Merge branch 'release/1.14.5'

* release/1.14.5:
  changelog update
  1.14.5
  fixed test issue
  Updated changelog
  fixes #352
  changelog
  fixes #350
  fixes #347
  enable pretty print when serializing .xmi; related to #339
  replacing now also works from context menu; fixes #345; related to #149
  Bump build-helper-maven-plugin from 3.0.0 to 3.2.0
  Bump maven-antrun-plugin from 1.8 to 3.0.0
  Bump maven-shade-plugin from 3.2.1 to 3.2.4
  Bump mockito-core from 3.1.0 to 3.4.4
  1.15.0-SNAPSHOT
  Bump plexus-archiver from 4.1.0 to 4.2.2
  Bump version.javafx from 13.0.1 to 13.0.2
  Bump reflections from 0.9.11 to 0.9.12
  Bump guava from 28.1-jre to 28.2-jre

Author: Nils Reiter

CHANGELOG.md

@@ -3,6 +3,14 @@
 Issue numbers (e.g., #43) refer to GitHub issues:
 https://github.com/nilsreiter/CorefAnnotator/issues
 
+## 1.14.5
+
+- Fixed behaviour of de-emphasising singletons. Thanks @andreasvc #347
+- Fixed upating of status bar if selection changes #350
+- Fixed the bug that prevented automatically removing empty entities #352
+- XMI files are now pretty printed, making them more git-friendly. 
+  Thanks @andreasvc #339
+
 ## 1.14.4
 
 - Fixed a bug caused by old flags no longer being generated 

pom.xml

@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>de.unistuttgart.ims</groupId>
 	<artifactId>coref.annotator</artifactId>
-	<version>1.14.4</version>
+	<version>1.14.5</version>
 	<packaging>jar</packaging>
 	<name>CorefAnnotator</name>
 	<url>https://github.com/nilsreiter/CorefAnnotator/</url>
@@ -15,7 +15,7 @@
 		<version.eclipse>9.2.0</version.eclipse>
 		<maven.compiler.source>1.8</maven.compiler.source>
 		<maven.compiler.target>1.8</maven.compiler.target>
-		<version.javafx>13.0.1</version.javafx>
+		<version.javafx>13.0.2</version.javafx>
 	</properties>
 	<build>
 		<plugins>
@@ -87,7 +87,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-shade-plugin</artifactId>
-				<version>3.2.1</version>
+				<version>3.2.4</version>
 				<configuration>
 					<transformers>
 						<transformer
@@ -189,7 +189,7 @@
 				<plugins>
 					<plugin>
 						<artifactId>maven-antrun-plugin</artifactId>
-						<version>1.8</version>
+						<version>3.0.0</version>
 						<executions>
 							<execution>
 								<id>duplicate build directory</id>
@@ -231,7 +231,7 @@
 							<dependency>
 								<groupId>org.codehaus.plexus</groupId>
 								<artifactId>plexus-archiver</artifactId>
-								<version>4.1.0</version>
+								<version>4.2.2</version>
 							</dependency>
 							<dependency>
 								<groupId>org.apache.velocity</groupId>
@@ -253,7 +253,7 @@
 					<plugin>
 						<groupId>org.codehaus.mojo</groupId>
 						<artifactId>build-helper-maven-plugin</artifactId>
-						<version>3.0.0</version>
+						<version>3.2.0</version>
 						<executions>
 							<execution>
 								<id>quadrama-add-source</id>
@@ -317,7 +317,7 @@
 					<plugin>
 						<groupId>org.codehaus.mojo</groupId>
 						<artifactId>build-helper-maven-plugin</artifactId>
-						<version>3.0.0</version>
+						<version>3.2.0</version>
 						<executions>
 							<execution>
 								<id>creta-add-source</id>
@@ -365,7 +365,7 @@
 					<plugin>
 						<groupId>org.codehaus.mojo</groupId>
 						<artifactId>build-helper-maven-plugin</artifactId>
-						<version>3.0.0</version>
+						<version>3.2.0</version>
 						<executions>
 							<execution>
 								<id>sfb1391-add-source</id>
@@ -499,7 +499,7 @@
 		<dependency>
 			<groupId>com.google.guava</groupId>
 			<artifactId>guava</artifactId>
-			<version>28.1-jre</version>
+			<version>28.2-jre</version>
 		</dependency>
 
 		<dependency>
@@ -525,7 +525,7 @@
 		<dependency>
 			<groupId>org.reflections</groupId>
 			<artifactId>reflections</artifactId>
-			<version>0.9.11</version>
+			<version>0.9.12</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
@@ -594,7 +594,7 @@
 		<dependency>
 			<groupId>org.mockito</groupId>
 			<artifactId>mockito-core</artifactId>
-			<version>3.1.0</version>
+			<version>3.4.4</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>

src/main/java/de/unistuttgart/ims/coref/annotator/DocumentWindow.java

@@ -760,13 +760,26 @@ public void showSearch() {
 		searchPanel.setVisible(true);
 	}
 
+	@Override
+	protected void entityEventAdd(FeatureStructureEvent event) {
+		super.entityEventAdd(event);
+		updateStatusBar();
+	}
+
+	@Override
+	protected void entityEventRemove(FeatureStructureEvent event) {
+		super.entityEventRemove(event);
+		updateStatusBar();
+	}
+
 	@Override
 	protected void entityEventMove(FeatureStructureEvent event) {
 		for (FeatureStructure fs : event)
 			if (fs instanceof Mention) {
 				highlightManager.unUnderline((Annotation) fs);
 				highlightManager.underline((Mention) fs, new Color(((Entity) event.getArgument2()).getColor()));
 			}
+		updateStatusBar();
 	}
 
 	@Override
@@ -910,6 +923,33 @@ public void updateStyle(Object constant, Object value) {
 		switchStyle(currentStyle);
 	}
 
+	protected void updateStatusBar() {
+		int low = Math.min(textPane.getSelectionStart(), textPane.getSelectionEnd());
+		int high = Math.max(textPane.getSelectionStart(), textPane.getSelectionEnd());
+
+		MutableSet<Mention> mentions = Sets.mutable.empty();
+		if (getDocumentModel() != null && getDocumentModel().getCoreferenceModel() != null) {
+
+			// nothing is selected: show all mentions cursor is part of
+			MutableSet<? extends Annotation> annotations = Sets.mutable
+					.withAll(getDocumentModel().getCoreferenceModel().getMentions(low));
+			mentions = annotations.selectInstancesOf(Mention.class);
+
+			// something is selected
+			if (low != high) {
+				ImmutableSet<Mention> ms = getDocumentModel().getCoreferenceModel().getMentionsBetween(low, high)
+						.selectInstancesOf(Mention.class);
+				mentions.addAllIterable(ms);
+			}
+			setCollectionPanel(mentions.collect(m -> {
+				EntityPanel ep = new EntityPanel(getDocumentModel(), m.getEntity());
+				Annotator.app.getPreferences().addPreferenceChangeListener(ep);
+				getDocumentModel().getCoreferenceModel().addCoreferenceModelListener(ep);
+				return ep;
+			}));
+		}
+	}
+
 	@Override
 	public void switchStyle(StylePlugin sv) {
 		switchStyle(sv, sv.getBaseStyle());
@@ -1480,34 +1520,10 @@ class TextCaretListener implements CaretListener {
 
 		@Override
 		public void caretUpdate(CaretEvent e) {
-			int dot = e.getDot();
-			int mark = e.getMark();
-			int low = Math.min(dot, mark);
-			int high = Math.max(dot, mark);
-
-			MutableSet<Mention> mentions = Sets.mutable.empty();
-			if (getDocumentModel() != null && getDocumentModel().getCoreferenceModel() != null) {
-
-				// nothing is selected: show all mentions cursor is part of
-				MutableSet<? extends Annotation> annotations = Sets.mutable
-						.withAll(getDocumentModel().getCoreferenceModel().getMentions(low));
-				mentions = annotations.selectInstancesOf(Mention.class);
-
-				// something is selected
-				if (dot != mark) {
-					ImmutableSet<Mention> ms = getDocumentModel().getCoreferenceModel().getMentionsBetween(low, high)
-							.selectInstancesOf(Mention.class);
-					mentions.addAllIterable(ms);
-				}
-				setCollectionPanel(mentions.collect(m -> {
-					EntityPanel ep = new EntityPanel(getDocumentModel(), m.getEntity());
-					Annotator.app.getPreferences().addPreferenceChangeListener(ep);
-					getDocumentModel().getCoreferenceModel().addCoreferenceModelListener(ep);
-					return ep;
-				}));
-			}
+
+			updateStatusBar();
 			if (getDocumentModel() != null)
-				highlightSegmentInTOC(dot);
+				highlightSegmentInTOC(e.getDot());
 
 		}
 
@@ -1607,7 +1623,13 @@ else if (anno instanceof DetachedMentionPart)
 						mi.addActionListener(new ActionListener() {
 							@Override
 							public void actionPerformed(ActionEvent e) {
-								getDocumentModel().edit(new AddMentionsToEntity(entity, getSelection()));
+								if (Annotator.app.getPreferences().getBoolean(Constants.CFG_REPLACE_MENTION, false)
+										&& getSelectedAnnotations(Mention.class).size() == 1) {
+									getDocumentModel().edit(
+											new MoveMentionsToEntity(entity, getSelectedAnnotations(Mention.class)));
+								} else {
+									getDocumentModel().edit(new AddMentionsToEntity(entity, getSelection()));
+								}
 							}
 						});
 						mi.setIcon(FontIcon.of(MaterialDesign.MDI_ACCOUNT, new Color(entity.getColor())));

src/main/java/de/unistuttgart/ims/coref/annotator/document/CoreferenceModel.java

@@ -320,6 +320,13 @@ protected synchronized void edit(CoreferenceModelOperation operation) {
 				return addTo(op.getEntity(), sp);
 			}));
 			fireEvent(Event.get(this, Event.Type.Add, op.getEntity(), op.getMentions()));
+			int newNumberOfMentions = getSize(op.getEntity());
+			// may trigger underlining in gray if singleton
+			if (getSpecialHandlingForSingletons() && newNumberOfMentions - op.getMentions().size() == 1
+					&& newNumberOfMentions > 1) {
+				fireEvent(Event.get(this, Event.Type.Update, op.getEntity()));
+				fireEvent(Event.get(this, Event.Type.Update, get(op.getEntity())));
+			}
 		} else if (operation instanceof AttachPart) {
 			AttachPart op = (AttachPart) operation;
 			op.setPart(addTo(op.getMention(), op.getSpan()));
@@ -328,6 +335,21 @@ protected synchronized void edit(CoreferenceModelOperation operation) {
 			MoveMentionsToEntity op = (MoveMentionsToEntity) operation;
 			op.getMentions().forEach(m -> moveTo(op.getTarget(), m));
 			fireEvent(Event.get(this, Event.Type.Move, op.getSource(), op.getTarget(), op.getMentions()));
+			// may trigger underlining in gray if singleton
+			if (getSpecialHandlingForSingletons()) {
+				int numberOfMentionsMoved = op.getMentions().size();
+				// handle the source
+				if (getSize(op.getSource()) == 1) {
+					fireEvent(Event.get(this, Event.Type.Update, op.getSource()));
+					fireEvent(Event.get(this, Event.Type.Update, get(op.getSource())));
+				}
+				// target
+				if (getSize(op.getTarget()) - numberOfMentionsMoved == 1) {
+					fireEvent(Event.get(this, Event.Type.Update, op.getTarget()));
+					fireEvent(Event.get(this, Event.Type.Update, get(op.getTarget())));
+				}
+			}
+
 		} else if (operation instanceof MoveMentionPartToMention) {
 			MoveMentionPartToMention op = (MoveMentionPartToMention) operation;
 			op.getObjects().forEach(d -> {
@@ -465,6 +487,22 @@ protected void edit(RemoveMention op) {
 			}
 		});
 		fireEvent(Event.get(this, Event.Type.Remove, op.getEntity(), op.getFeatureStructures()));
+
+		// may trigger underlining in gray if singleton
+		if (getSpecialHandlingForSingletons()) {
+			if (getSize(op.getEntity()) == 1) {
+				fireEvent(Event.get(this, Event.Type.Update, op.getEntity()));
+				fireEvent(Event.get(this, Event.Type.Update, get(op.getEntity())));
+			}
+		}
+
+		// remove entity if its empty
+		Entity e = op.getEntity();
+		if (entityMentionMap.get(e).isEmpty() && getPreferences().getBoolean(Constants.CFG_DELETE_EMPTY_ENTITIES,
+				Defaults.CFG_DELETE_EMPTY_ENTITIES)) {
+			remove(e);
+			op.setEntityAutoDeleted(true);
+		}
 		registerEdit(op);
 	}
 
@@ -560,6 +598,10 @@ public ImmutableList<Entity> getSingletons() {
 				.select(e -> getMentions(e).size() == 1).toList().toImmutable();
 	}
 
+	protected int getSize(Entity e) {
+		return get(e).size();
+	}
+
 	public ImmutableList<Entity> getEntities(final EntitySorter entitySorter) {
 
 		MutableSet<Entity> eset = Sets.mutable.withAll(JCasUtil.select(documentModel.getJcas(), Entity.class));
@@ -650,6 +692,11 @@ public Preferences getPreferences() {
 		return documentModel.getPreferences();
 	}
 
+	private boolean getSpecialHandlingForSingletons() {
+		return getPreferences().getBoolean(Constants.CFG_UNDERLINE_SINGLETONS_IN_GRAY,
+				Defaults.CFG_UNDERLINE_SINGLETONS_IN_GRAY);
+	}
+
 	public String getToolTipText(FeatureStructure featureStructure) {
 		if (featureStructure instanceof EntityGroup) {
 			StringBuilder b = new StringBuilder();
@@ -969,6 +1016,11 @@ private void undo(DuplicateMentions op) {
 	}
 
 	private void undo(RemoveMention op) {
+		if (op.isEntityAutoDeleted()) {
+			op.getEntity().addToIndexes();
+			fireEvent(Event.get(this, Event.Type.Add, null, op.getEntity()));
+		}
+
 		// re-create all mentions and set them to the op
 		op.getFeatureStructures().forEach(m -> {
 			m.addToIndexes();

src/main/java/de/unistuttgart/ims/coref/annotator/document/op/RemoveMention.java

@@ -9,6 +9,7 @@
 public class RemoveMention extends AbstractRemoveOperation<Mention> implements CoreferenceModelOperation {
 	Entity entity;
 	ImmutableList<Span> spans;
+	boolean entityAutoDeleted = false;
 
 	public RemoveMention(Mention... mention) {
 		super(mention);
@@ -51,4 +52,18 @@ public void setMentions(ImmutableList<Mention> mention) {
 	public ImmutableList<Mention> getMentions() {
 		return getFeatureStructures();
 	}
+
+	/**
+	 * @return the entityAutoDeleted
+	 */
+	public boolean isEntityAutoDeleted() {
+		return entityAutoDeleted;
+	}
+
+	/**
+	 * @param entityAutoDeleted the entityAutoDeleted to set
+	 */
+	public void setEntityAutoDeleted(boolean entityAutoDeleted) {
+		this.entityAutoDeleted = entityAutoDeleted;
+	}
 }

src/main/java/de/unistuttgart/ims/coref/annotator/worker/SaveJCasWorker.java

@@ -37,7 +37,7 @@ protected Object doInBackground() throws Exception {
 				os = new GZIPOutputStream(new FileOutputStream(file));
 			}
 			if (os != null)
-				XmiCasSerializer.serialize(jcas.getCas(), os);
+				XmiCasSerializer.serialize(jcas.getCas(), null, os, true, null);
 		} finally {
 			if (os != null)
 				os.close();