Merge branch 'release/32.x'

* release/32.x:
  #4787 - When re-merging a document CASMetadata is not retained
  #4785 - Upgrade dependencies

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

@@ -21,7 +21,6 @@
 import static org.apache.uima.fit.util.CasUtil.getType;
 import static org.apache.uima.fit.util.FSUtil.setFeature;
 
-import java.io.IOException;
 import java.lang.invoke.MethodHandles;
 import java.util.Optional;
 
@@ -64,7 +63,6 @@ public static void clearCasMetadata(CAS aCas) throws IllegalStateException
 
     public static void addOrUpdateCasMetadata(CAS aCas, long aTimeStamp, SourceDocument aDocument,
             String aUsername)
-        throws IOException
     {
         // If the type system of the CAS does not yet support CASMetadata, then we do not add it
         // and wait for the next regular CAS upgrade before we include this data.
@@ -81,7 +79,7 @@ public static void addOrUpdateCasMetadata(CAS aCas, long aTimeStamp, SourceDocum
         FeatureStructure cmd;
         var cmds = aCas.select(CASMetadata.class).toList();
         if (cmds.size() > 1) {
-            throw new IOException("CAS contains more than one CASMetadata instance!");
+            throw new IllegalStateException("CAS contains more than one CASMetadata instance!");
         }
 
         if (cmds.size() == 1) {

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

@@ -20,12 +20,12 @@
 import static java.lang.System.currentTimeMillis;
 import static java.util.concurrent.TimeUnit.MINUTES;
 import static java.util.stream.Collectors.toList;
+import static org.apache.commons.lang3.StringUtils.isEmpty;
 
 import java.util.List;
 import java.util.Objects;
 
 import org.apache.commons.lang3.Validate;
-import org.apache.uima.cas.CAS;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
@@ -37,9 +37,7 @@
 
 import de.tudarmstadt.ukp.clarin.webanno.api.annotation.config.AnnotationAutoConfiguration;
 import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationFeature;
-import de.tudarmstadt.ukp.clarin.webanno.model.AnnotationLayer;
 import de.tudarmstadt.ukp.clarin.webanno.model.Project;
-import de.tudarmstadt.ukp.inception.rendering.Renderer;
 import de.tudarmstadt.ukp.inception.rendering.pipeline.RenderStep;
 import de.tudarmstadt.ukp.inception.rendering.request.RenderRequest;
 import de.tudarmstadt.ukp.inception.rendering.vmodel.VDocument;
@@ -95,41 +93,42 @@ public void render(VDocument aResponse, RenderRequest aRequest)
     {
         log.trace("Prerenderer.render()");
 
-        CAS cas = aRequest.getCas();
+        var cas = aRequest.getCas();
+        var documentText = cas.getDocumentText();
+
         Validate.notNull(cas, "CAS cannot be null");
 
-        String documentText = cas.getDocumentText();
-        int renderBegin = Math.max(0, aRequest.getWindowBeginOffset());
-        int renderEnd = Math.min(documentText.length(), aRequest.getWindowEndOffset());
+        if (aRequest.getVisibleLayers().isEmpty() || isEmpty(documentText)) {
+            return;
+        }
+
+        var renderBegin = Math.max(0, aRequest.getWindowBeginOffset());
+        var renderEnd = Math.min(documentText.length(), aRequest.getWindowEndOffset());
         aResponse.setText(documentText.substring(renderBegin, renderEnd));
         aResponse.setWindowBegin(renderBegin);
         aResponse.setWindowEnd(renderEnd);
 
-        if (aRequest.getVisibleLayers().isEmpty()) {
-            return;
-        }
-
-        long start = System.currentTimeMillis();
-        Project project = aRequest.getProject();
+        var start = System.currentTimeMillis();
+        var project = aRequest.getProject();
 
         // Listing the features once is faster than repeatedly hitting the DB to list features for
         // every layer.
-        List<AnnotationFeature> supportedFeatures = supportedFeaturesCache.get(project);
-        List<AnnotationFeature> allFeatures = allFeaturesCache.get(project);
+        var supportedFeatures = supportedFeaturesCache.get(project);
+        var allFeatures = allFeaturesCache.get(project);
 
         // Render (custom) layers
-        for (AnnotationLayer layer : aRequest.getVisibleLayers()) {
-            List<AnnotationFeature> layerSupportedFeatures = supportedFeatures.stream() //
+        for (var layer : aRequest.getVisibleLayers()) {
+            var layerSupportedFeatures = supportedFeatures.stream() //
                     .filter(feature -> feature.getLayer().equals(layer)) //
                     .collect(toList());
-            List<AnnotationFeature> layerAllFeatures = allFeatures.stream() //
+            var layerAllFeatures = allFeatures.stream() //
                     .filter(feature -> feature.getLayer().equals(layer)) //
                     .collect(toList());
             // We need to pass in *all* the annotation features here because we also to that in
             // other places where we create renderers - and the set of features must always be
             // the same because otherwise the IDs of armed slots would be inconsistent
             LayerSupport<?, ?> layerSupport = layerSupportRegistry.getLayerSupport(layer);
-            Renderer renderer = layerSupport.createRenderer(layer, () -> layerAllFeatures);
+            var renderer = layerSupport.createRenderer(layer, () -> layerAllFeatures);
             renderer.render(cas, layerSupportedFeatures, aResponse, renderBegin, renderEnd);
         }
 

inception/inception-api-annotation/src/main/java/de/tudarmstadt/ukp/inception/editor/state/AnnotatorStateImpl.java

@@ -363,6 +363,18 @@ public void setPageBegin(CAS aCas, int aOffset)
     @Override
     public void setVisibleUnits(List<Unit> aUnits, int aTotalUnitCount)
     {
+        if (aUnits.isEmpty()) {
+            unitCount = 0;
+            visibleUnits = aUnits;
+            firstVisibleUnitIndex = 0;
+            lastVisibleUnitIndex = 0;
+            focusUnitIndex = 0;
+            windowBeginOffset = 0;
+            windowEndOffset = 0;
+            fireViewStateChanged();
+            return;
+        }
+
         unitCount = aTotalUnitCount;
         visibleUnits = aUnits;
         firstVisibleUnitIndex = aUnits.get(0).getIndex();

inception/inception-api-render/src/main/java/de/tudarmstadt/ukp/inception/rendering/paging/PagingStrategy.java

@@ -99,7 +99,11 @@ default Unit unitAtIndex(CAS aCas, int aIndex)
             index = 1;
         }
 
-        List<Unit> units = units(aCas);
+        var units = units(aCas);
+
+        if (units.isEmpty()) {
+            return null;
+        }
 
         if (index > units.size()) {
             index = units.size();
@@ -128,8 +132,10 @@ default List<Unit> unitsStartingAtOffset(CAS aCas, int aOffset, int aCount)
      */
     default void moveToUnit(AnnotatorViewState aState, CAS aCas, int aIndex, FocusPosition aPos)
     {
-        Unit unit = unitAtIndex(aCas, aIndex);
-        moveToOffset(aState, aCas, unit.getBegin(), aPos);
+        var unit = unitAtIndex(aCas, aIndex);
+        if (unit != null) {
+            moveToOffset(aState, aCas, unit.getBegin(), aPos);
+        }
     }
 
     default void moveToPreviousPage(AnnotatorViewState aState, CAS aCas, FocusPosition aPos)

inception/inception-curation/src/main/java/de/tudarmstadt/ukp/inception/curation/merge/CasMerge.java

@@ -63,6 +63,7 @@
 import com.github.benmanes.caffeine.cache.Caffeine;
 import com.github.benmanes.caffeine.cache.LoadingCache;
 
+import de.tudarmstadt.ukp.clarin.webanno.api.type.CASMetadata;
 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.DiffResult;
@@ -80,6 +81,7 @@
 import de.tudarmstadt.ukp.inception.annotation.feature.link.LinkFeatureTraits;
 import de.tudarmstadt.ukp.inception.annotation.layer.relation.RelationAdapter;
 import de.tudarmstadt.ukp.inception.annotation.layer.span.SpanAdapter;
+import de.tudarmstadt.ukp.inception.annotation.storage.CasMetadataUtils;
 import de.tudarmstadt.ukp.inception.curation.merge.strategy.DefaultMergeStrategy;
 import de.tudarmstadt.ukp.inception.curation.merge.strategy.MergeStrategy;
 import de.tudarmstadt.ukp.inception.rendering.vmodel.VID;
@@ -206,7 +208,7 @@ public Set<LogMessage> clearAndMergeCas(DiffResult aDiff, SourceDocument aTarget
         throws UIMAException
     {
         // Remove any annotations from the target CAS - keep type system, sentences and tokens
-        clearAnnotations(aTargetDocument.getProject(), aTargetCas);
+        clearAnnotations(aTargetDocument, aTargetCas);
 
         return mergeCas(aDiff, aTargetDocument, aTargetUsername, aTargetCas, aCasMap);
     }
@@ -432,15 +434,14 @@ public Set<LogMessage> mergeCas(DiffResult aDiff, SourceDocument aTargetDocument
      * Removes all annotations except {@link Token} and {@link Sentence} annotations - but from
      * these also only the offsets are kept and all other features are cleared.
      * 
-     * @param aProject
-     *            the project to which the CAS belongs.
-     * 
+     * @param aDocument
+     *            the document to which the CAS belongs.
      * @param aCas
      *            the CAS to clear.
      * @throws UIMAException
      *             if there was a problem clearing the CAS.
      */
-    private void clearAnnotations(Project aProject, CAS aCas) throws UIMAException
+    private void clearAnnotations(SourceDocument aDocument, CAS aCas) throws UIMAException
     {
         // Copy the CAS - basically we do this just to keep the full type system information
         var backup = WebAnnoCasUtil.createCasCopy(aCas);
@@ -456,10 +457,18 @@ private void clearAnnotations(Project aProject, CAS aCas) throws UIMAException
             createDocumentMetadata(aCas);
         }
 
+        var casMetadataType = aCas.getTypeSystem().getType(CASMetadata._TypeName);
+        if (casMetadataType != null && exists(backup, casMetadataType)) {
+            var casMetadata = backup.select(CASMetadata.class).single();
+            var timestamp = casMetadata.getLastChangedOnDisk();
+            var username = casMetadata.getUsername();
+            CasMetadataUtils.addOrUpdateCasMetadata(aCas, timestamp, aDocument, username);
+        }
+
         aCas.setDocumentLanguage(backup.getDocumentLanguage()); // DKPro Core Issue 435
         aCas.setDocumentText(backup.getDocumentText());
 
-        transferSegmentation(aProject, aCas, backup);
+        transferSegmentation(aDocument.getProject(), aCas, backup);
     }
 
     /**

inception/inception-diag/src/main/java/de/tudarmstadt/ukp/clarin/webanno/diag/checks/CASMetadataTypeIsPresentCheck.java

@@ -35,9 +35,15 @@ public class CASMetadataTypeIsPresentCheck
     @Override
     public boolean check(Project aProject, CAS aCas, List<LogMessage> aMessages)
     {
-        if (aCas.getTypeSystem().getType(CASMetadata.class.getName()) == null) {
-            aMessages.add(LogMessage.warn(this, "CAS needs upgrade to support CASMetadata which is "
+        if (aCas.getTypeSystem().getType(CASMetadata._TypeName) == null) {
+            aMessages.add(LogMessage.info(this, "CAS needs upgrade to support CASMetadata which is "
                     + "required to detect concurrent modifications to CAS files."));
+            return true;
+        }
+
+        if (aCas.select(CASMetadata.class).isEmpty()) {
+            aMessages.add(LogMessage.warn(this,
+                    "CAS contains no CASMetadata. Cannot check concurrent access."));
         }
 
         // This is an informative check - not critical, so we always pass it.

inception/inception-diag/src/main/java/de/tudarmstadt/ukp/clarin/webanno/diag/checks/NegativeSizeAnnotationsCheck.java

@@ -35,7 +35,7 @@ public boolean check(Project aProject, CAS aCas, List<LogMessage> aMessages)
     {
         boolean ok = true;
 
-        for (Annotation ann : aCas.select(Annotation.class)) {
+        for (var ann : aCas.select(Annotation.class)) {
             if (ann.getBegin() > ann.getEnd()) {
                 aMessages.add(error(this, "[%s] at [%d-%d] has negative size (starts after ending)",
                         ann.getType().getName(), ann.getBegin(), ann.getEnd()));