Merge branch 'main' into refactoring/4904-Upgrade-to-RDF4J-5.x

* main: (114 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 ... % Conflicts: % pom.xml
inception-project · Sep 8, 2024 · 0c6a273 · 0c6a273
2 parents 784f125 + f08cb31
commit 0c6a273
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diff --git a/.gitattributes b/.gitattributes
@@ -13,6 +13,8 @@
 
 # Make sure that these files are treated as binary so that newlines are preserved.
 #   overrides GIT's determination if a file is text or not
+*.zip binary
+*.gz binary
 *.bin binary
 *.dump binary
 *.xcas binary

diff --git a/.github/workflows/maven.yml b/.github/workflows/maven.yml
@@ -17,20 +17,38 @@ on:
 jobs:
   build:
     strategy:
+      fail-fast: false
       matrix:
         os: [ubuntu-latest, windows-latest]
         jdk: [17]
 
     runs-on: ${{ matrix.os }}
 
     steps:
-    - uses: actions/checkout@v4
+    - name: Checkout repository
+      uses: actions/checkout@v4
+      with:
+        ref: ${{ github.head_ref || github.ref }}
+
     - name: Set up JDK ${{ matrix.jdk }}
       uses: actions/setup-java@v4
       with:
         java-version: ${{ matrix.jdk }}
         distribution: 'temurin'
         cache: maven
+
+    - name: Set up cache date
+      run: echo "CACHE_DATE=$(date +'%Y-%m-%d')" >> $GITHUB_ENV
+
+    - name: Cache Maven repository
+      id: maven-cache
+      uses: actions/cache@v4
+      with:
+        path: ~/.m2/repository
+        key: ${{ runner.os }}-maven-${{ hashFiles('**/pom.xml') }}-${{ env.CACHE_DATE }}
+        restore-keys: |
+          ${{ runner.os }}-maven-
+
     - name: Build with Maven
       run: mvn --no-transfer-progress -B clean verify --file pom.xml
 

diff --git a/.gitignore b/.gitignore
@@ -25,3 +25,4 @@ dependency-reduced-pom.xml
 **/src/main/ts/package.json
 **/src/main/ts/package-lock.json
 local/
+.asciidoctorconfig.adoc
diff --git a/...main/java/de/tudarmstadt/ukp/inception/active/learning/sidebar/ActiveLearningSidebar.java b/...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;
@@ -75,7 +73,7 @@
 import de.tudarmstadt.ukp.clarin.webanno.model.ReorderableTag;
 import de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument;
 import de.tudarmstadt.ukp.clarin.webanno.security.UserDao;
-import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.AnnotationPage;
+import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.AnnotationPageBase2;
 import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.sidebar.AnnotationSidebar_ImplBase;
 import de.tudarmstadt.ukp.inception.active.learning.ActiveLearningService;
 import de.tudarmstadt.ukp.inception.active.learning.ActiveLearningServiceImpl;
@@ -182,7 +180,7 @@ public class ActiveLearningSidebar
 
     private final WebMarkupContainer alMainContainer;
 
-    private AnnotationPage annotationPage;
+    private AnnotationPageBase2 annotationPage;
     private BootstrapModalDialog dialog;
     private FeatureEditor editor;
     private Form<Void> recommendationForm;
@@ -199,11 +197,10 @@ enum FeatureDetailEditorUpdateFlag
         KEEP_SELECTED_ANNOTATION_AND_VIEW, CLEAR_SELECTED_ANNOTATION_AND_JUMP_TO_SUGGESTION
     }
 
-    public ActiveLearningSidebar(String aId, IModel<AnnotatorState> aModel,
-            AnnotationActionHandler aActionHandler, CasProvider aCasProvider,
-            AnnotationPage aAnnotationPage)
+    public ActiveLearningSidebar(String aId, AnnotationActionHandler aActionHandler,
+            CasProvider aCasProvider, AnnotationPageBase2 aAnnotationPage)
     {
-        super(aId, aModel, aActionHandler, aCasProvider, aAnnotationPage);
+        super(aId, aActionHandler, aCasProvider, aAnnotationPage);
 
         annotationPage = aAnnotationPage;
 
@@ -993,10 +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();
     }
 

diff --git a/...va/de/tudarmstadt/ukp/inception/active/learning/sidebar/ActiveLearningSidebarFactory.java b/...va/de/tudarmstadt/ukp/inception/active/learning/sidebar/ActiveLearningSidebarFactory.java
@@ -23,7 +23,7 @@
 
 import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasProvider;
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
-import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.AnnotationPage;
+import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.AnnotationPageBase2;
 import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.sidebar.AnnotationSidebarFactory_ImplBase;
 import de.tudarmstadt.ukp.clarin.webanno.ui.annotation.sidebar.AnnotationSidebar_ImplBase;
 import de.tudarmstadt.ukp.inception.active.learning.config.ActiveLearningAutoConfiguration;
@@ -80,11 +80,9 @@ public boolean applies(AnnotatorState aState)
     }
 
     @Override
-    public AnnotationSidebar_ImplBase create(String aId, IModel<AnnotatorState> aModel,
-            AnnotationActionHandler aActionHandler, CasProvider aCasProvider,
-            AnnotationPage aAnnotationPage)
+    public AnnotationSidebar_ImplBase create(String aId, AnnotationActionHandler aActionHandler,
+            CasProvider aCasProvider, AnnotationPageBase2 aAnnotationPage)
     {
-        return new ActiveLearningSidebar(aId, aModel, aActionHandler, aCasProvider,
-                aAnnotationPage);
+        return new ActiveLearningSidebar(aId, aActionHandler, aCasProvider, aAnnotationPage);
     }
 }
diff --git a/...c/test/java/de/tudarmstadt/ukp/inception/recommendation/api/model/LearningRecordTest.java b/...c/test/java/de/tudarmstadt/ukp/inception/recommendation/api/model/LearningRecordTest.java
@@ -17,23 +17,21 @@
  */
 package de.tudarmstadt.ukp.inception.recommendation.api.model;
 
+import static java.util.Arrays.fill;
 import static org.assertj.core.api.Assertions.assertThat;
 
-import java.util.Arrays;
-
 import org.junit.jupiter.api.Test;
 
 public class LearningRecordTest
 {
-
     @Test
     public void thatTokenTextIsTruncated()
     {
-        char[] charArray = new char[300];
-        Arrays.fill(charArray, 'X');
-        String longTokenText = new String(charArray);
+        var charArray = new char[300];
+        fill(charArray, 'X');
+        var longTokenText = new String(charArray);
 
-        LearningRecord sut = new LearningRecord();
+        var sut = new LearningRecord();
         sut.setTokenText(longTokenText);
 
         assertThat(sut.getTokenText()).as("TokenText has been truncated").hasSize(255);

diff --git a/...n-agreement/src/main/java/de/tudarmstadt/ukp/clarin/webanno/agreement/AgreementUtils.java b/...n-agreement/src/main/java/de/tudarmstadt/ukp/clarin/webanno/agreement/AgreementUtils.java
@@ -48,10 +48,10 @@
 import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.CasDiff;
 import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.Configuration;
 import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.ConfigurationSet;
-import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.LinkCompareBehavior;
 import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.Tag;
 import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.relation.RelationDiffAdapter;
 import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.relation.RelationPosition;
+import de.tudarmstadt.ukp.inception.annotation.feature.link.LinkFeatureMultiplicityMode;
 
 public class AgreementUtils
 {
@@ -295,23 +295,33 @@ private static Object extractValueForAgreement(Configuration cfg, String user,
     }
 
     private static Object extractLinkFeatureValueForAgreement(FeatureStructure aFs, String aFeature,
-            int aLinkIndex, LinkCompareBehavior aLCB)
+            int aLinkIndex, LinkFeatureMultiplicityMode aLCB)
     {
         @SuppressWarnings("unchecked")
         var links = (ArrayFS<FeatureStructure>) aFs
                 .getFeatureValue(aFs.getType().getFeatureByBaseName(aFeature));
         var link = links.get(aLinkIndex);
 
         switch (aLCB) {
-        case LINK_TARGET_AS_LABEL:
+        case ONE_TARGET_MULTIPLE_ROLES: {
             // FIXME The target feature name should be obtained from the feature definition!
             var target = (AnnotationFS) link
                     .getFeatureValue(link.getType().getFeatureByBaseName("target"));
 
             return target.getBegin() + "-" + target.getEnd() + " [" + target.getCoveredText() + "]";
-        case LINK_ROLE_AS_LABEL:
+        }
+        case MULTIPLE_TARGETS_ONE_ROLE:
             // FIXME The role feature name should be obtained from the feature definition!
             return link.getStringValue(link.getType().getFeatureByBaseName("role"));
+        case MULTIPLE_TARGETS_MULTIPLE_ROLES: {
+            // FIXME The role feature name should be obtained from the feature definition!
+            // FIXME The target feature name should be obtained from the feature definition!
+            var target = (AnnotationFS) link
+                    .getFeatureValue(link.getType().getFeatureByBaseName("target"));
+            return link.getStringValue(link.getType().getFeatureByBaseName("role")) + "@"
+                    + target.getBegin() + "-" + target.getEnd() + " [" + target.getCoveredText()
+                    + "]";
+        }
         default:
             throw new IllegalStateException("Unknown link target comparison mode [" + aLCB + "]");
         }

diff --git a/...ain/java/de/tudarmstadt/ukp/clarin/webanno/agreement/measures/DefaultAgreementTraits.java b/...ain/java/de/tudarmstadt/ukp/clarin/webanno/agreement/measures/DefaultAgreementTraits.java
@@ -17,12 +17,8 @@
  */
 package de.tudarmstadt.ukp.clarin.webanno.agreement.measures;
 
-import static de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.LinkCompareBehavior.LINK_TARGET_AS_LABEL;
-
 import java.io.Serializable;
 
-import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.LinkCompareBehavior;
-
 public class DefaultAgreementTraits
     implements Serializable
 {
@@ -31,18 +27,6 @@ public class DefaultAgreementTraits
     private boolean limitToFinishedDocuments = false;
     private boolean excludeIncomplete;
 
-    private LinkCompareBehavior linkCompareBehavior = LINK_TARGET_AS_LABEL;
-
-    public LinkCompareBehavior getLinkCompareBehavior()
-    {
-        return linkCompareBehavior;
-    }
-
-    public void setLinkCompareBehavior(LinkCompareBehavior aLinkCompareBehavior)
-    {
-        linkCompareBehavior = aLinkCompareBehavior;
-    }
-
     public boolean isLimitToFinishedDocuments()
     {
         return limitToFinishedDocuments;

diff --git a/...va/de/tudarmstadt/ukp/clarin/webanno/agreement/measures/DefaultAgreementTraitsEditor.java b/...va/de/tudarmstadt/ukp/clarin/webanno/agreement/measures/DefaultAgreementTraitsEditor.java
@@ -28,16 +28,16 @@
 import org.apache.wicket.model.CompoundPropertyModel;
 import org.apache.wicket.model.IModel;
 
-import de.tudarmstadt.ukp.clarin.webanno.curation.casdiff.LinkCompareBehavior;
 import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
 import de.tudarmstadt.ukp.clarin.webanno.model.LinkMode;
+import de.tudarmstadt.ukp.inception.annotation.feature.link.LinkFeatureMultiplicityMode;
 
 public class DefaultAgreementTraitsEditor<T extends DefaultAgreementTraits>
     extends Panel
 {
     private static final long serialVersionUID = 7780019891761754494L;
 
-    private final DropDownChoice<LinkCompareBehavior> linkCompareBehaviorDropDown;
+    private final DropDownChoice<LinkFeatureMultiplicityMode> linkCompareBehaviorDropDown;
 
     private final Form<T> form;
 
@@ -59,7 +59,7 @@ protected void onSubmit()
         };
 
         linkCompareBehaviorDropDown = new DropDownChoice<>("linkCompareBehavior",
-                asList(LinkCompareBehavior.values()), new EnumChoiceRenderer<>(this));
+                asList(LinkFeatureMultiplicityMode.values()), new EnumChoiceRenderer<>(this));
         linkCompareBehaviorDropDown.add(
                 visibleWhen(aFeature.map(f -> LinkMode.NONE != f.getLinkMode()).orElse(false)));
         linkCompareBehaviorDropDown.setOutputMarkupPlaceholderTag(true);

diff --git a/...tudarmstadt/ukp/clarin/webanno/agreement/measures/DefaultAgreementTraitsEditor.properties b/...tudarmstadt/ukp/clarin/webanno/agreement/measures/DefaultAgreementTraitsEditor.properties
@@ -19,7 +19,7 @@ linkCompareBehavior = Link treatment
 LinkCompareBehavior.LINK_ROLE_AS_LABEL   = Use link role as label
 LinkCompareBehavior.LINK_TARGET_AS_LABEL = Use link target as label
 
-excludeIncomplete = Exclude incomplete
+excludeIncomplete = Only consider positions annotated by all annotators
 
-limitToFinishedDocuments = Limit to finished documents
+limitToFinishedDocuments = Only consider finished documents
 
diff --git a/...armstadt/ukp/clarin/webanno/agreement/measures/cohenkappa/CohenKappaAgreementMeasure.java b/...armstadt/ukp/clarin/webanno/agreement/measures/cohenkappa/CohenKappaAgreementMeasure.java
@@ -52,11 +52,10 @@ public CohenKappaAgreementMeasure(AnnotationFeature aFeature, DefaultAgreementTr
     public FullCodingAgreementResult getAgreement(Map<String, CAS> aCasMap)
     {
         var feature = getFeature();
-        var traits = getTraits();
 
         var adapters = getDiffAdapters(annotationService, asList(feature.getLayer()));
 
-        var diff = doDiff(adapters, traits.getLinkCompareBehavior(), aCasMap);
+        var diff = doDiff(adapters, aCasMap);
 
         var tagset = annotationService.listTags(feature.getTagset()).stream() //
                 .map(Tag::getName) //

diff --git a/...mstadt/ukp/clarin/webanno/agreement/measures/fleisskappa/FleissKappaAgreementMeasure.java b/...mstadt/ukp/clarin/webanno/agreement/measures/fleisskappa/FleissKappaAgreementMeasure.java
@@ -53,11 +53,10 @@ public FleissKappaAgreementMeasure(AnnotationFeature aFeature, DefaultAgreementT
     public FullCodingAgreementResult getAgreement(Map<String, CAS> aCasMap)
     {
         var feature = getFeature();
-        var traits = getTraits();
 
         var adapters = getDiffAdapters(annotationService, asList(feature.getLayer()));
 
-        var diff = doDiff(adapters, traits.getLinkCompareBehavior(), aCasMap);
+        var diff = doDiff(adapters, aCasMap);
 
         var tagset = annotationService.listTags(feature.getTagset()).stream() //
                 .map(Tag::getName) //

diff --git a/...larin/webanno/agreement/measures/krippendorffalpha/KrippendorffAlphaAgreementMeasure.java b/...larin/webanno/agreement/measures/krippendorffalpha/KrippendorffAlphaAgreementMeasure.java
@@ -59,7 +59,7 @@ public FullCodingAgreementResult getAgreement(Map<String, CAS> aCasMap)
 
         var adapters = getDiffAdapters(annotationService, asList(feature.getLayer()));
 
-        var diff = doDiff(adapters, traits.getLinkCompareBehavior(), aCasMap);
+        var diff = doDiff(adapters, aCasMap);
 
         var tagset = annotationService.listTags(feature.getTagset()).stream() //
                 .map(Tag::getName) //

diff --git a/...ement/measures/krippendorffalphaunitizing/KrippendorffAlphaUnitizingAgreementMeasure.java b/...ement/measures/krippendorffalphaunitizing/KrippendorffAlphaUnitizingAgreementMeasure.java
@@ -17,6 +17,7 @@
  */
 package de.tudarmstadt.ukp.clarin.webanno.agreement.measures.krippendorffalphaunitizing;
 
+import java.lang.invoke.MethodHandles;
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.Map;
@@ -27,6 +28,8 @@
 import org.apache.uima.jcas.tcas.Annotation;
 import org.dkpro.statistics.agreement.unitizing.KrippendorffAlphaUnitizingAgreement;
 import org.dkpro.statistics.agreement.unitizing.UnitizingAnnotationStudy;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import de.tudarmstadt.ukp.clarin.webanno.agreement.measures.AgreementMeasure_ImplBase;
 import de.tudarmstadt.ukp.clarin.webanno.agreement.measures.DefaultAgreementTraits;
@@ -38,6 +41,8 @@ public class KrippendorffAlphaUnitizingAgreementMeasure
             FullUnitizingAgreementResult, //
             DefaultAgreementTraits>
 {
+    private static final Logger LOG = LoggerFactory.getLogger(MethodHandles.lookup().lookupClass());
+
     public KrippendorffAlphaUnitizingAgreementMeasure(AnnotationFeature aFeature,
             DefaultAgreementTraits aTraits)
     {
@@ -90,6 +95,9 @@ public FullUnitizingAgreementResult getAgreement(Map<String, CAS> aCasMap)
             }
         }
 
+        LOG.trace("Units in study : {}", study.getUnitCount());
+        LOG.trace("Raters im study: {}", study.getRaterCount());
+
         var result = new FullUnitizingAgreementResult(typeName, getFeature().getName(), study,
                 new ArrayList<>(aCasMap.keySet()), getTraits().isExcludeIncomplete());
 

diff --git a/...de/tudarmstadt/ukp/clarin/webanno/agreement/results/coding/FullCodingAgreementResult.java b/...de/tudarmstadt/ukp/clarin/webanno/agreement/results/coding/FullCodingAgreementResult.java
@@ -35,7 +35,6 @@ public class FullCodingAgreementResult
 
     protected final DiffResult diff;
     protected final List<ConfigurationSet> allSets;
-    protected final boolean excludeIncomplete;
 
     public FullCodingAgreementResult(String aType, String aFeature, DiffResult aDiff,
             ICodingAnnotationStudy aStudy, List<String> aCasGroupIds,
@@ -45,7 +44,6 @@ public FullCodingAgreementResult(String aType, String aFeature, DiffResult aDiff
 
         allSets = aTaggedConfigurations;
         diff = aDiff;
-        excludeIncomplete = aExcludeIncomplete;
     }
 
     public boolean noPositions()