Examples with TagReference de.catma.document.annotation.TagReference used on opensource projects

Example 11 with TagReference

use of de.catma.document.annotation.TagReference in project catma by forTEXT.

the class GraphWriter method addTagReferences.

void addTagReferences(String revisionHash, Vertex collectionV, List<TagReference> tagReferences) {
    final ArrayListMultimap<TagInstance, Range> tagInstancesAndRanges = ArrayListMultimap.create();
    tagReferences.forEach(tagReference -> {
        tagInstancesAndRanges.put(tagReference.getTagInstance(), tagReference.getRange());
    });
    Map<String, Vertex> tagNodesById = new HashMap<>();
    Set<String> availablePropertyDefIds = new HashSet<>();
    for (TagInstance ti : tagInstancesAndRanges.keySet()) {
        List<Range> ranges = tagInstancesAndRanges.get(ti);
        List<Integer> flatRanges = ranges.stream().sorted().flatMap(range -> Stream.of(range.getStartPoint(), range.getEndPoint())).collect(Collectors.toList());
        if (ti.getAuthor() == null) {
            ti.setAuthor(user.getIdentifier());
        }
        String tagsetId = ti.getTagsetId();
        String tagId = ti.getTagDefinitionId();
        Vertex tagInstanceV = graph.addVertex(nt(TagInstance));
        tagInstanceV.property("tagInstanceId", ti.getUuid());
        tagInstanceV.property("author", ti.getAuthor());
        tagInstanceV.property("timestamp", ti.getTimestamp());
        tagInstanceV.property("ranges", flatRanges);
        collectionV.addEdge(rt(hasInstance), tagInstanceV);
        Vertex tagV = tagNodesById.get(tagId);
        GraphTraversalSource g = graph.traversal();
        if (tagV == null) {
            GraphTraversal<Vertex, Vertex> traversal = g.V().has(nt(ProjectRevision), "revisionHash", revisionHash).outE(rt(hasTagset)).inV().has(nt(Tagset), "tagsetId", tagsetId).outE(rt(hasTag)).inV().has(nt(Tag), "tagId", tagId);
            if (traversal.hasNext()) {
                tagV = traversal.next();
                tagNodesById.put(tagId, tagV);
            }
        }
        if (tagV != null) {
            // usually the Tag should always be present,
            // because we delete stale Annotations when loading the Collection from git
            // if we hit an orphan Annotation at this stage it gets ignored
            // until the next sync might bring the corresponding Tag
            tagV.addEdge(rt(hasInstance), tagInstanceV);
            for (Property property : ti.getUserDefinedProperties()) {
                if (availablePropertyDefIds.contains(property.getPropertyDefinitionId()) || g.V(tagV).outE(rt(hasProperty)).inV().has(nt(Property), "uuid", property.getPropertyDefinitionId()).hasNext()) {
                    Vertex annoPropertyV = graph.addVertex(nt(AnnotationProperty));
                    annoPropertyV.property("uuid", property.getPropertyDefinitionId());
                    annoPropertyV.property("values", property.getPropertyValueList());
                    tagInstanceV.addEdge(rt(hasProperty), annoPropertyV);
                    availablePropertyDefIds.add(property.getPropertyDefinitionId());
                }
            }
        }
    }
}

Example 12 with TagReference

use of de.catma.document.annotation.TagReference 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 13 with TagReference

use of de.catma.document.annotation.TagReference 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 14 with TagReference

use of de.catma.document.annotation.TagReference in project catma by forTEXT.

the class GitMarkupCollectionHandler method getBothModifiedAnnotationConflict.

private AnnotationConflict getBothModifiedAnnotationConflict(String projectId, String collectionId, String serializedConflictingAnnotation) throws Exception {
    String masterVersion = serializedConflictingAnnotation.replaceAll("\\Q<<<<<<< HEAD\\E(\\r\\n|\\r|\\n)", "").replaceAll("\\Q=======\\E(\\r\\n|\\r|\\n|.)*?\\Q>>>>>>> \\E.+?(\\r\\n|\\r|\\n)", "");
    String devVersion = serializedConflictingAnnotation.replaceAll("\\Q<<<<<<< HEAD\\E(\\r\\n|\\r|\\n|.)*?\\Q=======\\E(\\r\\n|\\r|\\n)", "").replaceAll("\\Q>>>>>>> \\E.+?(\\r\\n|\\r|\\n)", "");
    JsonLdWebAnnotation masterVersionJsonLdWebAnnotation = new SerializationHelper<JsonLdWebAnnotation>().deserialize(masterVersion, JsonLdWebAnnotation.class);
    JsonLdWebAnnotation devVersionJsonLdWebAnnotation = new SerializationHelper<JsonLdWebAnnotation>().deserialize(devVersion, JsonLdWebAnnotation.class);
    List<TagReference> masterTagReferences = masterVersionJsonLdWebAnnotation.toTagReferenceList(projectId, collectionId);
    List<TagReference> devTagReferences = devVersionJsonLdWebAnnotation.toTagReferenceList(projectId, collectionId);
    AnnotationConflict annotationConflict = new AnnotationConflict(devTagReferences.get(0).getTagInstance(), devTagReferences, masterTagReferences.get(0).getTagInstance(), masterTagReferences);
    return annotationConflict;
}

Example 15 with TagReference

use of de.catma.document.annotation.TagReference in project catma by forTEXT.

the class GitMarkupCollectionHandler method getDeleteByUsAnnotationConflict.

private AnnotationConflict getDeleteByUsAnnotationConflict(String projectId, String collectionId, String serializedConflictingAnnotation) throws Exception {
    JsonLdWebAnnotation devVersionJsonLdWebAnnotation = new SerializationHelper<JsonLdWebAnnotation>().deserialize(serializedConflictingAnnotation, JsonLdWebAnnotation.class);
    List<TagReference> devTagReferences = devVersionJsonLdWebAnnotation.toTagReferenceList(projectId, collectionId);
    AnnotationConflict annotationConflict = new AnnotationConflict(devTagReferences.get(0).getTagInstance(), devTagReferences, null, Collections.emptyList());
    return annotationConflict;
}