Merge branch 'release/2.1.0'

* release/2.1.0: Updated changelog 2.1.0 and updated Changelog Fix #380 Downgrade slf4j-nop to match managed version of log4j Fix reflection warning by adding multi-release manifest entry Fix #381 Implement CSV export for ExportMultipleFiles tool Update dependencies Use Java 11 and fix duplicate dependencies appropriately
nilsreiter · Apr 8, 2022 · b3f2db8 · b3f2db8
2 parents 088d6a9 + f798114
commit b3f2db8
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,6 +3,15 @@
 Issue numbers (e.g., #43) refer to GitHub issues:
 https://github.com/nilsreiter/CorefAnnotator/issues
 
+## 2.1.0
+
+- New: Multiple files can be exported at once into CSV format #370
+- Fixes an issue that made deleted annotations to re-appear if the file is re-opened #380
+- Fixes an issue that caused a freeze when deleting an annotation #381
+- Updated some dependencies
+
+Thanks Börge for taking care of these!
+
 ## 2.0.1
 
 - Fixes an issue that prevented expanding the tree properly in some imported files #373

diff --git a/pom.xml b/pom.xml
@@ -4,7 +4,7 @@
 	<modelVersion>4.0.0</modelVersion>
 	<groupId>de.unistuttgart.ims</groupId>
 	<artifactId>coref.annotator</artifactId>
-	<version>2.0.1</version>
+	<version>2.1.0</version>
 	<packaging>jar</packaging>
 	<name>CorefAnnotator</name>
 	<url>https://github.com/nilsreiter/CorefAnnotator/</url>
@@ -13,12 +13,18 @@
 		<version.dkpro>2.2.0</version.dkpro>
 		<version.ikonli>12.2.0</version.ikonli>
 		<version.eclipse>10.2.0</version.eclipse>
-		<maven.compiler.source>1.8</maven.compiler.source>
-		<maven.compiler.target>1.8</maven.compiler.target>
 		<version.javafx>14.0.2.1</version.javafx>
 	</properties>
 	<build>
 		<plugins>
+			<plugin>
+				<groupId>org.apache.maven.plugins</groupId>
+				<artifactId>maven-compiler-plugin</artifactId>
+				<version>3.8.1</version>
+				<configuration>
+					<release>11</release>
+				</configuration>
+			</plugin>
 			<plugin>
 				<groupId>org.apache.uima</groupId>
 				<artifactId>jcasgen-maven-plugin</artifactId>
@@ -80,6 +86,7 @@
 							<manifestEntries>
 								<Main-Class>de.unistuttgart.ims.coref.annotator.Annotator</Main-Class>
 								<Build-Number>${project.version}</Build-Number>
+								<Multi-Release>true</Multi-Release>
 							</manifestEntries>
 						</transformer>
 						<transformer
@@ -436,7 +443,7 @@
 		<dependency>
 			<groupId>org.reflections</groupId>
 			<artifactId>reflections</artifactId>
-			<version>0.9.12</version>
+			<version>0.10.2</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
@@ -471,16 +478,22 @@
 		<dependency>
 			<groupId>org.dkpro.core</groupId>
 			<artifactId>dkpro-core-stanfordnlp-gpl</artifactId>
+			<exclusions>
+				<exclusion>
+					<groupId>xml-apis</groupId>
+					<artifactId>xml-apis</artifactId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.json</groupId>
 			<artifactId>json</artifactId>
-			<version>20151123</version>
+			<version>20210307</version>
 		</dependency>
 		<dependency>
 			<groupId>de.unistuttgart.ims.uima.io</groupId>
 			<artifactId>generic-xml-reader</artifactId>
-			<version>2.0.0</version>
+			<version>2.0.1</version>
 		</dependency>
 		<dependency>
 			<groupId>com.lexicalscope.jewelcli</groupId>
@@ -490,7 +503,7 @@
 		<dependency>
 			<groupId>org.mockito</groupId>
 			<artifactId>mockito-core</artifactId>
-			<version>3.4.4</version>
+			<version>4.1.0</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
@@ -506,12 +519,18 @@
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi</artifactId>
-			<version>4.1.2</version>
+			<version>5.1.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.poi</groupId>
 			<artifactId>poi-ooxml</artifactId>
-			<version>4.1.2</version>
+			<version>5.1.0</version>
+			<exclusions>
+				<exclusion>
+					<artifactId>xml-apis</artifactId>
+					<groupId>xml-apis</groupId>
+				</exclusion>
+			</exclusions>
 		</dependency>
 		<dependency>
 			<groupId>org.knowm.xchart</groupId>
@@ -521,7 +540,7 @@
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-csv</artifactId>
-			<version>1.8</version>
+			<version>1.9.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.slf4j</groupId>

diff --git a/src/main/java/de/unistuttgart/ims/coref/annotator/Annotator.java b/src/main/java/de/unistuttgart/ims/coref/annotator/Annotator.java
@@ -465,8 +465,7 @@ private MutableList<File> getRecentFilesFromPreferences() {
 
 	private void recentFiles2Preferences(MutableList<File> recentFiles) {
 		StringBuilder sb = new StringBuilder();
-		for (int index = 0; index < recentFiles.size(); index++) {
-			File file = recentFiles.get(index);
+		for (File file : recentFiles) {
 			if (sb.length() > 0) {
 				sb.append(File.pathSeparator);
 			}
@@ -481,7 +480,6 @@ public JMenu getRecentFilesMenu() {
 		for (int i = 0; i < Math.min(20, recentFiles.size()); i++)
 			m.add(new SelectedFileOpenAction(this, recentFiles.get(i)));
 		return m;
-
 	}
 
 	public Preferences getPreferences() {

diff --git a/src/main/java/de/unistuttgart/ims/coref/annotator/DocumentWindow.java b/src/main/java/de/unistuttgart/ims/coref/annotator/DocumentWindow.java
@@ -1610,27 +1610,33 @@ protected JMenu getMentionItem(Mention m) {
 			StringBuilder b = new StringBuilder();
 			b.append(m.getAddress());
 
-			String surf = UimaUtil.getCoveredText(m);
-			surf = StringUtils.abbreviateMiddle(surf, "...", 20);
-
-			if (m.getEntity().getLabel() != null)
-				b.append(": ")
-						.append(StringUtils.abbreviateMiddle(
-								getDocumentModel().getCoreferenceModel().getLabel(m.getEntity()), "...",
-								Constants.UI_MAX_STRING_WIDTH_IN_MENU));
-
+			String mention = StringUtils
+					.abbreviateMiddle(UimaUtil.getCoveredText(m), "...", 20);
+
+			if (m.getEntity().getLabel() != null) {
+				String entity = StringUtils.abbreviateMiddle(
+						getDocumentModel().getCoreferenceModel().getLabel(m.getEntity()), "...",
+						Constants.UI_MAX_STRING_WIDTH_IN_MENU / 2);
+				b.append(String.format(": %s (%s)", mention, entity));
+			}
+
 			JMenu mentionMenu = new JMenu(b.toString());
 			mentionMenu.setIcon(FontIcon.of(MaterialDesign.MDI_ACCOUNT, new Color(m.getEntity().getColor())));
 			Action a = new ShowMentionInTreeAction(DocumentWindow.this, m);
-			mentionMenu.add('"' + surf + '"');
+			mentionMenu.add(String.format("\"%s\"", mention));
+			mentionMenu.getItem(mentionMenu.getItemCount() - 1).setEnabled(false);
 			mentionMenu.add(a);
 			mentionMenu.add(new DeleteAction(DocumentWindow.this, m));
-			if (m.getSurface().size() > 0)
+
+			if (m.getSurface().size() > 1) {
 				for (MentionSurface ms : m.getSurface()) {
-					JMenu mentionSurfaceMenu = new JMenu(StringUtils.abbreviateMiddle(ms.getCoveredText(), "...", 20));
+					JMenu mentionSurfaceMenu = new JMenu(StringUtils.abbreviateMiddle(
+							ms.getCoveredText(), "...",
+							Constants.UI_MAX_STRING_WIDTH_IN_MENU));
 					mentionSurfaceMenu.add(new DeleteAction(DocumentWindow.this, ms));
 					mentionMenu.add(mentionSurfaceMenu);
 				}
+			}
 
 			return mentionMenu;
 		}

diff --git a/src/main/java/de/unistuttgart/ims/coref/annotator/document/CoreferenceModel.java b/src/main/java/de/unistuttgart/ims/coref/annotator/document/CoreferenceModel.java
@@ -153,7 +153,7 @@ protected Entity createEntity(String l) {
 		e.setLabel(l);
 		e.setFlags(new EmptyFSList<Flag>(documentModel.getJcas()));
 		e.setMembers(new FSArray<Entity>(documentModel.getJcas(), 0));
-		e.addToIndexes();
+		e.addToIndexes(getJCas());
 		return e;
 	}
 
@@ -257,8 +257,8 @@ protected synchronized void edit(CoreferenceModelOperation operation) {
 			for (; i < arr.size(); i++) {
 				arr.set(i, newMembers.get(i - oldSize));
 			}
-			arr.addToIndexes();
-			op.getEntityGroup().removeFromIndexes();
+			arr.addToIndexes(getJCas());
+			op.getEntityGroup().removeFromIndexes(getJCas());
 			op.getEntityGroup().setMembers(arr);
 			updateEntityGroupLabel(op.getEntityGroup());
 			fireEvent(Event.get(this, Event.Type.Add, op.getEntityGroup(), op.getEntities()));
@@ -454,7 +454,7 @@ protected void edit(RemoveMentionSurface op) {
 			fireEvent(Event.get(this, Type.Remove, m, ms));
 			mentions.add(m);
 			spans.add(new Span(ms));
-			ms.removeFromIndexes();
+			ms.removeFromIndexes(getJCas());
 			characterPosition2AnnotationMap.remove(ms);
 		});
 		op.setMention(mentions.toImmutable());
@@ -737,7 +737,7 @@ public void initialPainting() {
 		}
 		for (Mention mention : JCasUtil.select(documentModel.getJcas(), Mention.class)) {
 			entityMentionMap.put(mention.getEntity(), mention);
-			mention.getEntity().addToIndexes();
+			mention.getEntity().addToIndexes(getJCas());
 			registerAnnotation(mention);
 			fireEvent(Event.get(this, Event.Type.Add, mention.getEntity(), mention));
 
@@ -763,7 +763,7 @@ private Entity merge(Iterable<Entity> nodes) {
 					entityMentionMap.get(n).toSet().forEach(m -> moveTo(tgt, m));
 
 					entityMentionMap.removeAll(n);
-					n.removeFromIndexes();
+					n.removeFromIndexes(getJCas());
 				}
 			}
 		return biggest;
@@ -809,7 +809,7 @@ private void remove(Entity entity) {
 		for (Mention m : entityMentionMap.get(entity)) {
 			for (MentionSurface ms : m.getSurface())
 				characterPosition2AnnotationMap.remove(ms);
-			m.removeFromIndexes();
+			m.removeFromIndexes(getJCas());
 			// TODO: remove parts
 		}
 		for (Entity group : entityEntityGroupMap.get(entity)) {
@@ -822,7 +822,7 @@ private void remove(Entity entity) {
 
 		fireEvent(Event.get(this, Event.Type.Remove, null, entity));
 		entityMentionMap.removeAll(entity);
-		entity.removeFromIndexes();
+		entity.removeFromIndexes(getJCas());
 		Annotator.logger.traceExit();
 	}
 
@@ -831,7 +831,7 @@ private void remove(Mention m, boolean autoRemove) {
 		for (MentionSurface ms : m.getSurface())
 			characterPosition2AnnotationMap.remove(ms);
 		entityMentionMap.remove(entity, m);
-		m.removeFromIndexes();
+		m.removeFromIndexes(getJCas());
 		if (autoRemove && entityMentionMap.get(entity).isEmpty() && getPreferences()
 				.getBoolean(Constants.CFG_DELETE_EMPTY_ENTITIES, Defaults.CFG_DELETE_EMPTY_ENTITIES)) {
 			remove(entity);
@@ -869,7 +869,7 @@ protected void undo(AddSpanToMention op) {
 		MentionSurface ms = op.getMentionSurface();
 		UimaUtil.removeMentionSurface(ms.getMention(), ms);
 		fireEvent(Event.get(this, Event.Type.Remove, ms.getMention(), ms));
-		ms.removeFromIndexes();
+		ms.removeFromIndexes(getJCas());
 		characterPosition2AnnotationMap.remove(ms);
 	}
 
@@ -933,7 +933,7 @@ protected void undo(CoreferenceModelOperation operation) {
 			RemoveDuplicateMentionsInEntities op = (RemoveDuplicateMentionsInEntities) operation;
 
 			op.getFeatureStructures().forEach(m -> {
-				m.addToIndexes();
+				m.addToIndexes(getJCas());
 				entityMentionMap.put(m.getEntity(), m);
 				registerAnnotation(m);
 				fireEvent(Event.get(this, Type.Add, m.getEntity(), m));
@@ -943,7 +943,7 @@ protected void undo(CoreferenceModelOperation operation) {
 		} else if (operation instanceof RemoveEntities) {
 			RemoveEntities op = (RemoveEntities) operation;
 			op.getFeatureStructures().forEach(e -> {
-				e.addToIndexes();
+				e.addToIndexes(getJCas());
 				if (op.entityEntityGroupMap.containsKey(e)) {
 					for (Entity group : op.entityEntityGroupMap.get(e)) {
 						group.setMembers(UimaUtil.addTo(documentModel.getJcas(), group.getMembers(), e));
@@ -967,15 +967,15 @@ protected void undo(CoreferenceModelOperation operation) {
 			}
 			op.getEntityGroup().setMembers(newArr);
 			updateEntityGroupLabel(op.getEntityGroup());
-			newArr.addToIndexes();
-			oldArr.removeFromIndexes();
+			newArr.addToIndexes(getJCas());
+			oldArr.removeFromIndexes(getJCas());
 		} else if (operation instanceof RemoveSingletons) {
 			undo((RemoveSingletons) operation);
 		} else if (operation instanceof MergeEntities) {
 			MergeEntities op = (MergeEntities) operation;
 			for (Entity oldEntity : op.getEntities()) {
 				if (op.getEntity() != oldEntity) {
-					oldEntity.addToIndexes();
+					oldEntity.addToIndexes(getJCas());
 					fireEvent(Event.get(this, Event.Type.Add, null, oldEntity));
 					for (Mention m : op.getPreviousState().get(oldEntity)) {
 						moveTo(oldEntity, m);
@@ -1008,13 +1008,13 @@ private void undo(DuplicateMentions op) {
 
 	private void undo(RemoveMention op) {
 		if (op.isEntityAutoDeleted()) {
-			op.getEntity().addToIndexes();
+			op.getEntity().addToIndexes(getJCas());
 			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();
+			m.addToIndexes(getJCas());
 			m.setEntity(op.getEntity());
 			entityMentionMap.put(op.getEntity(), m);
 			for (MentionSurface ms : m.getSurface())
@@ -1038,13 +1038,13 @@ private void undo(RemoveMentionSurface op) {
 	}
 
 	private void undo(RemoveSingletons op) {
-		op.getFeatureStructures().forEach(e -> e.addToIndexes());
+		op.getFeatureStructures().forEach(e -> e.addToIndexes(getJCas()));
 		op.getMentions().forEach(m -> {
 			entityMentionMap.put(m.getEntity(), m);
 			for (MentionSurface ms : m.getSurface())
 				characterPosition2AnnotationMap.add(ms);
-			m.addToIndexes();
-			m.getEntity().addToIndexes();
+			m.addToIndexes(getJCas());
+			m.getEntity().addToIndexes(getJCas());
 			fireEvent(Event.get(this, Event.Type.Add, null, m.getEntity()));
 			fireEvent(Event.get(this, Event.Type.Add, m.getEntity(), m));
 		});
@@ -1076,7 +1076,7 @@ protected void undo(RenameAllEntities operation) {
 	 */
 	protected void undo(MergeMentions operation) {
 		operation.getMentions().forEach(m -> {
-			m.addToIndexes();
+			m.addToIndexes(getJCas());
 			entityMentionMap.put(operation.getNewMention().getEntity(), m);
 			fireEvent(Event.get(this, Type.Add, m.getEntity(), m));
 		});

diff --git a/src/main/java/de/unistuttgart/ims/coref/annotator/document/EntityTreeModel.java b/src/main/java/de/unistuttgart/ims/coref/annotator/document/EntityTreeModel.java
@@ -123,9 +123,9 @@ public void entityEvent(FeatureStructureEvent event) {
 					if (etn != null) {
 						etn.removeAllChildren();
 						removeNodeFromParent(etn);
+						etn.modify();
 					}
 					fsMap.remove(event.getArgument(i));
-					etn.modify();
 				}
 			optResort();
 			break;