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

* main: (39 commits)
  No issue: Try to get build work on Windows
  No issue: Added gitattributes file
  #4618 - Resizing a span does not update annotations on disk
  #4616 - Option to disable displaying suggestions in sidebar curation mode
  #4554 - Allow displaying comments from annotators on hover when curating using curation sidebar on the annotation page
  No issue: Try to get build work on Windows
  #4610 - Annotations are misaligned when PDF pages vary in dimensions
  #4611 - Run the three SPARQL queries in the concept linker in parallel
  No issue: Added gitattributes file
  No issue: Enable matrix build
  #4557 - Bulk process page should not show processes from other projects
  #4596 - Ability to temporarily suspend recommenders
  #4603 - Bulk actions in search sidebar should not be greyed-out when in sidebar curation mode
  #4602 - Project-specific user preferences may be saved without a user
  #4603 - Bulk actions in search sidebar should not be greyed-out when in sidebar curation mode
  #4602 - Project-specific user preferences may be saved without a user
  #4600 - Error when exporting project during preference phase
  No issue: Fix example CSS file for custom XML format which was actually an SCSS file
  #4583 - Ability to configure layer visibility via a sidebar
  Remove <Proxy> directive as it shouldn't be necessary
  ...

% Conflicts:
%	inception/inception-diam/src/main/java/de/tudarmstadt/ukp/inception/diam/service/DiamWebsocketController.java
%	inception/inception-kb/src/test/java/de/tudarmstadt/ukp/inception/kb/FullTextIndexUpgradeTest.java
%	inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/config/RecommenderServiceAutoConfiguration.java
%	inception/inception-recommendation/src/main/java/de/tudarmstadt/ukp/inception/recommendation/footer/RecommendationEventFooterPanel.java
%	inception/inception-ui-scheduling/src/main/java/de/tudarmstadt/ukp/inception/ui/scheduling/TaskMonitorPanel.java
%	inception/inception-websocket/pom.xml

.gitattributes

@@ -0,0 +1,24 @@
+# Set the default behavior, in case people don't have core.autocrlf set.
+#   means that files that GIT determines to be text files, will be 
+#     converted from CRLF -> LF upon being added to the repo, and
+#     converted from LF -> LF or CRLF when checked out (depending on the platform, I think)
+# * text=auto
+
+# We force LF for all text files because we have Checkstyle set up in such a way
+# The "text" by itself says these files must be line-ending-conversion controlled on check-in / out
+#   The internal repo form for these is always lf, 
+#   The eol=lf means on check-out do nothing, and on check-in, if the file has crlf, convert to lf
+* text eol=lf
+# *.sh text eol=lf
+
+# 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
+*.bin binary
+*.dump binary
+*.xcas binary
+*.xmi binary
+#  next is probably the default
+*.pdf binary
+*.ser binary
+*.png binary
+*.jpg binary

.github/workflows/maven.yml

@@ -16,15 +16,19 @@ on:
 
 jobs:
   build:
+    strategy:
+      matrix:
+        os: [ubuntu-latest, windows-latest]
+        jdk: [17]
 
-    runs-on: ubuntu-latest
+    runs-on: ${{ matrix.os }}
 
     steps:
     - uses: actions/checkout@v4
-    - name: Set up JDK 17
+    - name: Set up JDK ${{ matrix.jdk }}
       uses: actions/setup-java@v4
       with:
-        java-version: '17'
+        java-version: ${{ matrix.jdk }}
         distribution: 'temurin'
         cache: maven
     - name: Build with Maven

inception/inception-active-learning/pom.xml

@@ -66,6 +66,10 @@
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-support</artifactId>
     </dependency>
+    <dependency>
+      <groupId>de.tudarmstadt.ukp.inception.app</groupId>
+      <artifactId>inception-preferences</artifactId>
+    </dependency>
     <dependency>
       <groupId>de.tudarmstadt.ukp.inception.app</groupId>
       <artifactId>inception-support-bootstrap</artifactId>
@@ -97,6 +101,10 @@
       <artifactId>commons-lang3</artifactId>
     </dependency>
 
+    <dependency>
+      <groupId>org.springframework</groupId>
+      <artifactId>spring-core</artifactId>
+    </dependency>
     <dependency>
       <groupId>org.springframework</groupId>
       <artifactId>spring-beans</artifactId>

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

@@ -31,6 +31,7 @@
 import de.tudarmstadt.ukp.inception.active.learning.log.ActiveLearningSuggestionOfferedAdapter;
 import de.tudarmstadt.ukp.inception.active.learning.sidebar.ActiveLearningSidebarFactory;
 import de.tudarmstadt.ukp.inception.documents.api.DocumentService;
+import de.tudarmstadt.ukp.inception.preferences.PreferencesService;
 import de.tudarmstadt.ukp.inception.recommendation.api.LearningRecordService;
 import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
 import de.tudarmstadt.ukp.inception.recommendation.config.RecommenderServiceAutoConfiguration;
@@ -73,7 +74,8 @@ public ActiveLearningSuggestionOfferedAdapter activeLearningSuggestionOfferedAda
 
     @Bean
     public ActiveLearningSidebarFactory activeLearningSidebarFactory(
-            RecommendationService aRecommendationService)
+            RecommendationService aRecommendationService, PreferencesService aPreferencesService,
+            UserDao aUserService)
     {
         return new ActiveLearningSidebarFactory(aRecommendationService);
     }

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

@@ -26,6 +26,10 @@
       </div>
       <div class="scrolling card-body flex-v-container">
 
+        <span wicket:id="notAvailableNotice" class="flex-content no-data-notice">
+          <wicket:message key="notAvailableNotice"/>
+        </span>
+
         <form wicket:id="sessionControlForm">
           <div class="input-group">
             <select class="form-select flex-content" wicket:id="selectLayer" data-container="body"/>

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

@@ -20,12 +20,14 @@
 import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasAccessMode.SHARED_READ_ONLY_ACCESS;
 import static de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasUpgradeMode.AUTO_CAS_UPGRADE;
 import static de.tudarmstadt.ukp.inception.active.learning.sidebar.ActiveLearningUserStateMetaData.CURRENT_AL_USER_STATE;
+import static de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService.KEY_RECOMMENDER_GENERAL_SETTINGS;
 import static de.tudarmstadt.ukp.inception.recommendation.api.model.AnnotationSuggestion.FLAG_REJECTED;
 import static de.tudarmstadt.ukp.inception.recommendation.api.model.AnnotationSuggestion.FLAG_SKIPPED;
 import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordUserAction.ACCEPTED;
 import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordUserAction.CORRECTED;
 import static de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecordUserAction.REJECTED;
 import static de.tudarmstadt.ukp.inception.support.lambda.LambdaBehavior.visibleWhen;
+import static de.tudarmstadt.ukp.inception.support.lambda.LambdaBehavior.visibleWhenNot;
 import static java.lang.String.format;
 import static java.util.Arrays.asList;
 import static java.util.stream.Collectors.toList;
@@ -92,6 +94,7 @@
 import de.tudarmstadt.ukp.inception.bootstrap.BootstrapModalDialog;
 import de.tudarmstadt.ukp.inception.documents.api.DocumentService;
 import de.tudarmstadt.ukp.inception.editor.action.AnnotationActionHandler;
+import de.tudarmstadt.ukp.inception.preferences.PreferencesService;
 import de.tudarmstadt.ukp.inception.recommendation.api.LearningRecordService;
 import de.tudarmstadt.ukp.inception.recommendation.api.RecommendationService;
 import de.tudarmstadt.ukp.inception.recommendation.api.event.AjaxRecommendationAcceptedEvent;
@@ -100,7 +103,6 @@
 import de.tudarmstadt.ukp.inception.recommendation.api.model.AnnotationSuggestion;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.LearningRecord;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.Offset;
-import de.tudarmstadt.ukp.inception.recommendation.api.model.Predictions;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.SpanSuggestion;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionDocumentGroup;
 import de.tudarmstadt.ukp.inception.recommendation.api.model.SuggestionGroup;
@@ -172,7 +174,9 @@ public class ActiveLearningSidebar
     private @SpringBean ApplicationEventPublisherHolder applicationEventPublisherHolder;
     private @SpringBean UserDao userService;
     private @SpringBean FeatureSupportRegistry featureSupportRegistry;
+    private @SpringBean PreferencesService preferencesService;
 
+    private IModel<Boolean> recommendersAvailable;
     private IModel<List<LearningRecord>> learningRecords;
     private CompoundPropertyModel<ActiveLearningServiceImpl.ActiveLearningUserState> alStateModel;
 
@@ -211,17 +215,26 @@ public ActiveLearningSidebar(String aId, IModel<AnnotatorState> aModel,
 
         // Set up the AL state in the page if it is not already there or if for some reason the
         // suggestions have completely disappeared (e.g. after a system restart)
-        AnnotatorState state = getModelObject();
-        Predictions predictions = state.getProject() != null
+        var state = getModelObject();
+        var predictions = state.getProject() != null
                 ? recommendationService.getPredictions(state.getUser(), state.getProject())
                 : null;
         if (aAnnotationPage.getMetaData(CURRENT_AL_USER_STATE) == null || predictions == null) {
-            ActiveLearningUserState alState = new ActiveLearningUserState();
+            var alState = new ActiveLearningUserState();
             alState.setStrategy(new UncertaintySamplingStrategy());
             alStateModel.setObject(alState);
         }
 
-        add(sessionControlForm = createSessionControlForm());
+        recommendersAvailable = LoadableDetachableModel.of(this::isRecommendersAvailable);
+
+        var notAvailableNotice = new WebMarkupContainer("notAvailableNotice");
+        notAvailableNotice.add(visibleWhenNot(recommendersAvailable));
+        add(notAvailableNotice);
+
+        sessionControlForm = createSessionControlForm();
+        sessionControlForm.add(visibleWhen(() -> alStateModel.getObject().isDoExistRecommenders()
+                && recommendersAvailable.getObject()));
+        add(sessionControlForm);
 
         alMainContainer = new WebMarkupContainer(CID_MAIN_CONTAINER);
         alMainContainer.setOutputMarkupId(true);
@@ -230,19 +243,48 @@ public ActiveLearningSidebar(String aId, IModel<AnnotatorState> aModel,
         alMainContainer.add(clearSkippedRecommendationForm());
         alMainContainer.add(createRecommendationOperationForm());
         alMainContainer.add(createLearningHistory());
+        alMainContainer.add(visibleWhen(recommendersAvailable));
         add(alMainContainer);
 
         dialog = new BootstrapModalDialog(CID_CONFIRMATION_DIALOG);
         dialog.trapFocus();
         add(dialog);
     }
 
+    @Override
+    protected void onDetach()
+    {
+        super.onDetach();
+        recommendersAvailable.detach();
+    }
+
+    private boolean isRecommendersAvailable()
+    {
+        var state = getModelObject();
+        var prefs = preferencesService.loadDefaultTraitsForProject(KEY_RECOMMENDER_GENERAL_SETTINGS,
+                state.getProject());
+
+        // Do not show predictions when viewing annotations of another user
+        if (!prefs.isShowRecommendationsWhenViewingOtherUser()
+                && !Objects.equals(state.getUser(), userService.getCurrentUser())) {
+            return false;
+        }
+
+        // Do not show predictions when viewing annotations of curation user
+        if (!prefs.isShowRecommendationsWhenViewingCurationUser()
+                && Objects.equals(state.getUser(), userService.getCurationUser())) {
+            return false;
+        }
+
+        return true;
+    }
+
     private Label createNoRecommendersMessage()
     {
         if (!alStateModel.getObject().isSessionActive()) {
             // Use the currently selected layer from the annotation detail editor panel as the
             // default choice in the active learning mode.
-            List<AnnotationLayer> layersWithRecommenders = listLayersWithRecommenders();
+            var layersWithRecommenders = listLayersWithRecommenders();
             if (layersWithRecommenders.contains(getModelObject().getDefaultAnnotationLayer())) {
                 alStateModel.getObject().setLayer(getModelObject().getDefaultAnnotationLayer());
             }
@@ -258,7 +300,7 @@ else if (!layersWithRecommenders.isEmpty()) {
             }
         }
 
-        Label noRecommendersMessage = new Label(CID_NO_RECOMMENDERS, "None of the layers have any "
+        var noRecommendersMessage = new Label(CID_NO_RECOMMENDERS, "None of the layers have any "
                 + "recommenders configured. Please set the recommenders first in the Project "
                 + "Settings.");
         noRecommendersMessage
@@ -268,9 +310,9 @@ else if (!layersWithRecommenders.isEmpty()) {
 
     private Form<Void> createSessionControlForm()
     {
-        Form<Void> form = new Form<>(CID_SESSION_CONTROL_FORM);
+        var form = new Form<Void>(CID_SESSION_CONTROL_FORM);
 
-        DropDownChoice<AnnotationLayer> layersDropdown = new DropDownChoice<>(CID_SELECT_LAYER);
+        var layersDropdown = new DropDownChoice<AnnotationLayer>(CID_SELECT_LAYER);
         layersDropdown.setModel(alStateModel.bind("layer"));
         layersDropdown.setChoices(LoadableDetachableModel.of(this::listLayersWithRecommenders));
         layersDropdown.setChoiceRenderer(new LambdaChoiceRenderer<>(AnnotationLayer::getUiName));
@@ -284,7 +326,6 @@ private Form<Void> createSessionControlForm()
                 .add(visibleWhen(() -> !alStateModel.getObject().isSessionActive())));
         form.add(new LambdaAjaxLink(CID_STOP_SESSION_BUTTON, this::actionStopSession)
                 .add(visibleWhen(() -> alStateModel.getObject().isSessionActive())));
-        form.add(visibleWhen(() -> alStateModel.getObject().isDoExistRecommenders()));
 
         return form;
     }

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

@@ -23,3 +23,4 @@ delta=\u0394
 history=History
 session=Session
 activeLearning=Active Learning
+notAvailableNotice=Currently not available

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

@@ -19,7 +19,7 @@
 
 import org.apache.wicket.Component;
 import org.apache.wicket.model.IModel;
-import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.core.annotation.Order;
 
 import de.tudarmstadt.ukp.clarin.webanno.api.casstorage.CasProvider;
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
@@ -37,12 +37,12 @@
  * {@link ActiveLearningAutoConfiguration#activeLearningSidebarFactory}.
  * </p>
  */
+@Order(4000)
 public class ActiveLearningSidebarFactory
     extends AnnotationSidebarFactory_ImplBase
 {
     private final RecommendationService recommendationService;
 
-    @Autowired
     public ActiveLearningSidebarFactory(RecommendationService aRecommendationService)
     {
         recommendationService = aRecommendationService;

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

@@ -51,7 +51,7 @@ public ActiveLearningSidebarIcon(String aId, IModel<AnnotatorState> aState)
 
         setOutputMarkupId(true);
 
-        queue(new Icon("icon", FontAwesome5IconType.robot_s));
+        queue(new Icon("icon", FontAwesome5IconType.font_s));
         queue(new Icon("badge", LoadableDetachableModel.of(this::getStateIcon))
                 .add(new ClassAttributeModifier()
                 {

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

@@ -24,6 +24,7 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Set;
+import java.util.stream.DoubleStream;
 
 import de.tudarmstadt.ukp.clarin.webanno.agreement.results.coding.FullCodingAgreementResult;
 import de.tudarmstadt.ukp.clarin.webanno.agreement.results.unitizing.FullUnitizingAgreementResult;
@@ -124,10 +125,10 @@ public void merge(AgreementSummary aResult)
         }
 
         for (var e : aResult.allNull.entrySet()) {
-            allNull.merge(e.getKey(), e.getValue(), Boolean::logicalOr);
+            allNull.merge(e.getKey(), e.getValue(), Boolean::logicalAnd);
         }
 
-        empty |= aResult.empty;
+        empty &= aResult.empty;
 
         if (incompleteSetsByPosition >= 0 && aResult.incompleteSetsByPosition >= 0) {
             incompleteSetsByPosition += aResult.incompleteSetsByPosition;
@@ -208,9 +209,26 @@ public List<String> getCasGroupIds()
         return casGroupIds;
     }
 
+    private DoubleStream usableAgreements()
+    {
+        return agreements.stream() //
+                .mapToDouble(a -> a) //
+                .filter(v -> !Double.isNaN(v)); // skip documents for which we have no agreement
+    }
+
     public double getAgreement()
     {
-        return agreements.stream().mapToDouble(a -> a).average().orElse(Double.NaN);
+        return usableAgreements().average().orElse(Double.NaN);
+    }
+
+    public long getTotalAgreementsCount()
+    {
+        return agreements.size();
+    }
+
+    public long getUsableAgreementsCount()
+    {
+        return usableAgreements().count();
     }
 
     public String getType()

inception/inception-agreement/src/main/java/de/tudarmstadt/ukp/clarin/webanno/agreement/results/coding/PairwiseCodingAgreementTable.java

@@ -244,7 +244,9 @@ else if ((incLabel + incPos) == result.getRelevantSetCount()) {
 
         var tooltipTitle = aRater1.getUiName() + " ↔ " + aRater2.getUiName();
 
-        var tooltipContent = "Positions annotated:\n"
+        var tooltipContent = String.format("Documents counted: %d/%d%n",
+                result.getUsableAgreementsCount(), result.getTotalAgreementsCount())
+                + "Positions annotated:\n"
                 + String.format("- %s: %d/%d%n", aRater1.getUiName(),
                         result.getNonNullCount(casGroupId1), result.getItemCount(casGroupId1))
                 + String.format("- %s: %d/%d%n", aRater2.getUiName(),

inception/inception-agreement/src/main/java/de/tudarmstadt/ukp/clarin/webanno/agreement/results/unitizing/PairwiseUnitizingAgreementTable.java

@@ -203,7 +203,9 @@ else if (noDataRater2) {
 
         var tooltipTitle = aRater1.getUiName() + " ↔ " + aRater2.getUiName();
 
-        var tooltipContent = "Positions annotated:\n"
+        var tooltipContent = String.format("Documents counted: %d/%d%n",
+                result.getUsableAgreementsCount(), result.getTotalAgreementsCount())
+                + "Positions annotated:\n"
                 + String.format("- %s: %d/%d%n", aRater1.getUiName(),
                         result.getNonNullCount(casGroupId1), result.getItemCount(casGroupId1))
                 + String.format("- %s: %d/%d%n", aRater2.getUiName(),

inception/inception-annotation-storage-api/src/main/java/de/tudarmstadt/ukp/clarin/webanno/api/casstorage/CasStorageService.java

@@ -180,4 +180,6 @@ Optional<Long> verifyCasTimestamp(SourceDocument aDocument, String aUser,
     void forceActionOnCas(SourceDocument aDocument, String aUser, CasStorageServiceLoader aLoader,
             CasStorageServiceAction aAction, boolean aSave)
         throws IOException;
+
+    Optional<Long> getCasFileSize(SourceDocument aDocument, String aUser) throws IOException;
 }

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

@@ -875,6 +875,25 @@ public boolean existsCas(SourceDocument aDocument, String aUser) throws IOExcept
         }
     }
 
+    @Override
+    public Optional<Long> getCasFileSize(SourceDocument aDocument, String aUser) throws IOException
+    {
+        Validate.notNull(aDocument, "Source document must be specified");
+        Validate.notBlank(aUser, "User must be specified");
+
+        // Ensure that the CAS is not being re-written and temporarily unavailable while we check
+        // for its existence
+        try (var access = new WithExclusiveAccess(aDocument, aUser)) {
+            return driver.getCasFileSize(aDocument, aUser);
+        }
+        catch (IOException e) {
+            throw e;
+        }
+        catch (Exception e) {
+            throw new IOException(e);
+        }
+    }
+
     private class WithExclusiveAccess
         implements AutoCloseable
     {

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

@@ -48,4 +48,6 @@ Optional<CasStorageMetadata> getCasMetadata(SourceDocument aDocument, String aUs
     Optional<Long> verifyCasTimestamp(SourceDocument aDocument, String aUser,
             long aExpectedTimeStamp, String aContextAction)
         throws IOException, ConcurentCasModificationException;
+
+    Optional<Long> getCasFileSize(SourceDocument aDocument, String aUser) throws IOException;
 }