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

Example 16 with TagReference

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

the class GitMarkupCollectionHandler method getDeleteByThemAnnotationConflict.

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

Example 17 with TagReference

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

the class TaggerView method tagInstanceAdded.

public void tagInstanceAdded(ClientTagInstance clientTagInstance) {
    AnnotationCollection collection = annotationPanel.getSelectedEditableCollection();
    if (collection == null) {
        // shouldn't happen, but just in case
        Notification.show("Info", "Please make sure you have an editable Collection available " + "and select this Collection as 'currently being edited'! " + "Your Annotation hasn't been saved!", Type.ERROR_MESSAGE);
    } else {
        TagLibrary tagLibrary = collection.getTagLibrary();
        TagDefinition tagDef = tagLibrary.getTagDefinition(clientTagInstance.getTagDefinitionID());
        TagInstance ti = new TagInstance(clientTagInstance.getInstanceID(), tagDef.getUuid(), project.getUser().getIdentifier(), ZonedDateTime.now().format(DateTimeFormatter.ofPattern(Version.DATETIMEPATTERN)), tagDef.getUserDefinedPropertyDefinitions(), tagDef.getTagsetDefinitionUuid());
        List<TagReference> tagReferences = new ArrayList<TagReference>();
        try {
            String userMarkupCollectionUuid = collection.getId();
            for (TextRange tr : clientTagInstance.getRanges()) {
                Range r = new Range(tr.getStartPos(), tr.getEndPos());
                TagReference ref = new TagReference(ti, sourceDocument.getUuid(), r, userMarkupCollectionUuid);
                tagReferences.add(ref);
            }
            final Annotation annotation = new Annotation(ti, tagReferences, collection, tagLibrary.getTagPath(tagDef));
            if (!tagDef.getUserDefinedPropertyDefinitions().isEmpty()) {
                EditAnnotationPropertiesDialog editAnnotationPropertiesDialog = new EditAnnotationPropertiesDialog(project, annotation, new SaveCancelListener<List<Property>>() {

                    @Override
                    public void savePressed(List<Property> notOfInterest) {
                        userMarkupCollectionManager.addTagReferences(tagReferences, collection);
                    }
                });
                editAnnotationPropertiesDialog.show();
            } else {
                userMarkupCollectionManager.addTagReferences(tagReferences, collection);
            }
        } catch (URISyntaxException e) {
            errorHandler.showAndLogError("Error adding Annotations!", e);
        }
    }
}

Example 18 with TagReference

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

the class KwicPanel method annotateSelection.

@SuppressWarnings("unchecked")
private void annotateSelection(Set<QueryResultRow> selectedRows, WizardContext result) throws Exception {
    List<Property> properties = (List<Property>) result.get(AnnotationWizardContextKey.PROPERTIES);
    Map<String, AnnotationCollectionReference> collectionRefsByDocId = (Map<String, AnnotationCollectionReference>) result.get(AnnotationWizardContextKey.COLLECTIONREFS_BY_DOCID);
    TagDefinition tag = (TagDefinition) result.get(AnnotationWizardContextKey.TAG);
    AnnotationCollectionManager collectionManager = new AnnotationCollectionManager(project);
    for (AnnotationCollectionReference ref : collectionRefsByDocId.values()) {
        collectionManager.add(project.getUserMarkupCollection(ref));
    }
    for (QueryResultRow row : selectedRows) {
        AnnotationCollectionReference collectionRef = collectionRefsByDocId.get(row.getSourceDocumentId());
        TagInstance tagInstance = new TagInstance(idGenerator.generate(), tag.getUuid(), project.getUser().getIdentifier(), ZonedDateTime.now().format(DateTimeFormatter.ofPattern(Version.DATETIMEPATTERN)), tag.getUserDefinedPropertyDefinitions(), tag.getTagsetDefinitionUuid());
        List<TagReference> tagReferences = new ArrayList<TagReference>();
        for (Property protoProp : properties) {
            tagInstance.getUserDefinedPropetyByUuid(protoProp.getPropertyDefinitionId()).setPropertyValueList(protoProp.getPropertyValueList());
        }
        Set<Range> ranges = row.getRanges();
        for (Range range : ranges) {
            TagReference tagReference = new TagReference(tagInstance, row.getSourceDocumentId(), range, collectionRef.getId());
            tagReferences.add(tagReference);
        }
        collectionManager.addTagReferences(tagReferences, collectionRef.getId());
    }
}

Example 19 with TagReference

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

the class Tagger method setVisible.

public void setVisible(List<TagReference> tagReferences, boolean visible) {
    Map<String, ClientTagInstance> tagInstancesByInstanceID = new HashMap<String, ClientTagInstance>();
    for (TagReference tagReference : tagReferences) {
        List<TextRange> textRanges = new ArrayList<TextRange>();
        textRanges.add(new TextRange(tagReference.getRange().getStartPoint(), tagReference.getRange().getEndPoint()));
        ClientTagInstance tagInstance = tagInstancesByInstanceID.get(tagReference.getTagInstanceId());
        if (tagInstance == null) {
            TagDefinition tagDefinition = project.getTagManager().getTagLibrary().getTagDefinition(tagReference.getTagDefinitionId());
            tagInstancesByInstanceID.put(tagReference.getTagInstanceId(), new ClientTagInstance(tagReference.getTagDefinitionId(), tagReference.getTagInstanceId(), tagDefinition == null ? "FFFFFF" : ColorConverter.toHex(tagDefinition.getColor()), textRanges));
        } else {
            tagInstance.addRanges(textRanges);
        }
    }
    setTagInstancesVisible(tagInstancesByInstanceID.values(), visible);
}

Example 20 with TagReference

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

the class CorpusImporter method importCorpus.

/**
 * !BACKGROUND THREAD! No direct UI code here!
 *
 * @param progressListener
 * @param corpusFile
 * @param documentMetadataList
 * @param tempDir
 * @param ui
 * @param project
 * @return
 * @throws Exception
 */
public Void importCorpus(final ProgressListener progressListener, final File corpusFile, final List<CorpusImportDocumentMetadata> documentMetadataList, final String tempDir, final UI ui, final Project project) throws Exception {
    progressListener.setProgress("Importing Corpus");
    GZIPInputStream gzipIs = new GZIPInputStream(new FileInputStream(corpusFile));
    try (TarArchiveInputStream taIs = new TarArchiveInputStream(gzipIs)) {
        TarArchiveEntry entry = taIs.getNextTarEntry();
        while (entry != null) {
            final String entryName = entry.getName();
            final String[] pathParts = entry.getName().split(Pattern.quote("/"));
            final String documentIdPart = pathParts[2];
            final String documentId = documentIdPart.substring(documentIdPart.indexOf("__") + 3);
            final String idUri = "catma://" + documentId;
            if (pathParts[3].equals("annotationcollections")) {
                progressListener.setProgress("Importing Collection %1$s", pathParts[4]);
                ui.accessSynchronously(() -> {
                    try {
                        final ByteArrayOutputStream buffer = new ByteArrayOutputStream();
                        IOUtils.copy(taIs, buffer);
                        SourceDocument document = project.getSourceDocument(documentId);
                        Pair<AnnotationCollection, List<TagsetDefinitionImportStatus>> loadResult = project.loadAnnotationCollection(new ByteArrayInputStream(buffer.toByteArray()), document);
                        List<TagsetDefinitionImportStatus> tagsetDefinitionImportStatusList = loadResult.getSecond();
                        final AnnotationCollection annotationCollection = loadResult.getFirst();
                        Optional<TagsetDefinition> optIntrinsicTagset = annotationCollection.getTagLibrary().getTagsetDefinitions().stream().filter(tagsetDef -> tagsetDef.getName().equals("Intrinsic Markup")).findFirst();
                        if (optIntrinsicTagset.isPresent()) {
                            TagsetDefinition intrinsicTagset = optIntrinsicTagset.get();
                            List<TagReference> intrinsicAnnotations = annotationCollection.getTagReferences(intrinsicTagset);
                            if (!intrinsicAnnotations.isEmpty()) {
                                annotationCollection.removeTagReferences(intrinsicAnnotations);
                            }
                            annotationCollection.getTagLibrary().remove(intrinsicTagset);
                            tagsetDefinitionImportStatusList.stream().filter(status -> status.getTagset().equals(intrinsicTagset)).findFirst().ifPresent(status -> status.setDoImport(false));
                        }
                        tagsetDefinitionImportStatusList.stream().filter(status -> status.getTagset().isEmpty()).forEach(status -> status.setDoImport(false));
                        if (!annotationCollection.isEmpty()) {
                            project.importCollection(tagsetDefinitionImportStatusList, annotationCollection);
                        }
                    } catch (Exception e) {
                        Logger.getLogger(ProjectView.class.getName()).log(Level.SEVERE, "Error importing the CATMA 5 Corpus: " + entryName, e);
                        String errorMsg = e.getMessage();
                        if ((errorMsg == null) || (errorMsg.trim().isEmpty())) {
                            errorMsg = "";
                        }
                        Notification.show("Error", String.format("Error importing the CATMA 5 Corpus! " + "This Collection will be skipped!\n The underlying error message was:\n%1$s", errorMsg), Type.ERROR_MESSAGE);
                    }
                });
            } else {
                final CorpusImportDocumentMetadata documentMetadata = documentMetadataList.stream().filter(metadata -> metadata.getSourceDocID().equals(idUri)).findFirst().orElse(null);
                final Locale locale = LocaleUtils.toLocale(documentMetadata.getSourceDocLocale());
                final boolean useApostrophe = Arrays.asList(documentMetadata.getSourceDocSepChars()).contains(String.valueOf(UploadFile.APOSTROPHE));
                final String title = (documentMetadata.getSourceDocName() == null || documentMetadata.getSourceDocName().isEmpty()) ? documentId : documentMetadata.getSourceDocName();
                progressListener.setProgress("Importing Document %1$s", title);
                final File tempFile = new File(new File(tempDir), documentId);
                if (tempFile.exists()) {
                    tempFile.delete();
                }
                try (FileOutputStream fos = new FileOutputStream(tempFile)) {
                    IOUtils.copy(taIs, fos);
                }
                ui.accessSynchronously(() -> {
                    IDGenerator idGenerator = new IDGenerator();
                    IndexInfoSet indexInfoSet = new IndexInfoSet(Collections.emptyList(), useApostrophe ? Lists.newArrayList(UploadFile.APOSTROPHE) : Collections.emptyList(), locale);
                    TechInfoSet techInfoSet = new TechInfoSet(documentId, FileType.TEXT.getMimeType(), tempFile.toURI());
                    ContentInfoSet contentInfoSet = new ContentInfoSet(documentMetadata.getSourceDocAuthor(), documentMetadata.getSourceDocDescription(), documentMetadata.getSourceDocPublisher(), title);
                    techInfoSet.setCharset(Charset.forName("UTF-8"));
                    SourceDocumentInfo documentInfo = new SourceDocumentInfo(indexInfoSet, contentInfoSet, techInfoSet);
                    AbstractSourceContentHandler handler = null;
                    boolean loadIntrinsicMarkup = false;
                    if (entryName.endsWith("xml2")) {
                        handler = new XML2ContentHandler();
                        loadIntrinsicMarkup = true;
                    } else if (entryName.endsWith("xml")) {
                        handler = new OldXMLContentHandler();
                        loadIntrinsicMarkup = true;
                    } else {
                        handler = new StandardContentHandler();
                    }
                    handler.setSourceDocumentInfo(documentInfo);
                    SourceDocument document = new SourceDocument(documentId, handler);
                    try {
                        project.insert(document, false);
                        if (loadIntrinsicMarkup) {
                            final TagManager tagmanager = new TagManager(new TagLibrary());
                            XmlMarkupCollectionSerializationHandler markupHandler = new XmlMarkupCollectionSerializationHandler(tagmanager, (XML2ContentHandler) handler, project.getUser().getIdentifier());
                            try (FileInputStream fis = new FileInputStream(tempFile)) {
                                AnnotationCollection intrinsicMarkupCollection = markupHandler.deserialize(document, idGenerator.generateCollectionId(), fis);
                                Collection<TagsetImport> tagsetImports = new ArrayList<TagsetImport>();
                                String defaultIntrinsicXMLElmentsName = "Default Intrinsic XML Elements";
                                for (TagsetDefinition tagset : tagmanager.getTagLibrary()) {
                                    if (!tagset.isEmpty()) {
                                        TagsetDefinition targetTagset = project.getTagManager().getTagLibrary().getTagsetDefinition(tagset.getUuid());
                                        boolean inProject = false;
                                        if (targetTagset == null) {
                                            targetTagset = tagset;
                                        } else {
                                            inProject = true;
                                        }
                                        String namespace = tagset.getName() == null ? "none" : tagset.getName();
                                        if (tagset.getName() == null) {
                                            tagset.setName(defaultIntrinsicXMLElmentsName);
                                        }
                                        TagsetImport tagsetImport = new TagsetImport(namespace, tagset, targetTagset, inProject ? TagsetImportState.WILL_BE_MERGED : TagsetImportState.WILL_BE_CREATED);
                                        tagsetImports.add(tagsetImport);
                                    }
                                }
                                // Creating Tagsets
                                tagsetImports.stream().filter(ti -> ti.getImportState().equals(TagsetImportState.WILL_BE_CREATED)).forEach(tagsetImport -> {
                                    if (project.getTagManager().getTagLibrary().getTagsetDefinition(tagsetImport.getTargetTagset().getUuid()) != null) {
                                        // already imported, so it will be a merge
                                        tagsetImport.setImportState(TagsetImportState.WILL_BE_MERGED);
                                    } else {
                                        TagsetDefinition extractedTagset = tagsetImport.getExtractedTagset();
                                        try {
                                            project.importTagsets(Collections.singletonList(new TagsetDefinitionImportStatus(extractedTagset, project.inProjectHistory(extractedTagset.getUuid()), project.getTagManager().getTagLibrary().getTagsetDefinition(extractedTagset.getUuid()) != null)));
                                        } catch (Exception e) {
                                            Logger.getLogger(ProjectView.class.getName()).log(Level.SEVERE, String.format("Error importing tagset %1$s with ID %2$s", extractedTagset.getName(), extractedTagset.getUuid()), e);
                                            String errorMsg = e.getMessage();
                                            if ((errorMsg == null) || (errorMsg.trim().isEmpty())) {
                                                errorMsg = "";
                                            }
                                            Notification.show("Error", String.format("Error importing tagset %1$s! " + "This tagset will be skipped!\n The underlying error message was:\n%2$s", extractedTagset.getName(), errorMsg), Type.ERROR_MESSAGE);
                                        }
                                    }
                                });
                                // Merging Tagsets
                                tagsetImports.stream().filter(ti -> ti.getImportState().equals(TagsetImportState.WILL_BE_MERGED)).forEach(tagsetImport -> {
                                    TagsetDefinition targetTagset = project.getTagManager().getTagLibrary().getTagsetDefinition(tagsetImport.getTargetTagset().getUuid());
                                    for (TagDefinition tag : tagsetImport.getExtractedTagset()) {
                                        Optional<TagDefinition> optionalTag = targetTagset.getTagDefinitionsByName(tag.getName()).findFirst();
                                        if (optionalTag.isPresent()) {
                                            TagDefinition existingTag = optionalTag.get();
                                            tag.getUserDefinedPropertyDefinitions().forEach(pd -> {
                                                if (existingTag.getPropertyDefinition(pd.getName()) == null) {
                                                    project.getTagManager().addUserDefinedPropertyDefinition(existingTag, new PropertyDefinition(pd));
                                                }
                                            });
                                            List<TagReference> tagReferences = intrinsicMarkupCollection.getTagReferences(tag);
                                            intrinsicMarkupCollection.removeTagReferences(tagReferences);
                                            Multimap<TagInstance, TagReference> referencesByInstance = ArrayListMultimap.create();
                                            tagReferences.forEach(tr -> referencesByInstance.put(tr.getTagInstance(), tr));
                                            for (TagInstance incomingTagInstance : referencesByInstance.keySet()) {
                                                TagInstance newTagInstance = new TagInstance(idGenerator.generate(), existingTag.getUuid(), incomingTagInstance.getAuthor(), incomingTagInstance.getTimestamp(), existingTag.getUserDefinedPropertyDefinitions(), targetTagset.getUuid());
                                                for (Property oldProp : incomingTagInstance.getUserDefinedProperties()) {
                                                    String oldPropDefId = oldProp.getPropertyDefinitionId();
                                                    PropertyDefinition oldPropDef = tag.getPropertyDefinitionByUuid(oldPropDefId);
                                                    PropertyDefinition existingPropDef = existingTag.getPropertyDefinition(oldPropDef.getName());
                                                    newTagInstance.addUserDefinedProperty(new Property(existingPropDef.getUuid(), oldProp.getPropertyValueList()));
                                                }
                                                ArrayList<TagReference> newReferences = new ArrayList<>();
                                                referencesByInstance.get(incomingTagInstance).forEach(tr -> {
                                                    try {
                                                        newReferences.add(new TagReference(newTagInstance, tr.getTarget().toString(), tr.getRange(), tr.getUserMarkupCollectionUuid()));
                                                    } catch (URISyntaxException e) {
                                                        e.printStackTrace();
                                                    }
                                                });
                                                intrinsicMarkupCollection.addTagReferences(newReferences);
                                            }
                                        } else {
                                            tag.setTagsetDefinitionUuid(targetTagset.getUuid());
                                            project.getTagManager().addTagDefinition(targetTagset, tag);
                                        }
                                    }
                                });
                                project.importCollection(Collections.emptyList(), intrinsicMarkupCollection);
                            }
                            if (tempFile.exists()) {
                                tempFile.delete();
                            }
                        }
                    } catch (Exception e) {
                        Logger.getLogger(ProjectView.class.getName()).log(Level.SEVERE, "Error importing the CATMA 5 Corpus: " + entryName, e);
                        String errorMsg = e.getMessage();
                        if ((errorMsg == null) || (errorMsg.trim().isEmpty())) {
                            errorMsg = "";
                        }
                        Notification.show("Error", String.format("Error importing the CATMA 5 Corpus! " + "This Document will be skipped!\n The underlying error message was:\n%1$s", errorMsg), Type.ERROR_MESSAGE);
                    }
                });
            }
            entry = taIs.getNextTarEntry();
        }
    }
    return null;
}