This class needs to be public so surefire don't crash running the tests

README.md

@@ -1,23 +1,87 @@
-# Introduction
-
-CATMA is a web based application for text annotation and analysis.
-
-It has two main components: an annotation component that allows the user to annotate text and an analysis component that supports pattern analysis of text and annotations in combination through a custom but easy query language and a data visualization facility based on [Vega](https://vega.github.io/vega/). 
-
-It also allows the project-centric management of text corpora, annotation collections, tagsets and team members. 
-
-CATMA uses a Gitlab instance as its backend to store and manage the project's resources and team. All resources are versioned and available through either the CATMA web interface or the Gitlab REST API.
-
-# Installation & Setup
-
-CATMA uses a stock Gitlab installation with the following mandatory configuration:
-
-The default dev ops pipeline needs to be switched off.
-The default branch protection needs to be "partially protected".
-
-The CATMA war file can be build with 
-`mvn clean compile package`
-
-CATMA is tested with the jetty servlet container. 
-
-Copy and configure the catma.properties file from the resource folder to the web app root folder.
+# Introduction
+
+CATMA is a web based application for text annotation and analysis.
+
+It has two main components: an annotation component that allows the user to annotate text and an analysis component that supports pattern analysis of text and annotations in combination through a custom but easy query language and a data visualization facility based on [Vega](https://vega.github.io/vega/).
+
+It also allows the project-centric management of text corpora, annotation collections, tagsets and team members.
+
+CATMA uses a Gitlab instance as its backend to store and manage the project's resources and team. All resources are versioned and available through either the CATMA web interface or the Gitlab REST API.
+
+# Requirements
+ * jdk11 or lower, ideally jdk8
+  * say on debian 12/bookworm, you wanna get jdk from oldstable, so you don't have to change libc6
+ * maven
+ * docker
+
+# Installation & Setup
+First, you need to get some dependencies dealt with:
+```
+git clone https://github.com/forTEXT/serverside-elements.git # some bundled dependency that is patched
+cd serverside-elements
+mvn compile package
+mvn install:install-file -Dfile=elements/target/elements-0.2.3-CATMA.jar -DpomFile=elements/pom.xml
+cd ..
+git clone https://github.com/forTEXT/gitlab4j-api.git # some other patched dependency
+cd gitlab4j-api
+mvn compile package
+mvn install:install-file -Dfile=target/gitlab4j-api-5.1.0-SNAPSHOT.jar -DpomFile=pom.xml
+cd ..
+sudo docker pull gitlab/gitlab-ce
+echo > docker-compose.yml """
+services:
+  gitlab-server:
+    image: 'gitlab/gitlab-ce'
+    container_name: gitlab-server
+    ports:
+      - '8088:80'
+    environment:
+      GITLAB_ROOT_EMAIL: '[email protected]'
+      GITLAB_ROOT_PASSWORD: 'Abcd@0123456789 CHANGE THIS'
+    volumes:
+      - ./gitlab/config:/etc/gitlab
+      - ./gitlab/data:/var/opt/gitlab
+"""
+sudo docker compose up
+```
+
+This has downloaded a gitlab docker insancen. When the virtual machine in which gitlab
+runs will be started you should be able to configure in your browser at localhost:8088.
+You then need to change the configuration this way:
+ * The default dev ops pipeline needs to be switched off.
+   * That is in settings => CI/CD => Continuous integration and development => remove
+     the tickmark before "Default to Auto DevOps pipeline for all projects"
+ * The default branch protection needs to be disabled
+   * Settings => Repository => Default branch => Initial branch protection needs to be
+     set to not protected
+ * Then you need to go in your user settings and create and access token for the API
+   for the root account
+   * User settings => access tokens
+
+```
+git clone https://github.com/forTEXT/catma
+cd catma
+cp src/main/resources/catma.properties .
+```
+
+You probably wanna change some config option in catma.properties ; namely, if you
+plan on just running catma via maven for testing purposes, you probably want
+to set the BASE_URL to http://localhost:8080/catma/. Also you need to configure the
+gitlab access token and server url.
+
+Then you can:
+```
+mvn clean compile package
+```
+As maven runs tests after the compilation, the gitlab link gets extensively tested,
+so you need that link to run so you can compile the catma jar file.
+
+Copy and configure the catma.properties file from the resource folder to the web app root folder.
+```
+cp catma.properties src/main/webapp/catma.properties
+```
+
+CATMA is tested with the jetty servlet container. To run it, you just have to type:
+```
+mvn jetty:run
+```

src/main/java/de/catma/repository/git/GitProjectHandler.java

@@ -211,6 +211,24 @@ public String createOrUpdateTag(String tagsetId, TagDefinition tagDefinition, St
 		}
 	}
 
+	public String moveTagAndUpdateAnnotations(TagsetDefinition tsdFrom, TagsetDefinition tsdTo, TagDefinition tdFrom, TagDefinition tdTo, Multimap<String, TagInstance> tagInstancesByCollectionId, String commitMsg) throws IOException {
+		try (LocalGitRepositoryManager localGitRepoManager = localGitRepositoryManager) {
+			localGitRepoManager.open(projectReference.getNamespace(), projectReference.getProjectId());
+			GitTagsetHandler gitTagsetHandler = new GitTagsetHandler(
+					localGitRepoManager,
+					projectPath,
+					remoteGitServerManager.getUsername(),
+					remoteGitServerManager.getEmail()
+			);
+			String projectRevision = gitTagsetHandler.moveTagDefinition(tdFrom, tdTo, commitMsg);
+
+			localGitRepoManager.push(jGitCredentialsManager);
+
+			return projectRevision;
+		}
+	}
+
+
 	public String removeTagAndAnnotations(TagDefinition tagDefinition, Multimap<String, TagInstance> tagInstancesByCollectionId) throws IOException {
 		try (LocalGitRepositoryManager localGitRepoManager = localGitRepositoryManager) {
 			localGitRepoManager.open(projectReference.getNamespace(), projectReference.getProjectId());

src/main/java/de/catma/repository/git/GitTagsetHandler.java

@@ -171,6 +171,77 @@ public ContentInfoSet getContentInfoSet(String tagsetId) throws IOException {
 
 		return contentInfoSet;
 	}
+
+	/**
+	 * Moves a tag definition between one or multiple tagsets identified by <code>tagsetId</code>.
+	 *
+	 * @param tdFrom {@link TagDefinition} source
+	 * @param tdTo {@link TagDefinition} destination
+	 * @param commitMsg commit message
+	 * @return the new project revision hash
+	 * @throws IOException if an error occurs during the move of the tag definition
+	 */
+	public String moveTagDefinition(
+			TagDefinition tdFrom,
+			TagDefinition tdTo,
+			String commitMsg
+	) throws IOException {
+		String pdj = "/propertydefs.json";
+		String common =	String.format("%s/%s/", this.projectDirectory.getAbsolutePath(), GitProjectHandler.TAGSETS_DIRECTORY_NAME);
+		String fromTagsetDir = String.format("%s/%s/", common, tdFrom.getTagsetDefinitionUuid());
+		String toTagsetDir = String.format("%s/%s/", common, tdTo.getTagsetDefinitionUuid());
+
+		/* This work like it seems: all the folders having subdirectories have a folder
+		at the root of the tagset folder containing the subitems. This mean that the
+		hiearchy isn't stored as it is in the UI. */
+		String fromPath = fromTagsetDir +
+			(StringUtils.isEmpty(tdFrom.getParentUuid()) ? "" : (tdFrom.getParentUuid() + "/"))
+			+ tdFrom.getUuid();
+		String toPath = toTagsetDir +
+			(StringUtils.isEmpty(tdTo.getParentUuid()) ? "" : (tdTo.getParentUuid() + "/"))
+			+ tdTo.getUuid();
+		File from = Paths.get(fromPath).toFile();
+		File to = Paths.get(toPath).toFile();
+		if ((StringUtils.isEmpty(tdFrom.getParentUuid()) && StringUtils.isEmpty(tdTo.getParentUuid())) ||
+			(!StringUtils.isEmpty(tdFrom.getParentUuid()) && !StringUtils.isEmpty(tdTo.getParentUuid()))) {
+			/* if we move from an item in a tree somewhere to an item in a tree somewhere else, or if we
+				move a parent around in the root of the hierarchy, its fine, we just move the folder
+                                around */
+			FileUtils.moveDirectory(from, to);
+			this.localGitRepositoryManager.remove(Paths.get(fromPath + pdj).toFile());
+			this.localGitRepositoryManager.remove(from);
+		}
+		if (StringUtils.isEmpty(tdFrom.getParentUuid()) && !StringUtils.isEmpty(tdTo.getParentUuid())) {
+			/* if we moved from the root to an object lower in the hierarchy, we need to bring the children back down 
+			(if it has any) */
+			/* There shouldn't be a subdir with the name of the current tag UUID in its parent folder */
+			to.mkdirs();
+			FileUtils.moveFile(Paths.get(fromPath+pdj).toFile(), Paths.get(toPath+pdj).toFile());
+			/* That leaves the children in the root of the tagset under the directory with the name of
+                        their parent, which is what we wanted anyways */
+			this.localGitRepositoryManager.remove(Paths.get(fromPath + pdj).toFile());
+		}
+		if (StringUtils.isEmpty(tdTo.getParentUuid()) && !StringUtils.isEmpty(tdFrom.getParentUuid())) {
+			/* If we moved back to the root, our children are already in a directory called with our UUID at the root,
+			we need to not squish them, so we only move the propertydefs there */
+			FileUtils.moveFile(Paths.get(fromPath+pdj).toFile(), Paths.get(toPath+pdj).toFile());
+			this.localGitRepositoryManager.remove(Paths.get(fromPath + pdj).toFile());
+		}
+
+		GitTagDefinition gitTagDefinition = new GitTagDefinition(tdTo);
+		String serializedGitTagDefinition =
+				new SerializationHelper<GitTagDefinition>().serialize(gitTagDefinition);
+
+		String projectRevision = this.localGitRepositoryManager.addAndCommit(
+			Paths.get(toPath + pdj).toFile(),
+			serializedGitTagDefinition.getBytes(StandardCharsets.UTF_8),
+			commitMsg,
+			this.username,
+			this.email);
+		System.out.println("Deletion test commit:" + projectRevision);
+		return projectRevision;
+	}
+
 
 	/**
 	 * Creates a tag definition within the tagset identified by <code>tagsetId</code>.
@@ -187,6 +258,9 @@ public String createOrUpdateTagDefinition(
 			String commitMsg
 	) throws IOException {
 
+		/* This work like it seems: all the folders having subdirectories have a folder
+		at the root of the tagset folder containing the subitems. This mean that the
+		hiearchy isn't stored as it is in the UI. */
 		String targetPropertyDefinitionsFileRelativePath =
 			(StringUtils.isEmpty(tagDefinition.getParentUuid()) ? "" : (tagDefinition.getParentUuid() + "/"))
 			+ tagDefinition.getUuid()

src/main/java/de/catma/repository/git/GraphWorktreeProject.java

@@ -449,6 +449,30 @@ else if (evt.getNewValue() == null) { // TagDefinition was deleted
 		};
 		tagManager.addPropertyChangeListener(TagManagerEvent.tagDefinitionChanged, tagDefinitionChangedListener);
 
+		PropertyChangeListener tagDefinitionMovedListener = new PropertyChangeListener() {
+			public void propertyChange(final PropertyChangeEvent evt) {
+				if (!tagManagerListenersEnabled) {
+					return;
+				}
+
+				try {
+					@SuppressWarnings("unchecked")
+					final Pair<TagsetDefinition, TagDefinition> newVal = (Pair<TagsetDefinition, TagDefinition>) evt.getNewValue();
+					final Pair<TagsetDefinition, TagDefinition> oldVal = (Pair<TagsetDefinition, TagDefinition>) evt.getOldValue();
+					moveTagDefinition((TagsetDefinition)(oldVal.getFirst()), (TagsetDefinition)(newVal.getFirst()), (TagDefinition)(oldVal.getSecond()), (TagDefinition)(newVal.getSecond()));
+				}
+				catch (Exception e) {
+					propertyChangeSupport.firePropertyChange(
+							ProjectEvent.exceptionOccurred.name(),
+							null,
+							e
+					);
+				}
+			}
+		};
+
+		tagManager.addPropertyChangeListener(TagManagerEvent.tagDefinitionMoved, tagDefinitionMovedListener);
+
 		PropertyChangeListener userDefinedPropertyChangedListener = new PropertyChangeListener() {
 			public void propertyChange(PropertyChangeEvent evt) {
 				if (!tagManagerListenersEnabled) {
@@ -692,26 +716,27 @@ private void removeTagsetDefinition(TagsetDefinition tagsetDefinition) throws Ex
 		graphProjectHandler.updateProjectRevision(oldRootRevisionHash, rootRevisionHash);
 	}
 
-	private void addTagDefinition(TagDefinition tagDefinition, TagsetDefinition tagsetDefinition) throws Exception {
+	private void updateTagDefinition(TagDefinition tagDefinition, TagsetDefinition tagsetDefinition) throws Exception {
 		if (isReadOnly()) {
 			throw new IllegalStateException(
 					String.format(
-							"Project \"%1$s\" is in read-only mode! Cannot add tag \"%2$s\" to tagset \"%3$s\".",
+							"Project \"%1$s\" is in read-only mode! Cannot update tag \"%2$s\" with ID %3$s in tagset \"%4$s\".",
 							projectReference.getName(),
 							tagDefinition.getName(),
+							tagDefinition.getUuid(),
 							tagsetDefinition.getName()
 					)
 			);
 		}
 
 		String oldRootRevisionHash = rootRevisionHash;
 
-		// create tag in repo and commit
+		// update tag in repo and commit
 		rootRevisionHash = gitProjectHandler.createOrUpdateTag(
 				tagsetDefinition.getUuid(),
 				tagDefinition,
 				String.format(
-						"Added tag \"%1$s\" with ID %2$s to tagset \"%3$s\" with ID %4$s",
+						"Updated tag \"%1$s\" with ID %2$s in tagset \"%3$s\" with ID %4$s",
 						tagDefinition.getName(),
 						tagDefinition.getUuid(),
 						tagsetDefinition.getName(),
@@ -723,27 +748,25 @@ private void addTagDefinition(TagDefinition tagDefinition, TagsetDefinition tags
 		graphProjectHandler.updateProjectRevision(oldRootRevisionHash, rootRevisionHash);
 	}
 
-	private void updateTagDefinition(TagDefinition tagDefinition, TagsetDefinition tagsetDefinition) throws Exception {
+	private void addTagDefinition(TagDefinition tagDefinition, TagsetDefinition tagsetDefinition) throws Exception {
 		if (isReadOnly()) {
 			throw new IllegalStateException(
 					String.format(
-							"Project \"%1$s\" is in read-only mode! Cannot update tag \"%2$s\" with ID %3$s in tagset \"%4$s\".",
+							"Project \"%1$s\" is in read-only mode! Cannot add tag \"%2$s\" to tagset \"%3$s\".",
 							projectReference.getName(),
 							tagDefinition.getName(),
-							tagDefinition.getUuid(),
 							tagsetDefinition.getName()
 					)
 			);
 		}
-
 		String oldRootRevisionHash = rootRevisionHash;
 
-		// update tag in repo and commit
+		// create tag in repo and commit
 		rootRevisionHash = gitProjectHandler.createOrUpdateTag(
 				tagsetDefinition.getUuid(),
 				tagDefinition,
 				String.format(
-						"Updated tag \"%1$s\" with ID %2$s in tagset \"%3$s\" with ID %4$s",
+						"Added tag \"%1$s\" with ID %2$s to tagset \"%3$s\" with ID %4$s",
 						tagDefinition.getName(),
 						tagDefinition.getUuid(),
 						tagsetDefinition.getName(),
@@ -755,6 +778,44 @@ private void updateTagDefinition(TagDefinition tagDefinition, TagsetDefinition t
 		graphProjectHandler.updateProjectRevision(oldRootRevisionHash, rootRevisionHash);
 	}
 
+	private void moveTagDefinition(TagsetDefinition tsdFrom, TagsetDefinition tsdTo, TagDefinition tdFrom, TagDefinition tdTo) throws Exception {
+		if (isReadOnly()) {
+			throw new IllegalStateException(
+					String.format(
+							"Project \"%1$s\" is in read-only mode! Cannot move tag \"%2$s\" with ID %3$s from tagset \"%4$s\".",
+							projectReference.getName(),
+							tdTo.getName(),
+							tdTo.getUuid(),
+							tsdTo.getName()
+					)
+			);
+		}
+
+		String oldRootRevisionHash = rootRevisionHash;
+
+		Multimap<String, TagReference> tagReferencesByCollectionId = graphProjectHandler.getTagReferencesByCollectionId(tdFrom);
+		Multimap<String, TagInstance> tagInstancesByCollectionId = Multimaps.transformValues(
+				tagReferencesByCollectionId, TagReference::getTagInstance
+		);
+
+		// update tag in repo and commit
+		rootRevisionHash = gitProjectHandler.moveTagAndUpdateAnnotations(
+				tsdFrom, tsdTo, tdFrom, tdTo,
+				tagInstancesByCollectionId,
+				String.format(
+						"Moved tag \"%1$s\" with ID %2$s from tagset \"%3$s\" with ID %4$s to tagset \"%5$s\" with id %6$s",
+						tdTo.getName(),
+						tdTo.getUuid(),
+						tsdFrom.getName(),
+						tsdFrom.getUuid(),
+						tsdTo.getName(),
+						tsdTo.getUuid()
+				)
+		);
+		// update revision hash on GraphProjectHandler
+		graphProjectHandler.updateProjectRevision(oldRootRevisionHash, rootRevisionHash);
+	}
+
 	private void removeTagDefinition(TagDefinition tagDefinition, TagsetDefinition tagsetDefinition) throws Exception {
 		if (isReadOnly()) {
 			throw new IllegalStateException(