Examples with JsonLdWebAnnotation de.catma.repository.git.serialization.models.json_ld.JsonLdWebAnnotation used on opensource projects

Example 1 with JsonLdWebAnnotation

use of de.catma.repository.git.serialization.models.json_ld.JsonLdWebAnnotation in project catma by forTEXT.

the class GitMarkupCollectionHandlerTest method createTagInstance.

@Test
public void createTagInstance() throws Exception {
    try (JGitRepoManager jGitRepoManager = new JGitRepoManager(this.catmaProperties.getProperty(RepositoryPropertyKey.GitBasedRepositoryBasePath.name()), this.catmaUser)) {
        this.directoriesToDeleteOnTearDown.add(jGitRepoManager.getRepositoryBasePath());
        HashMap<String, Object> getJsonLdWebAnnotationResult = JsonLdWebAnnotationTest.getJsonLdWebAnnotation(jGitRepoManager, this.gitLabServerManager, this.catmaUser);
        JsonLdWebAnnotation jsonLdWebAnnotation = (JsonLdWebAnnotation) getJsonLdWebAnnotationResult.get("jsonLdWebAnnotation");
        String projectId = (String) getJsonLdWebAnnotationResult.get("projectUuid");
        String markupCollectionId = (String) getJsonLdWebAnnotationResult.get("userMarkupCollectionUuid");
        String tagsetId = (String) getJsonLdWebAnnotationResult.get("tagsetDefinitionUuid");
        String tagInstanceId = (String) getJsonLdWebAnnotationResult.get("tagInstanceUuid");
        this.projectsToDeleteOnTearDown.add(projectId);
        // add the tagset to the markup collection
        GitMarkupCollectionHandler gitMarkupCollectionHandler = new GitMarkupCollectionHandler(jGitRepoManager, this.gitLabServerManager);
        // TODO: use the real tagset hash - currently the handler does not validate it at all
        gitMarkupCollectionHandler.addTagset(projectId, markupCollectionId, tagsetId, "fakeTagsetVersion");
        // the JGitRepoManager instance should always be in a detached state after GitMarkupCollectionHandler calls
        // return
        assertFalse(jGitRepoManager.isAttached());
        // create the tag instance
        gitMarkupCollectionHandler.createTagInstance(projectId, markupCollectionId, jsonLdWebAnnotation);
        // the JGitRepoManager instance should always be in a detached state after GitMarkupCollectionHandler
        // calls return
        assertFalse(jGitRepoManager.isAttached());
        String projectRootRepositoryName = GitProjectManager.getProjectRootRepositoryName(projectId);
        jGitRepoManager.open(projectId, projectRootRepositoryName);
        File expectedTagInstanceJsonFilePath = new File(jGitRepoManager.getRepositoryWorkTree(), String.format("%s/%s/annotations/%s.json", GitProjectHandler.MARKUP_COLLECTION_SUBMODULES_DIRECTORY_NAME, markupCollectionId, tagInstanceId));
        assert expectedTagInstanceJsonFilePath.exists();
        assert expectedTagInstanceJsonFilePath.isFile();
        String expectedTagInstanceJsonFileContents = JsonLdWebAnnotationTest.EXPECTED_SERIALIZED_ANNOTATION.replaceAll("[\n\t]", "");
        expectedTagInstanceJsonFileContents = String.format(expectedTagInstanceJsonFileContents, getJsonLdWebAnnotationResult.get("projectRootRepositoryName"), getJsonLdWebAnnotationResult.get("tagsetDefinitionUuid"), getJsonLdWebAnnotationResult.get("tagDefinitionUuid"), getJsonLdWebAnnotationResult.get("userPropertyDefinitionUuid"), getJsonLdWebAnnotationResult.get("systemPropertyDefinitionUuid"), getJsonLdWebAnnotationResult.get("userMarkupCollectionUuid"), getJsonLdWebAnnotationResult.get("tagInstanceUuid"), getJsonLdWebAnnotationResult.get("sourceDocumentUuid"));
        assertEquals(expectedTagInstanceJsonFileContents, FileUtils.readFileToString(expectedTagInstanceJsonFilePath, StandardCharsets.UTF_8));
    }
}

Example 2 with JsonLdWebAnnotation

use of de.catma.repository.git.serialization.models.json_ld.JsonLdWebAnnotation in project catma by forTEXT.

the class GitMarkupCollectionHandlerTest method open.

@Test
public void open() throws Exception {
    // TODO: don't hardcode anything in assertions (markup collection name...)
    try (JGitRepoManager jGitRepoManager = new JGitRepoManager(this.catmaProperties.getProperty(RepositoryPropertyKey.GitBasedRepositoryBasePath.name()), this.catmaUser)) {
        this.directoriesToDeleteOnTearDown.add(jGitRepoManager.getRepositoryBasePath());
        HashMap<String, Object> getJsonLdWebAnnotationResult = JsonLdWebAnnotationTest.getJsonLdWebAnnotation(jGitRepoManager, this.gitLabServerManager, this.catmaUser);
        JsonLdWebAnnotation jsonLdWebAnnotation = (JsonLdWebAnnotation) getJsonLdWebAnnotationResult.get("jsonLdWebAnnotation");
        String projectId = (String) getJsonLdWebAnnotationResult.get("projectUuid");
        String markupCollectionId = (String) getJsonLdWebAnnotationResult.get("userMarkupCollectionUuid");
        String tagsetId = (String) getJsonLdWebAnnotationResult.get("tagsetDefinitionUuid");
        this.projectsToDeleteOnTearDown.add(projectId);
        // add the tagset to the markup collection
        GitMarkupCollectionHandler gitMarkupCollectionHandler = new GitMarkupCollectionHandler(jGitRepoManager, this.gitLabServerManager);
        // TODO: use the real tagset hash - currently the handler does not validate it at all
        gitMarkupCollectionHandler.addTagset(projectId, markupCollectionId, tagsetId, "fakeTagsetVersion");
        // the JGitRepoManager instance should always be in a detached state after GitMarkupCollectionHandler calls
        // return
        assertFalse(jGitRepoManager.isAttached());
        // create the tag instance within the markup collection
        gitMarkupCollectionHandler.createTagInstance(projectId, markupCollectionId, jsonLdWebAnnotation);
        // the JGitRepoManager instance should always be in a detached state after GitMarkupCollectionHandler calls
        // return
        assertFalse(jGitRepoManager.isAttached());
        UserMarkupCollection markupCollection = gitMarkupCollectionHandler.open(projectId, markupCollectionId);
        // the JGitRepoManager instance should always be in a detached state after GitMarkupCollectionHandler
        // calls return
        assertFalse(jGitRepoManager.isAttached());
        assertNotNull(markupCollection);
        assertEquals("Test Markup Collection", markupCollection.getContentInfoSet().getTitle());
        assertEquals(2, markupCollection.getTagReferences().size());
        assertTrue(markupCollection.getTagReferences().get(0).getRange().equals(new Range(12, 18)));
        assertNotNull(markupCollection.getRevisionHash());
    }
}

Example 3 with JsonLdWebAnnotation

use of de.catma.repository.git.serialization.models.json_ld.JsonLdWebAnnotation in project catma by forTEXT.

the class GitMarkupCollectionHandler method openTagReferences.

private ArrayList<TagReference> openTagReferences(String projectId, String markupCollectionId, String collectionName, File parentDirectory, ProgressListener progressListener, AtomicInteger counter) throws Exception {
    ArrayList<TagReference> tagReferences = new ArrayList<>();
    List<String> contents = Arrays.asList(parentDirectory.list());
    for (String item : contents) {
        File target = new File(parentDirectory, item);
        // if it is a directory, recurse into it adding results to the current tagReferences list
        if (target.isDirectory() && !target.getName().equalsIgnoreCase(".git")) {
            tagReferences.addAll(this.openTagReferences(projectId, markupCollectionId, collectionName, target, progressListener, counter));
        } else // if item is <CATMA_UUID>.json, read it into a list of TagReference objects
        if (target.isFile() && isTagInstanceFilename(target.getName())) {
            counter.incrementAndGet();
            if (counter.intValue() % 1000 == 0) {
                progressListener.setProgress("Loading Annotations %1$s %2$d", collectionName, counter.intValue());
            }
            String serialized = readFileToString(target, StandardCharsets.UTF_8);
            JsonLdWebAnnotation jsonLdWebAnnotation = new SerializationHelper<JsonLdWebAnnotation>().deserialize(serialized, JsonLdWebAnnotation.class);
            tagReferences.addAll(jsonLdWebAnnotation.toTagReferenceList(projectId, markupCollectionId));
        }
    }
    return tagReferences;
}

Example 4 with JsonLdWebAnnotation

use of de.catma.repository.git.serialization.models.json_ld.JsonLdWebAnnotation in project catma by forTEXT.

the class GitMarkupCollectionHandler method getCollection.

public AnnotationCollection getCollection(String projectId, String collectionId, TagLibrary tagLibrary, ProgressListener progressListener, boolean hasWritePermission, Function<String, Boolean> hasTagsetIdReadPermissionGetter) throws Exception {
    try (ILocalGitRepositoryManager localGitRepoManager = this.localGitRepositoryManager) {
        String projectRootRepositoryName = GitProjectManager.getProjectRootRepositoryName(projectId);
        localGitRepoManager.open(projectId, projectRootRepositoryName);
        String markupCollectionSubmoduleRelDir = GitProjectHandler.ANNOTATION_COLLECTION_SUBMODULES_DIRECTORY_NAME + "/" + collectionId;
        File markupCollectionSubmoduleAbsPath = new File(localGitRepoManager.getRepositoryWorkTree().toString(), markupCollectionSubmoduleRelDir);
        String markupCollectionRevisionHash = localGitRepoManager.getSubmoduleHeadRevisionHash(markupCollectionSubmoduleRelDir);
        // can't call open on an attached instance
        localGitRepoManager.detach();
        File markupCollectionHeaderFile = new File(markupCollectionSubmoduleAbsPath, HEADER_FILE_NAME);
        String serializedMarkupCollectionHeaderFile = FileUtils.readFileToString(markupCollectionHeaderFile, StandardCharsets.UTF_8);
        GitMarkupCollectionHeader markupCollectionHeader = new SerializationHelper<GitMarkupCollectionHeader>().deserialize(serializedMarkupCollectionHeaderFile, GitMarkupCollectionHeader.class);
        ContentInfoSet contentInfoSet = new ContentInfoSet(markupCollectionHeader.getAuthor(), markupCollectionHeader.getDescription(), markupCollectionHeader.getPublisher(), markupCollectionHeader.getName());
        AtomicInteger counter = new AtomicInteger();
        ArrayList<TagReference> tagReferences = this.openTagReferences(projectId, collectionId, contentInfoSet.getTitle(), markupCollectionSubmoduleAbsPath, progressListener, counter);
        // handle orphan Annotations
        ArrayListMultimap<TagInstance, TagReference> tagInstances = ArrayListMultimap.create();
        Set<String> orphanAnnotationIds = new HashSet<>();
        Iterator<TagReference> tagReferenceIterator = tagReferences.iterator();
        while (tagReferenceIterator.hasNext()) {
            TagReference tagReference = tagReferenceIterator.next();
            if (!orphanAnnotationIds.contains(tagReference.getTagInstanceId())) {
                String tagsetId = tagReference.getTagInstance().getTagsetId();
                boolean readPermission = hasTagsetIdReadPermissionGetter.apply(tagsetId);
                TagsetDefinition tagset = tagLibrary.getTagsetDefinition(tagsetId);
                String tagId = tagReference.getTagDefinitionId();
                if (readPermission && (tagset == null || tagset.isDeleted(tagId))) {
                    // Tag/Tagset has been deleted, we remove the stale Annotation as well
                    orphanAnnotationIds.add(tagReference.getTagInstanceId());
                    tagReferenceIterator.remove();
                } else {
                    // other orphan Annotations get ignored upon indexing
                    // until the corresponding Tag or its "deletion" info come along
                    tagInstances.put(tagReference.getTagInstance(), tagReference);
                }
            }
        }
        if (hasWritePermission) {
            removeTagInstances(projectId, collectionId, orphanAnnotationIds);
        }
        // handle orphan Properties
        if (hasWritePermission) {
            for (TagInstance tagInstance : tagInstances.keySet()) {
                TagsetDefinition tagset = tagLibrary.getTagsetDefinition(tagInstance.getTagsetId());
                if (tagset != null) {
                    Collection<Property> properties = tagInstance.getUserDefinedProperties();
                    for (Property property : new HashSet<>(properties)) {
                        // deleted property?
                        if (tagset.isDeleted(property.getPropertyDefinitionId())) {
                            // yes, we remove the stale property
                            tagInstance.removeUserDefinedProperty(property.getPropertyDefinitionId());
                            // and save the change
                            JsonLdWebAnnotation annotation = new JsonLdWebAnnotation(CATMAPropertyKey.GitLabServerUrl.getValue(), projectId, tagInstances.get(tagInstance), tagLibrary);
                            createTagInstance(projectId, collectionId, annotation);
                        }
                    }
                }
            }
        }
        AnnotationCollection userMarkupCollection = new AnnotationCollection(collectionId, contentInfoSet, tagLibrary, tagReferences, markupCollectionHeader.getSourceDocumentId(), markupCollectionHeader.getSourceDocumentVersion());
        userMarkupCollection.setRevisionHash(markupCollectionRevisionHash);
        return userMarkupCollection;
    }
}

Example 5 with JsonLdWebAnnotation

use of de.catma.repository.git.serialization.models.json_ld.JsonLdWebAnnotation in project catma by forTEXT.

the class GitMarkupCollectionHandler method createTagInstance.

/**
 * Creates a tag instance (annotation) within the markup collection identified by <code>markupCollectionId</code>.
 * <p>
 * NB: This method purposefully does NOT perform any Git add/commit operations as it is expected to be called a very
 * large number of times when a graph worktree is written to disk.
 *
 * @param projectId the ID of the project that contains the markup collection within which the tag instance should
 *                  be created
 * @param markupCollectionId the ID of the markup collection within which to create the tag instance
 * @param annotation a {@link JsonLdWebAnnotation} object representing the tag instance
 * @return the tag instance UUID contained within the <code>annotation</code> argument
 * @throws IOException if an error occurs while creating the tag instance
 */
public String createTagInstance(String projectId, String markupCollectionId, JsonLdWebAnnotation annotation) throws IOException {
    // TODO: check that the tag instance is for the correct document
    try (ILocalGitRepositoryManager localGitRepoManager = this.localGitRepositoryManager) {
        String projectRootRepositoryName = GitProjectManager.getProjectRootRepositoryName(projectId);
        String collectionGitRepositoryName = projectRootRepositoryName + "/" + GitProjectHandler.ANNOTATION_COLLECTION_SUBMODULES_DIRECTORY_NAME + "/" + markupCollectionId;
        localGitRepoManager.open(projectId, collectionGitRepositoryName);
        // write the serialized tag instance to the markup collection submodule
        File targetTagInstanceFilePath = new File(localGitRepoManager.getRepositoryWorkTree(), "annotations/" + annotation.getTagInstanceUuid() + ".json");
        String serializedTagInstance = new SerializationHelper<JsonLdWebAnnotation>().serialize(annotation);
        try (FileOutputStream fileOutputStream = FileUtils.openOutputStream(targetTagInstanceFilePath)) {
            fileOutputStream.write(serializedTagInstance.getBytes(StandardCharsets.UTF_8));
        }
    // not doing Git add/commit, see method doc comment
    }
    return annotation.getTagInstanceUuid();
}