Merge branch 'main' into bugfix/4668-Rejecting-predictions-using-Apac…

…he-Annotator-editor

* main: (330 commits)
  [maven-release-plugin] prepare for next development iteration
  [maven-release-plugin] prepare release inception-34.0
  No issue: Mention MS SQL and PosgreSQL as experimental DB options
  No issue: Fix versions after merge
  #5043 - Ability to specify token breaking zones when calling tokenizer
  #5064 - Project template for PHI annotation
  #5071 - Better document which layers are supported by which formats
  #5061 - Multiple synchronous recommenders only the last one wins
  #5064 - Project template for PHI annotation
  #5068 - Show annotation sidebar by default
  #5033 - Ability to configure recommenders interactively on the annotation page
  #5066 - Increase default number of rows for brat editors
  #5056 - Ability to configure additional languages for knowledge bases
  #4909 - Upgrade dependencies
  #5056 - Ability to configure additional languages for knowledge bases
  #4909 - Upgrade dependencies
  No issue: Actually, document-metadata doesn't seem to be experimental after all...
  No issue: Set version to 35.0-SNAPSHOT
  [maven-release-plugin] prepare for next development iteration
  [maven-release-plugin] prepare release inception-33.7
  ...

.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

.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
 

.gitignore

@@ -25,3 +25,4 @@ dependency-reduced-pom.xml
 **/src/main/ts/package.json
 **/src/main/ts/package-lock.json
 local/
+.asciidoctorconfig.adoc

Jenkinsfile

@@ -130,7 +130,7 @@ pipeline {
             script {
               def mavenCommand = 'mvn ' +
                 params.extraMavenArguments +
-                ' -B -Dmaven.test.failure.ignore=true -Pjacoco,full-tests clean verify javadoc:javadoc'
+                ' -B -Dmaven.test.failure.ignore=true -Pjacoco clean verify javadoc:javadoc'
 
               if (isUnix()) {
                 sh script: mavenCommand

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>35.0-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-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;
@@ -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();
     }
 

inception/inception-active-learning/src/main/java/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);
     }
 }

inception/inception-active-learning/src/main/resources/META-INF/spring.factories → inception/inception-active-learning/src/main/resources/META-INF/spring/org.springframework.boot.autoconfigure.AutoConfiguration.imports

@@ -1,2 +1 @@
-org.springframework.boot.autoconfigure.EnableAutoConfiguration=\
 de.tudarmstadt.ukp.inception.active.learning.config.ActiveLearningAutoConfiguration

inception/inception-active-learning/src/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);

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>35.0-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>
@@ -88,6 +97,10 @@
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-annotation-storage-api</artifactId>
     </dependency>
+    <dependency>
+      <groupId>de.tudarmstadt.ukp.inception.app</groupId>
+      <artifactId>inception-layer-docmetadata</artifactId>
+    </dependency>
 
     <dependency>
       <groupId>org.dkpro.statistics</groupId>
@@ -126,8 +139,8 @@
       <artifactId>wicket-bootstrap-core</artifactId>
     </dependency>
     <dependency>
-      <groupId>com.googlecode.wicket-jquery-ui</groupId>
-      <artifactId>wicket-jquery-ui-core</artifactId>
+      <groupId>org.wicketstuff</groupId>
+      <artifactId>wicketstuff-jquery-ui-core</artifactId>
     </dependency>
     <dependency>
       <groupId>org.wicketstuff</groupId>
@@ -160,6 +173,11 @@
       <artifactId>dkpro-core-io-xmi-asl</artifactId>
       <scope>test</scope>
     </dependency>
+    <dependency>
+      <groupId>de.tudarmstadt.ukp.inception.app</groupId>
+      <artifactId>inception-constraints</artifactId>
+      <scope>test</scope>
+    </dependency>
     <dependency>
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-io-webanno-tsv</artifactId>

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;
     }
 }