Examples with FormatSupport de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport used on opensource projects

Example 1 with FormatSupport

use of de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport in project webanno by webanno.

the class AnnotationDocumentExporter method exportAnnotationDocumentContents.

private void exportAnnotationDocumentContents(ProjectExportRequest aRequest, ProjectExportTaskMonitor aMonitor, ExportedProject aExProject, File aStage) throws UIMAException, ClassNotFoundException, IOException {
    Project project = aRequest.getProject();
    // The export process may store project-related information in this context to ensure it
    // is looked up only once during the bulk operation and the DB is not hit too often.
    Map<Pair<Project, String>, Object> bulkOperationContext = new HashMap<>();
    List<SourceDocument> documents = documentService.listSourceDocuments(project);
    int i = 1;
    int initProgress = aMonitor.getProgress();
    // Create a map containing the annotation documents for each source document. Doing this
    // as one DB access before the main processing to avoid hammering the DB in the loops
    // below.
    Map<SourceDocument, List<AnnotationDocument>> srcToAnnIdx = documentService.listAnnotationDocuments(project).stream().collect(groupingBy(doc -> doc.getDocument(), toList()));
    // Cache user lookups to avoid constantly hitting the database
    LoadingCache<String, User> usersCache = Caffeine.newBuilder().build(key -> userRepository.get(key));
    for (SourceDocument srcDoc : documents) {
        try (CasStorageSession session = CasStorageSession.openNested()) {
            // If the initial CAS does not exist yet, it must be created before export.
            if (!documentService.existsInitialCas(srcDoc)) {
                documentService.createOrReadInitialCas(srcDoc);
            }
            File targetDir = new File(aStage, ANNOTATION_CAS_FOLDER + srcDoc.getName());
            forceMkdir(targetDir);
            File initialCasFile = documentService.getCasFile(srcDoc, INITIAL_CAS_PSEUDO_USER);
            copyFileToDirectory(initialCasFile, targetDir);
            log.info("Exported annotation document content for user [" + INITIAL_CAS_PSEUDO_USER + "] for source document [" + srcDoc.getId() + "] in project [" + project.getName() + "] with id [" + project.getId() + "]");
            // 
            // Export per-user annotation document
            // 
            // Determine which format to use for export
            String formatId = FORMAT_AUTO.equals(aRequest.getFormat()) ? srcDoc.getFormat() : aRequest.getFormat();
            FormatSupport format = importExportService.getWritableFormatById(formatId).orElseGet(() -> {
                FormatSupport fallbackFormat = new WebAnnoTsv3FormatSupport();
                aMonitor.addMessage(LogMessage.warn(this, "Annotation: [%s] No writer " + "found for original format [%s] - exporting as [%s] " + "instead.", srcDoc.getName(), formatId, fallbackFormat.getName()));
                return fallbackFormat;
            });
            // Export annotations from regular users
            for (AnnotationDocument annDoc : srcToAnnIdx.computeIfAbsent(srcDoc, key -> emptyList())) {
                // annotation document is not NEW/IGNORE
                if (usersCache.get(annDoc.getUser()) != null && !annDoc.getState().equals(AnnotationDocumentState.NEW) && !annDoc.getState().equals(AnnotationDocumentState.IGNORE)) {
                    File annSerDir = new File(aStage.getAbsolutePath() + ANNOTATION_CAS_FOLDER + srcDoc.getName());
                    File annDocDir = new File(aStage.getAbsolutePath() + ANNOTATION_ORIGINAL_FOLDER + srcDoc.getName());
                    forceMkdir(annSerDir);
                    forceMkdir(annDocDir);
                    File annSerFile = documentService.getCasFile(srcDoc, annDoc.getUser());
                    File annFile = null;
                    if (annSerFile.exists()) {
                        annFile = importExportService.exportAnnotationDocument(srcDoc, annDoc.getUser(), format, annDoc.getUser(), ANNOTATION, false, bulkOperationContext);
                    }
                    if (annSerFile.exists()) {
                        copyFileToDirectory(annSerFile, annSerDir);
                        copyFileToDirectory(annFile, annDocDir);
                        forceDelete(annFile);
                    }
                    log.info("Exported annotation document content for user [" + annDoc.getUser() + "] for source document [" + srcDoc.getId() + "] in project [" + project.getName() + "] with id [" + project.getId() + "]");
                }
            }
            // correction type projects.
            if (PROJECT_TYPE_AUTOMATION.equals(project.getMode()) || PROJECT_TYPE_CORRECTION.equals(project.getMode())) {
                File corrSerFile = documentService.getCasFile(srcDoc, CORRECTION_USER);
                if (corrSerFile.exists()) {
                    // Copy CAS - this is used when importing the project again
                    // Util WebAnno 3.4.x, the CORRECTION_USER CAS was exported to 'curation'
                    // and 'curation_ser'.
                    // Since WebAnno 3.5.x, the CORRECTION_USER CAS is exported to 'annotation'
                    // and 'annotation_ser'.
                    File curationSerDir = new File(aStage + ANNOTATION_AS_SERIALISED_CAS + srcDoc.getName());
                    forceMkdir(curationSerDir);
                    copyFileToDirectory(corrSerFile, curationSerDir);
                    // Copy secondary export format for convenience - not used during import
                    File curationDir = new File(aStage + ANNOTATION_ORIGINAL_FOLDER + srcDoc.getName());
                    forceMkdir(curationDir);
                    File corrFile = importExportService.exportAnnotationDocument(srcDoc, CORRECTION_USER, format, CORRECTION_USER, CORRECTION);
                    copyFileToDirectory(corrFile, curationDir);
                    forceDelete(corrFile);
                }
            }
        }
        aMonitor.setProgress(initProgress + (int) ceil(((double) i) / documents.size() * 80.0));
        i++;
    }
}

Example 2 with FormatSupport

use of de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport in project webanno by webanno.

the class CuratedDocumentsExporter method exportData.

/**
 * Copy, if exists, curation documents to a folder that will be exported as Zip file
 *
 * @param aStage
 *            The folder where curated documents are copied to be exported as Zip File
 */
@Override
public void exportData(ProjectExportRequest aRequest, ProjectExportTaskMonitor aMonitor, ExportedProject aExProject, File aStage) throws Exception {
    Project project = aRequest.getProject();
    // The export process may store project-related information in this context to ensure it
    // is looked up only once during the bulk operation and the DB is not hit too often.
    Map<Pair<Project, String>, Object> bulkOperationContext = new HashMap<>();
    // Get all the source documents from the project
    List<SourceDocument> documents = documentService.listSourceDocuments(project);
    int initProgress = aMonitor.getProgress() - 1;
    int i = 1;
    for (SourceDocument sourceDocument : documents) {
        File curationCasDir = new File(aStage, CURATION_CAS_FOLDER + sourceDocument.getName());
        forceMkdir(curationCasDir);
        File curationDir = new File(aStage, CURATION_FOLDER + sourceDocument.getName());
        forceMkdir(curationDir);
        // finished or also the ones that are in progress
        if ((aRequest.isIncludeInProgress() && CURATION_IN_PROGRESS.equals(sourceDocument.getState())) || CURATION_FINISHED.equals(sourceDocument.getState())) {
            File curationCasFile = documentService.getCasFile(sourceDocument, CURATION_USER);
            if (curationCasFile.exists()) {
                // Copy CAS - this is used when importing the project again
                copyFileToDirectory(curationCasFile, curationCasDir);
                // Determine which format to use for export
                String formatId = FORMAT_AUTO.equals(aRequest.getFormat()) ? sourceDocument.getFormat() : aRequest.getFormat();
                FormatSupport format = importExportService.getWritableFormatById(formatId).orElseGet(() -> {
                    FormatSupport fallbackFormat = new WebAnnoTsv3FormatSupport();
                    aMonitor.addMessage(LogMessage.warn(this, "Curation: [%s] No writer" + " found for original format [%s] - exporting as [%s] " + "instead.", sourceDocument.getName(), formatId, fallbackFormat.getName()));
                    return fallbackFormat;
                });
                // Copy secondary export format for convenience - not used during import
                try {
                    File curationFile = importExportService.exportAnnotationDocument(sourceDocument, CURATION_USER, format, CURATION_USER, CURATION, true, bulkOperationContext);
                    copyFileToDirectory(curationFile, curationDir);
                    forceDelete(curationFile);
                } catch (Exception e) {
                    // ExceptionUtils.getRootCauseMessage(e) );
                    throw new ProjectExportException("Aborting due to unrecoverable error while exporting!");
                }
            }
        }
        aMonitor.setProgress(initProgress + (int) ceil(((double) i) / documents.size() * 10.0));
        i++;
    }
}

Example 3 with FormatSupport

use of de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport in project webanno by webanno.

the class ImportExportServiceImpl method importCasFromFile.

@Override
public CAS importCasFromFile(File aFile, Project aProject, String aFormatId, TypeSystemDescription aFullProjectTypeSystem) throws UIMAException, IOException {
    TypeSystemDescription tsd = aFullProjectTypeSystem;
    if (tsd == null) {
        tsd = annotationService.getFullProjectTypeSystem(aProject);
    }
    // Prepare a CAS with the project type system
    CAS cas = CasFactory.createCas(tsd);
    // Convert the source document to CAS
    FormatSupport format = getReadableFormatById(aFormatId).orElseThrow(() -> new IOException("No reader available for format [" + aFormatId + "]"));
    CollectionReaderDescription readerDescription = format.getReaderDescription(tsd);
    addConfigurationParameters(readerDescription, ResourceCollectionReaderBase.PARAM_SOURCE_LOCATION, aFile.getParentFile().getAbsolutePath(), ResourceCollectionReaderBase.PARAM_PATTERNS, "[+]" + aFile.getName());
    CollectionReader reader = createReader(readerDescription);
    if (!reader.hasNext()) {
        throw new FileNotFoundException("Source file [" + aFile.getName() + "] not found in [" + aFile.getPath() + "]");
    }
    reader.getNext(cas);
    // Create sentence / token annotations if they are missing
    boolean hasTokens = exists(cas, getType(cas, Token.class));
    boolean hasSentences = exists(cas, getType(cas, Sentence.class));
    if (!hasSentences) {
        splitSentences(cas);
    }
    if (!hasTokens) {
        tokenize(cas);
    }
    if (!exists(cas, getType(cas, Token.class)) || !exists(cas, getType(cas, Sentence.class))) {
        throw new IOException("The document appears to be empty. Unable to detect any " + "tokens or sentences. Empty documents cannot be imported.");
    }
    return cas;
}

Example 4 with FormatSupport

use of de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport in project webanno by webanno.

the class ProjectExportCuratedDocumentsTask method exportCuratedDocuments.

/**
 * Copy, if exists, curation documents to a folder that will be exported as Zip file
 *
 * @param aCopyDir
 *            The folder where curated documents are copied to be exported as Zip File
 */
private void exportCuratedDocuments(ProjectExportRequest aModel, File aCopyDir, boolean aIncludeInProgress, ProjectExportTaskMonitor aMonitor) throws ProjectExportException, IOException {
    Project project = aModel.getProject();
    // Get all the source documents from the project
    List<de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument> documents = documentService.listSourceDocuments(project);
    // Determine which format to use for export.
    FormatSupport format;
    if (FORMAT_AUTO.equals(aModel.getFormat())) {
        format = new WebAnnoTsv3FormatSupport();
    } else {
        format = importExportService.getWritableFormatById(aModel.getFormat()).orElseGet(() -> {
            // aModel.getFormat());
            return new WebAnnoTsv3FormatSupport();
        });
    }
    int initProgress = aMonitor.getProgress() - 1;
    int i = 1;
    for (de.tudarmstadt.ukp.clarin.webanno.model.SourceDocument sourceDocument : documents) {
        File curationCasDir = new File(aCopyDir + CURATION_AS_SERIALISED_CAS + sourceDocument.getName());
        FileUtils.forceMkdir(curationCasDir);
        File curationDir = new File(aCopyDir + CURATION_FOLDER + sourceDocument.getName());
        FileUtils.forceMkdir(curationDir);
        // finished or also the ones that are in progress
        if ((aIncludeInProgress && SourceDocumentState.CURATION_IN_PROGRESS.equals(sourceDocument.getState())) || SourceDocumentState.CURATION_FINISHED.equals(sourceDocument.getState())) {
            File curationCasFile = documentService.getCasFile(sourceDocument, WebAnnoConst.CURATION_USER);
            if (curationCasFile.exists()) {
                // Copy CAS - this is used when importing the project again
                FileUtils.copyFileToDirectory(curationCasFile, curationCasDir);
                // Copy secondary export format for convenience - not used during import
                try {
                    File curationFile = importExportService.exportAnnotationDocument(sourceDocument, WebAnnoConst.CURATION_USER, format, WebAnnoConst.CURATION_USER, Mode.CURATION);
                    FileUtils.copyFileToDirectory(curationFile, curationDir);
                    FileUtils.forceDelete(curationFile);
                } catch (Exception e) {
                    // ExceptionUtils.getRootCauseMessage(e) );
                    throw new ProjectExportException("Aborting due to unrecoverable error while exporting!");
                }
            }
        }
        aMonitor.setProgress(initProgress + (int) Math.ceil(((double) i) / documents.size() * 10.0));
        i++;
    }
}

Example 5 with FormatSupport

use of de.tudarmstadt.ukp.clarin.webanno.api.format.FormatSupport in project webanno by webanno.

the class LegacyRemoteApiController method curationDocumentRead.

/**
 * Download curated document with requested parameters
 *
 * Test when running in Eclipse: Open your browser, paste following URL with appropriate values:
 *
 * http://USERNAME:PASSWORD@localhost:8080/webanno-webapp/api/projects/{aProjectId}/curationdoc/
 * {aSourceDocumentId}?format=xmi
 *
 * @param response
 *            HttpServletResponse.
 * @param aProjectId
 *            {@link Project} ID.
 * @param aSourceDocumentId
 *            {@link SourceDocument} ID.
 * @param aFormatId
 *            Export format.
 * @throws Exception
 *             if there was an error.
 */
@RequestMapping(value = "/" + PROJECTS + "/{" + PARAM_PROJECT_ID + "}/" + CURATION + "/{" + PARAM_DOCUMENT_ID + "}", method = RequestMethod.GET)
public void curationDocumentRead(HttpServletResponse response, @PathVariable(PARAM_PROJECT_ID) long aProjectId, @PathVariable(PARAM_DOCUMENT_ID) long aSourceDocumentId, @RequestParam(value = PARAM_FORMAT, required = false) String aFormatId) throws Exception {
    // Get current user
    String username = SecurityContextHolder.getContext().getAuthentication().getName();
    User user = userRepository.get(username);
    if (user == null) {
        response.sendError(HttpStatus.BAD_REQUEST.value(), "User [" + username + "] not found.");
        return;
    }
    // Get project
    Project project;
    try {
        project = projectRepository.getProject(aProjectId);
    } catch (NoResultException e) {
        response.sendError(HttpStatus.NOT_FOUND.value(), "Project" + aProjectId + "] not found.");
        return;
    }
    // Check for the access
    boolean hasAccess = projectRepository.isManager(project, user) || userRepository.isAdministrator(user);
    if (!hasAccess) {
        response.sendError(HttpStatus.FORBIDDEN.value(), "User [" + username + "] is not allowed to access project [" + aProjectId + "]");
        return;
    }
    // Get source document
    SourceDocument srcDocument;
    try {
        srcDocument = documentRepository.getSourceDocument(aProjectId, aSourceDocumentId);
    } catch (NoResultException e) {
        response.sendError(HttpStatus.NOT_FOUND.value(), "Source document [" + aSourceDocumentId + "] not found in project [" + aProjectId + "] not found.");
        return;
    }
    // Check if curation is complete
    if (!SourceDocumentState.CURATION_FINISHED.equals(srcDocument.getState())) {
        response.sendError(HttpStatus.NOT_FOUND.value(), "Curation of source document [" + aSourceDocumentId + "] not yet complete.");
        return;
    }
    String formatId;
    if (aFormatId == null) {
        formatId = srcDocument.getFormat();
    } else {
        formatId = aFormatId;
    }
    // Determine the format
    FormatSupport format = importExportService.getWritableFormatById(formatId).orElseGet(() -> {
        LOG.info("[{}] Format [{}] is not writable - exporting as WebAnno TSV3 instead.", srcDocument.getName(), formatId);
        return new WebAnnoTsv3FormatSupport();
    });
    // Temporary file of annotation document
    File downloadableFile = importExportService.exportAnnotationDocument(srcDocument, WebAnnoConst.CURATION_USER, format, srcDocument.getName(), Mode.CURATION);
    try {
        // Set mime type
        String mimeType = URLConnection.guessContentTypeFromName(downloadableFile.getName());
        if (mimeType == null) {
            LOG.info("mimetype is not detectable, will take default");
            mimeType = "application/octet-stream";
        }
        // Set response
        response.setContentType(mimeType);
        response.setContentType("application/force-download");
        response.setHeader("Content-Disposition", "inline; filename=\"" + downloadableFile.getName() + "\"");
        response.setContentLength((int) downloadableFile.length());
        InputStream inputStream = new BufferedInputStream(new FileInputStream(downloadableFile));
        FileCopyUtils.copy(inputStream, response.getOutputStream());
    } catch (Exception e) {
        LOG.info("Exception occured" + e.getMessage());
    } finally {
        if (downloadableFile.exists()) {
            downloadableFile.delete();
        }
    }
}