Merge branch 'main' into refactoring/4977-Clean-up-Knowledge-Base-UI-…

…code

* main: (42 commits)
  #5047 - Clean up layer detail UI a bit
  #4949 - Showing the start and end points of relations in left side bar
  No issue: Minor cleaning up
  #5043 - Ability to specify token breaking zones when calling tokenizer
  [maven-release-plugin] prepare for next development iteration
  [maven-release-plugin] prepare release inception-34.0-beta-6
  #5009 - Better handling of stacked annotations with link features in curation
  #5009 - Better handling of stacked annotations with link features in curation
  [maven-release-plugin] prepare for next development iteration
  [maven-release-plugin] prepare release inception-34.0-beta-6
  [maven-release-plugin] prepare for next development iteration
  [maven-release-plugin] prepare release inception-33.6
  #5040 - Improve feature form tab navigation
  #5037 - Show fraction of annotators that chose a certain label in curation sidebar mode
  #5035 - NBSPs should not be treated as tokens
  #5031 - ChatGPT recommender fails because format is not a supported parameter
  #5029 - Duplicate lines on the about page
  #5027 - Add more CSP configurations
  #4753 - Entity linker should skip already linked concepts
  #5007 - Lazy details on suggestions for multi-value concept features fail rendering
  ...

.github/workflows/maven.yml

@@ -42,7 +42,7 @@ jobs:
 
     - name: Cache Maven repository
       id: maven-cache
-      uses: actions/cache@v3
+      uses: actions/cache@v4
       with:
         path: ~/.m2/repository
         key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}-${{ env.CACHE_DATE }}

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

@@ -43,8 +43,6 @@
 import java.util.Optional;
 
 import org.apache.uima.cas.CAS;
-import org.apache.uima.cas.Feature;
-import org.apache.uima.cas.Type;
 import org.apache.uima.cas.text.AnnotationFS;
 import org.apache.uima.fit.util.CasUtil;
 import org.apache.wicket.Component;
@@ -992,10 +990,11 @@ private void actionSelectHistoryItem(AjaxRequestTarget aTarget, LearningRecord a
 
     private Optional<AnnotationFS> getMatchingAnnotation(CAS aCas, LearningRecord aRecord)
     {
-        Type type = CasUtil.getType(aCas, alStateModel.getObject().getLayer().getName());
-        Feature feature = type.getFeatureByBaseName(aRecord.getAnnotationFeature().getName());
+        var type = CasUtil.getType(aCas, alStateModel.getObject().getLayer().getName());
+        var feature = type.getFeatureByBaseName(aRecord.getAnnotationFeature().getName());
         return selectAt(aCas, type, aRecord.getOffsetBegin(), aRecord.getOffsetEnd()).stream()
-                .filter(fs -> aRecord.getAnnotation().equals(fs.getFeatureValueAsString(feature)))
+                .filter(fs -> Objects.equals(aRecord.getAnnotation(),
+                        fs.getFeatureValueAsString(feature)))
                 .findFirst();
     }
 

inception/inception-annotation-storage/src/main/java/de/tudarmstadt/ukp/inception/annotation/storage/CasKey.java

@@ -95,23 +95,31 @@ public boolean equals(final Object other)
             return false;
         }
         CasKey castOther = (CasKey) other;
-        return new EqualsBuilder().append(projectId, castOther.projectId)
-                .append(documentId, castOther.documentId).append(userId, castOther.userId)
+        return new EqualsBuilder() //
+                .append(projectId, castOther.projectId) //
+                .append(documentId, castOther.documentId) //
+                .append(userId, castOther.userId) //
                 .isEquals();
     }
 
     @Override
     public int hashCode()
     {
-        return new HashCodeBuilder().append(projectId).append(documentId).append(userId)
+        return new HashCodeBuilder() //
+                .append(projectId) //
+                .append(documentId) //
+                .append(userId) //
                 .toHashCode();
     }
 
     @Override
     public String toString()
     {
-        return new ToStringBuilder(this, ToStringStyle.NO_CLASS_NAME_STYLE).append("p", projectId)
-                .append("d", documentId).append("u", userId).toString();
+        return new ToStringBuilder(this, ToStringStyle.NO_CLASS_NAME_STYLE) //
+                .append("p", projectId) //
+                .append("d", documentId) //
+                .append("u", userId) //
+                .toString();
     }
 
     public static CasKey matchingAllFromProject(Project aProject)

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/page/AnnotationPageBase.java

@@ -379,7 +379,7 @@ protected void validateRequiredFeatures(AjaxRequestTarget aTarget, CAS aCas,
         var constraints = getModelObject().getConstraints();
 
         // Check each feature structure of this layer
-        var layerType = aAdapter.getAnnotationType(editorCas);
+        var layerType = aAdapter.getAnnotationType(editorCas).get();
         var annotationFsType = editorCas.getAnnotationType();
         try (var fses = editorCas.select(layerType)) {
             for (var fs : fses) {

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/annotation/rendering/LabelRenderer.java

@@ -22,11 +22,9 @@
 import org.springframework.core.annotation.Order;
 
 import de.tudarmstadt.ukp.clarin.webanno.api.annotation.config.AnnotationAutoConfiguration;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
 import de.tudarmstadt.ukp.inception.rendering.pipeline.RenderStep;
 import de.tudarmstadt.ukp.inception.rendering.request.RenderRequest;
 import de.tudarmstadt.ukp.inception.rendering.vmodel.VDocument;
-import de.tudarmstadt.ukp.inception.rendering.vmodel.VObject;
 
 /**
  * <p>
@@ -49,8 +47,8 @@ public String getId()
     @Override
     public void render(VDocument aVDoc, RenderRequest aRequest)
     {
-        for (AnnotationLayer layer : aVDoc.getAnnotationLayers()) {
-            for (VObject vobj : aVDoc.objects(layer.getId())) {
+        for (var layer : aVDoc.getAnnotationLayers()) {
+            for (var vobj : aVDoc.objects(layer.getId())) {
                 if (vobj.getLabelHint() != null) {
                     // Label hint was already set earlier - do not overwrite it!
                     continue;

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/inception/annotation/feature/bool/BooleanFeatureSupport.java

@@ -17,12 +17,14 @@
  */
 package de.tudarmstadt.ukp.inception.annotation.feature.bool;
 
+import static java.lang.Boolean.FALSE;
 import static java.util.Arrays.asList;
 import static java.util.Collections.unmodifiableList;
 
 import java.util.List;
 
 import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.FeatureStructure;
 import org.apache.wicket.MarkupContainer;
 import org.apache.wicket.model.IModel;
 
@@ -105,4 +107,11 @@ public String renderFeatureValue(AnnotationFeature aFeature, String aLabel)
             return "-" + aFeature.getUiName();
         }
     }
+
+    @SuppressWarnings("unchecked")
+    @Override
+    public <V> V getDefaultFeatureValue(AnnotationFeature aFeature, FeatureStructure aFS)
+    {
+        return (V) FALSE;
+    }
 }

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/inception/annotation/feature/link/LinkFeatureSupport.java

@@ -19,13 +19,15 @@
 
 import static de.tudarmstadt.ukp.clarin.webanno.model.LinkMode.WITH_ROLE;
 import static de.tudarmstadt.ukp.clarin.webanno.model.MultiValueMode.ARRAY;
+import static org.apache.commons.collections4.CollectionUtils.disjunction;
 import static org.apache.uima.cas.CAS.TYPE_NAME_FS_ARRAY;
 import static org.apache.uima.cas.CAS.TYPE_NAME_STRING;
 import static org.apache.uima.cas.CAS.TYPE_NAME_TOP;
 
 import java.lang.invoke.MethodHandles;
 import java.util.ArrayList;
 import java.util.Collection;
+import java.util.Collections;
 import java.util.List;
 
 import org.apache.commons.text.WordUtils;
@@ -59,6 +61,7 @@
 import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureSupport;
 import de.tudarmstadt.ukp.inception.schema.api.feature.FeatureType;
 import de.tudarmstadt.ukp.inception.schema.api.feature.LinkWithRoleModel;
+import de.tudarmstadt.ukp.inception.schema.api.feature.MaterializedLink;
 import de.tudarmstadt.ukp.inception.support.uima.ICasUtil;
 
 /**
@@ -207,14 +210,16 @@ public void generateFeature(TypeSystemDescription aTSD, TypeDescription aTD,
     public List<LinkWithRoleModel> getFeatureValue(AnnotationFeature aFeature, FeatureStructure aFS)
     {
         var linkFeature = aFS.getType().getFeatureByBaseName(aFeature.getName());
-
-        if (linkFeature == null) {
-            wrapFeatureValue(aFeature, aFS.getCAS(), null);
-        }
-
         return wrapFeatureValue(aFeature, aFS.getCAS(), aFS.getFeatureValue(linkFeature));
     }
 
+    @SuppressWarnings("unchecked")
+    @Override
+    public <V> V getDefaultFeatureValue(AnnotationFeature aFeature, FeatureStructure aFS)
+    {
+        return (V) Collections.emptyList();
+    }
+
     @Override
     public void setFeatureValue(CAS aCas, AnnotationFeature aFeature, int aAddress, Object aValue)
         throws AnnotationException
@@ -309,4 +314,26 @@ public String renderFeatureValue(AnnotationFeature aFeature, String aLabel)
         // Never render link feature labels
         return null;
     }
+
+    @Override
+    public boolean isCopyOnCurationMerge(AnnotationFeature aFeature)
+    {
+        // Links count as separate positions and should be merged separately
+        return false;
+    }
+
+    @Override
+    public boolean isFeatureValueEqual(AnnotationFeature aFeature, FeatureStructure aFS1,
+            FeatureStructure aFS2)
+    {
+        List<LinkWithRoleModel> links1 = getFeatureValue(aFeature, aFS1);
+        var matLinks1 = links1.stream()
+                .map(link -> MaterializedLink.toMaterializedLink(aFS1, aFeature, link)).toList();
+
+        List<LinkWithRoleModel> links2 = getFeatureValue(aFeature, aFS2);
+        var matLinks2 = links2.stream()
+                .map(link -> MaterializedLink.toMaterializedLink(aFS2, aFeature, link)).toList();
+
+        return disjunction(matLinks1, matLinks2).isEmpty();
+    }
 }

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/inception/annotation/feature/multistring/MultiValueStringFeatureSupport.java

@@ -111,6 +111,13 @@ public boolean accepts(AnnotationFeature aFeature)
                 && CAS.TYPE_NAME_STRING_ARRAY.equals(aFeature.getType());
     }
 
+    @SuppressWarnings("unchecked")
+    @Override
+    public <V> V getDefaultFeatureValue(AnnotationFeature aFeature, FeatureStructure aFS)
+    {
+        return (V) Collections.emptyList();
+    }
+
     @SuppressWarnings("unchecked")
     @Override
     public List<String> unwrapFeatureValue(AnnotationFeature aFeature, CAS aCAS, Object aValue)
@@ -307,4 +314,27 @@ public List<VLazyDetailGroup> lookupLazyDetails(AnnotationFeature aFeature, Obje
         }
         return asList(results);
     }
+
+    @Override
+    public <V> V getFeatureValue(AnnotationFeature aFeature, FeatureStructure aFS)
+    {
+        Object value;
+
+        var f = aFS.getType().getFeatureByBaseName(aFeature.getName());
+
+        if (f == null) {
+            value = null;
+        }
+        else if (f.getRange().isPrimitive()) {
+            value = FSUtil.getFeature(aFS, aFeature.getName(), Object.class);
+        }
+        else if (FSUtil.isMultiValuedFeature(aFS, f)) {
+            value = FSUtil.getFeature(aFS, aFeature.getName(), List.class);
+        }
+        else {
+            value = FSUtil.getFeature(aFS, aFeature.getName(), FeatureStructure.class);
+        }
+
+        return (V) wrapFeatureValue(aFeature, aFS.getCAS(), value);
+    }
 }

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/inception/annotation/feature/number/NumberFeatureSupport.java

@@ -25,6 +25,7 @@
 import java.util.stream.IntStream;
 
 import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.FeatureStructure;
 import org.apache.wicket.MarkupContainer;
 import org.apache.wicket.markup.html.panel.Panel;
 import org.apache.wicket.model.IModel;
@@ -137,4 +138,15 @@ public NumberFeatureTraits createDefaultTraits()
     {
         return new NumberFeatureTraits();
     }
+
+    @SuppressWarnings("unchecked")
+    @Override
+    public <V> V getDefaultFeatureValue(AnnotationFeature aFeature, FeatureStructure aFS)
+    {
+        return switch (aFeature.getType()) {
+        case CAS.TYPE_NAME_INTEGER -> (V) (Object) 0;
+        case CAS.TYPE_NAME_FLOAT -> (V) (Object) 0.0f;
+        default -> throw unsupportedFeatureTypeException(aFeature);
+        };
+    }
 }

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/inception/annotation/feature/string/StringFeatureSupport.java

@@ -236,4 +236,10 @@ public List<VLazyDetailGroup> lookupLazyDetails(AnnotationFeature aFeature, Obje
 
         return emptyList();
     }
+
+    @Override
+    public <V> V getDefaultFeatureValue(AnnotationFeature aFeature, FeatureStructure aFS)
+    {
+        return null;
+    }
 }

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/TypeAdapter_ImplBase.java

@@ -158,6 +158,15 @@ public final boolean isFeatureValueValid(AnnotationFeature aFeature, FeatureStru
         return featureSupport.isFeatureValueValid(aFeature, aFS);
     }
 
+    @Override
+    public final boolean isFeatureValueEqual(AnnotationFeature aFeature, FeatureStructure aFS1,
+            FeatureStructure aFS2)
+    {
+        var featureSupport = featureSupportRegistry.findExtension(aFeature).orElseThrow();
+
+        return featureSupport.isFeatureValueEqual(aFeature, aFS1, aFS2);
+    }
+
     @Override
     public final void setFeatureValue(SourceDocument aDocument, String aUsername, CAS aCas,
             int aAddress, AnnotationFeature aFeature, Object aValue)

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/chain/ChainAdapter.java

@@ -22,6 +22,7 @@
 import static de.tudarmstadt.ukp.inception.support.uima.WebAnnoCasUtil.isSame;
 import static java.lang.System.currentTimeMillis;
 import static java.util.Collections.emptyList;
+import static org.apache.uima.cas.text.AnnotationPredicates.colocated;
 
 import java.lang.invoke.MethodHandles;
 import java.util.ArrayList;
@@ -566,4 +567,32 @@ public Selection selectLink(AnnotationFS aAnno)
         selection.selectArc(new VID(aAnno, 1, VID.NONE, VID.NONE), aAnno, getNextLink(aAnno));
         return selection;
     }
+
+    @Override
+    public boolean isSamePosition(FeatureStructure aFS1, FeatureStructure aFS2)
+    {
+        if (aFS1 == null || aFS2 == null) {
+            return false;
+        }
+
+        if (!aFS1.getType().getName().equals(getAnnotationTypeName())) {
+            throw new IllegalArgumentException("Expected [" + getAnnotationTypeName()
+                    + "] but got [" + aFS1.getType().getName() + "]");
+        }
+
+        if (!aFS2.getType().getName().equals(getAnnotationTypeName())) {
+            throw new IllegalArgumentException("Expected [" + getAnnotationTypeName()
+                    + "] but got [" + aFS2.getType().getName() + "]");
+        }
+
+        if (aFS1 instanceof AnnotationFS ann1 && aFS2 instanceof AnnotationFS ann2) {
+            if (aFS1 == aFS2) {
+                return true;
+            }
+
+            return colocated(ann1, ann2);
+        }
+
+        throw new IllegalArgumentException("Feature structures need to be annotations");
+    }
 }

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/inception/annotation/layer/chain/ChainRenderer.java

@@ -145,7 +145,7 @@ public void render(RenderRequest aRequest, List<AnnotationFeature> aFeatures,
                 var nextLinkFs = (AnnotationFS) linkFs.getFeatureValue(linkNext);
 
                 // Is link after window? If yes, we can skip the rest of the chain
-                if (linkFs.getBegin() >= windowBegin) {
+                if (linkFs.getBegin() >= windowEnd) {
                     break; // Go to next chain
                 }