge on open document in curation mode
  #4774 - Ability to not reset curation when performing a manual merge (sidebar curation)
  #4772 - Repair to trim whitespace off annotations
  #4769 - Cannot export CAS RDF
  #4768 - Bulk curation
  #4766 - Add ID column to documents table in dev mode
  #4764 - No longer force-enable server-side timings when dev mode is disabled
  #4762 - Re-merging via the curation sidebar always uses the project settings instead of the dialog settings
  ...

% Conflicts:
%	inception/inception-dependencies/pom.xml
%	inception/inception-diam-editor/pom.xml
%	inception/inception-diam-editor/src/main/java/de/tudarmstadt/ukp/inception/diam/sidebar/DiamAnnotationBrowser.java
%	inception/inception-external-editor/src/main/java/de/tudarmstadt/ukp/inception/externaleditor/ExternalAnnotationEditorBase.java
%	inception/inception-remote/src/main/java/de/tudarmstadt/ukp/clarin/webanno/webapp/remoteapi/config/RemoteApiAutoConfiguration.java
%	inception/inception-search-core/src/main/java/de/tudarmstadt/ukp/inception/search/SearchServiceImpl.java
%	inception/inception-sharing/src/main/java/de/tudarmstadt/ukp/inception/sharing/config/InviteServiceAutoConfiguration.java
%	inception/inception-ui-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/annotation/detail/AnnotationDetailEditorPanel.java
%	inception/inception-ui-core/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/core/login/LoginPage.java
%	inception/inception-ui-curation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/ui/curation/config/CurationUIAutoConfiguration.java
%	inception/inception-ui-curation/src/main/java/de/tudarmstadt/ukp/inception/ui/curation/sidebar/config/CurationSidebarAutoConfiguration.java
%	inception/inception-ui-dashboard-activity/pom.xml
%	inception/inception-ui-kb/pom.xml
%	inception/inception-workload-dynamic/src/main/java/de/tudarmstadt/ukp/inception/workload/dynamic/annotation/DynamicWorkflowDocumentNavigationActionBarExtension.java
%	pom.xml

inception/inception-active-learning/pom.xml

@@ -20,7 +20,7 @@
   <parent>
     <groupId>de.tudarmstadt.ukp.inception.app</groupId>
     <artifactId>inception-app</artifactId>
-    <version>32.0-SNAPSHOT</version>
+    <version>33.0-SNAPSHOT</version>
     <relativePath>..</relativePath>
   </parent>
   <artifactId>inception-active-learning</artifactId>

inception/inception-active-learning/src/main/java/de/tudarmstadt/ukp/inception/active/learning/ActiveLearningServiceImpl.java

@@ -17,6 +17,7 @@
  */
 package de.tudarmstadt.ukp.inception.active.learning;
 
+import static de.tudarmstadt.ukp.clarin.webanno.model.AnnotationDocumentStateChangeFlag.EXPLICIT_ANNOTATOR_USER_ACTION;
 import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordChangeLocation.AL_SIDEBAR;
 import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordUserAction.ACCEPTED;
 import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordUserAction.CORRECTED;
@@ -224,7 +225,8 @@ public void acceptSpanSuggestion(SourceDocument aDocument, User aDataOwner,
         }
 
         // Save CAS after annotation has been created
-        documentService.writeAnnotationCas(cas, aDocument, aDataOwner, true);
+        documentService.writeAnnotationCas(cas, aDocument, aDataOwner,
+                EXPLICIT_ANNOTATOR_USER_ACTION);
 
         // Send an application event indicating if the user has accepted/skipped/corrected/rejected
         // the suggestion

inception/inception-active-learning/src/main/java/de/tudarmstadt/ukp/inception/active/learning/log/ActiveLearningRecommendationEventAdapter.java

@@ -38,9 +38,9 @@ public class ActiveLearningRecommendationEventAdapter
     implements EventLoggingAdapter<ActiveLearningRecommendationEvent>
 {
     @Override
-    public boolean accepts(Object aEvent)
+    public boolean accepts(Class<?> aEvent)
     {
-        return aEvent instanceof ActiveLearningRecommendationEvent;
+        return ActiveLearningRecommendationEvent.class.isAssignableFrom(aEvent);
     }
 
     @Override

inception/inception-active-learning/src/main/java/de/tudarmstadt/ukp/inception/active/learning/log/ActiveLearningSuggestionOfferedAdapter.java

@@ -22,7 +22,6 @@
 import java.util.stream.Collectors;
 
 import de.tudarmstadt.ukp.inception.active.learning.config.ActiveLearningAutoConfiguration;
-import de.tudarmstadt.ukp.inception.active.learning.event.ActiveLearningRecommendationEvent;
 import de.tudarmstadt.ukp.inception.active.learning.event.ActiveLearningSuggestionOfferedEvent;
 import de.tudarmstadt.ukp.inception.log.adapter.EventLoggingAdapter;
 import de.tudarmstadt.ukp.inception.log.model.AnnotationDetails;
@@ -39,9 +38,9 @@ public class ActiveLearningSuggestionOfferedAdapter
     implements EventLoggingAdapter<ActiveLearningSuggestionOfferedEvent>
 {
     @Override
-    public boolean accepts(Object aEvent)
+    public boolean accepts(Class<?> aEvent)
     {
-        return aEvent instanceof ActiveLearningRecommendationEvent;
+        return ActiveLearningSuggestionOfferedEvent.class.isAssignableFrom(aEvent);
     }
 
     @Override

inception/inception-agreement/pom.xml

@@ -20,16 +20,25 @@
   <parent>
     <groupId>de.tudarmstadt.ukp.inception.app</groupId>
     <artifactId>inception-app</artifactId>
-    <version>32.0-SNAPSHOT</version>
+    <version>33.0-SNAPSHOT</version>
   </parent>
+
   <artifactId>inception-agreement</artifactId>
   <name>INCEpTION - Core - Agreement</name>
-  <packaging>jar</packaging>
+
   <dependencies>
     <dependency>
       <groupId>org.apache.commons</groupId>
       <artifactId>commons-lang3</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-collections4</artifactId>
+    </dependency>
+    <dependency>
+      <groupId>org.apache.commons</groupId>
+      <artifactId>commons-math3</artifactId>
+    </dependency>
 
     <dependency>
       <groupId>org.apache.uima</groupId>
@@ -94,15 +103,6 @@
       <artifactId>dkpro-statistics-agreement</artifactId>
     </dependency>
 
-    <dependency>
-      <groupId>org.apache.commons</groupId>
-      <artifactId>commons-csv</artifactId>
-    </dependency>
-    <dependency>
-      <groupId>commons-io</groupId>
-      <artifactId>commons-io</artifactId>
-    </dependency>
-
     <!-- Spring dependencies -->
     <dependency>
       <groupId>org.springframework</groupId>

inception/inception-agreement/src/main/java/de/tudarmstadt/ukp/clarin/webanno/agreement/measures/krippendorffalphaunitizing/KrippendorffAlphaUnitizingAgreementTraits.java → inception/inception-agreement/src/main/java/de/tudarmstadt/ukp/clarin/webanno/agreement/AgreementResult_ImplBase.java

@@ -15,24 +15,34 @@
  * See the License for the specific language governing permissions and
  * limitations under the License.
  */
-package de.tudarmstadt.ukp.clarin.webanno.agreement.measures.krippendorffalphaunitizing;
+package de.tudarmstadt.ukp.clarin.webanno.agreement;
+
+import java.io.Serializable;
 
 import de.tudarmstadt.ukp.clarin.webanno.agreement.measures.DefaultAgreementTraits;
+import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
 
-public class KrippendorffAlphaUnitizingAgreementTraits
-    extends DefaultAgreementTraits
+public class AgreementResult_ImplBase
+    implements Serializable
 {
-    private static final long serialVersionUID = -3843837791046164173L;
+    private static final long serialVersionUID = -342895455350245379L;
+
+    private final AnnotationFeature feature;
+    private final DefaultAgreementTraits traits;
 
-    private boolean excludeIncomplete;
+    public AgreementResult_ImplBase(AnnotationFeature aFeature, DefaultAgreementTraits aTraits)
+    {
+        feature = aFeature;
+        traits = aTraits;
+    }
 
-    public boolean isExcludeIncomplete()
+    public AnnotationFeature getFeature()
     {
-        return excludeIncomplete;
+        return feature;
     }
 
-    public void setExcludeIncomplete(boolean aExcludeIncomplete)
+    public DefaultAgreementTraits getTraits()
     {
-        excludeIncomplete = aExcludeIncomplete;
+        return traits;
     }
 }

inception/inception-agreement/src/main/java/de/tudarmstadt/ukp/clarin/webanno/agreement/AgreementSummary.java

@@ -20,6 +20,7 @@
 import java.io.Serializable;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Map;
@@ -36,8 +37,7 @@ public class AgreementSummary
 
     private final String type;
     private final String feature;
-    private final boolean excludeIncomplete;
-    private final List<String> casGroupIds = new ArrayList<>();
+    private final Set<String> casGroupIds = new HashSet<>();
 
     private final List<Double> agreements = new ArrayList<>();
     private final Set<Object> categories = new LinkedHashSet<>();
@@ -52,43 +52,7 @@ public class AgreementSummary
     private int pluralitySets;
     private int relevantSetCount;
     private int completeSetCount;
-
-    public AgreementSummary remap(Map<String, String> aMapping)
-    {
-        return new AgreementSummary(this, aMapping);
-    }
-
-    private AgreementSummary(AgreementSummary aSummary, Map<String, String> aMapping)
-    {
-        type = aSummary.type;
-        feature = aSummary.feature;
-        excludeIncomplete = aSummary.excludeIncomplete;
-
-        aSummary.casGroupIds.stream().map(aMapping::get).sorted().forEach(casGroupIds::add);
-
-        agreements.addAll(aSummary.agreements);
-        categories.addAll(aSummary.categories);
-
-        for (var e : aSummary.itemCounts.entrySet()) {
-            itemCounts.put(aMapping.get(e.getKey()), e.getValue());
-        }
-
-        for (var e : aSummary.nonNullContentCounts.entrySet()) {
-            nonNullContentCounts.put(aMapping.get(e.getKey()), e.getValue());
-        }
-
-        for (var e : aSummary.allNull.entrySet()) {
-            allNull.put(aMapping.get(e.getKey()), e.getValue());
-        }
-
-        empty = aSummary.empty;
-
-        incompleteSetsByPosition = aSummary.incompleteSetsByPosition;
-        incompleteSetsByLabel = aSummary.incompleteSetsByLabel;
-        pluralitySets = aSummary.pluralitySets;
-        relevantSetCount = aSummary.relevantSetCount;
-        completeSetCount = aSummary.completeSetCount;
-    }
+    private int usedSetCount;
 
     public void merge(AgreementSummary aResult)
     {
@@ -102,17 +66,7 @@ public void merge(AgreementSummary aResult)
                     + feature + "] but encountered [" + aResult.feature + "]");
         }
 
-        if (excludeIncomplete != aResult.excludeIncomplete) {
-            throw new IllegalArgumentException(
-                    "All merged results must have the same excludeIncomplete [" + excludeIncomplete
-                            + "] but encountered [" + aResult.excludeIncomplete + "]");
-        }
-
-        if (!casGroupIds.equals(aResult.casGroupIds)) {
-            throw new IllegalArgumentException("All merged results must have the same casGroupIds "
-                    + casGroupIds + " but encountered " + aResult.casGroupIds);
-        }
-
+        casGroupIds.addAll(aResult.casGroupIds);
         agreements.addAll(aResult.agreements);
         categories.addAll(aResult.categories);
 
@@ -149,6 +103,10 @@ public void merge(AgreementSummary aResult)
         if (completeSetCount >= 0 && aResult.completeSetCount >= 0) {
             completeSetCount += aResult.completeSetCount;
         }
+
+        if (usedSetCount >= 0 && aResult.usedSetCount >= 0) {
+            usedSetCount += aResult.usedSetCount;
+        }
     }
 
     public static AgreementSummary of(Serializable aResult)
@@ -165,6 +123,19 @@ public static AgreementSummary of(Serializable aResult)
                 "Unsupported result type: [" + aResult.getClass().getName() + "]");
     }
 
+    public static AgreementSummary skipped(String aType, String aFeature)
+    {
+        return new AgreementSummary(aType, aFeature);
+    }
+
+    public AgreementSummary(String aType, String aFeature)
+    {
+        type = aType;
+        feature = aFeature;
+        agreements.add(Double.NaN);
+        empty = true;
+    }
+
     public AgreementSummary(FullUnitizingAgreementResult aResult)
     {
         this((FullAgreementResult_ImplBase<?>) aResult);
@@ -173,6 +144,7 @@ public AgreementSummary(FullUnitizingAgreementResult aResult)
         incompleteSetsByPosition = -1;
         relevantSetCount = -1;
         completeSetCount = -1;
+        usedSetCount = -1;
         pluralitySets = -1;
     }
 
@@ -183,16 +155,20 @@ public AgreementSummary(FullCodingAgreementResult aResult)
         incompleteSetsByLabel = aResult.getIncompleteSetsByLabel().size();
         incompleteSetsByPosition = aResult.getIncompleteSetsByPosition().size();
         pluralitySets = aResult.getPluralitySets().size();
-        relevantSetCount = aResult.getRelevantSetCount();
-        completeSetCount = aResult.getCompleteSetCount();
+        relevantSetCount = aResult.getRelevantSets().size();
+        completeSetCount = aResult.getCompleteSets().size();
+
+        usedSetCount = completeSetCount;
+        if (!aResult.isExcludeIncomplete()) {
+            usedSetCount += incompleteSetsByLabel + incompleteSetsByPosition;
+        }
     }
 
     private AgreementSummary(FullAgreementResult_ImplBase<?> aResult)
     {
         type = aResult.getType();
         feature = aResult.getFeature();
-        excludeIncomplete = aResult.isExcludeIncomplete();
-        aResult.casGroupIds.stream().sorted().forEach(casGroupIds::add);
+        casGroupIds.addAll(aResult.casGroupIds);
         agreements.add(aResult.agreement);
         aResult.getCategories().forEach(categories::add);
         empty = aResult.isEmpty();
@@ -206,7 +182,7 @@ private AgreementSummary(FullAgreementResult_ImplBase<?> aResult)
 
     public List<String> getCasGroupIds()
     {
-        return casGroupIds;
+        return casGroupIds.stream().sorted().toList();
     }
 
     private DoubleStream usableAgreements()
@@ -241,11 +217,6 @@ public String getFeature()
         return feature;
     }
 
-    public boolean isExcludeIncomplete()
-    {
-        return excludeIncomplete;
-    }
-
     public boolean isEmpty()
     {
         return empty;
@@ -295,4 +266,9 @@ public int getPluralitySets()
     {
         return pluralitySets;
     }
+
+    public int getUsedSetCount()
+    {
+        return usedSetCount;
+    }
 }