Examples with ExportedProject de.tudarmstadt.ukp.clarin.webanno.export.model.ExportedProject used on opensource projects

Example 1 with ExportedProject

use of de.tudarmstadt.ukp.clarin.webanno.export.model.ExportedProject 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 ExportedProject

use of de.tudarmstadt.ukp.clarin.webanno.export.model.ExportedProject in project webanno by webanno.

the class ProjectSettingsExporter method exportData.

@Override
public void exportData(ProjectExportRequest aRequest, ProjectExportTaskMonitor aMonitor, ExportedProject aExProject, File aStage) throws Exception {
    Project project = aRequest.getProject();
    aExProject.setDescription(project.getDescription());
    // In older versions of WebAnno, the mode was an enum which was serialized as upper-case
    // during export but as lower-case in the database. This is compensating for this case.
    aExProject.setMode(StringUtils.upperCase(project.getMode(), Locale.US));
    aExProject.setScriptDirection(project.getScriptDirection());
    aExProject.setVersion(project.getVersion());
    aExProject.setDisableExport(project.isDisableExport());
    aExProject.setCreated(project.getCreated());
    aExProject.setUpdated(project.getUpdated());
    aExProject.setAnonymousCuration(project.isAnonymousCuration());
}

Example 3 with ExportedProject

use of de.tudarmstadt.ukp.clarin.webanno.export.model.ExportedProject in project webanno by webanno.

the class CuratedDocumentsExporterTest method runImportAndFetchDocuments.

private List<Pair<SourceDocument, String>> runImportAndFetchDocuments(ZipFile aZipFile) throws Exception {
    ArgumentCaptor<SourceDocument> sourceDocCaptor = ArgumentCaptor.forClass(SourceDocument.class);
    ArgumentCaptor<String> usernameCaptor = ArgumentCaptor.forClass(String.class);
    // Import the project again
    ExportedProject exProject = ProjectExportServiceImpl.loadExportedProject(aZipFile);
    ProjectImportRequest importRequest = new ProjectImportRequest(true);
    sut.importData(importRequest, project, exProject, aZipFile);
    verify(casStorageService, atLeastOnce()).getCasFile(sourceDocCaptor.capture(), usernameCaptor.capture());
    List<Pair<SourceDocument, String>> importedCases = new ArrayList<>();
    List<SourceDocument> docs = sourceDocCaptor.getAllValues();
    List<String> users = usernameCaptor.getAllValues();
    for (int i = 0; i < docs.size(); i++) {
        importedCases.add(Pair.of(docs.get(i), users.get(i)));
    }
    return importedCases;
}

Example 4 with ExportedProject

use of de.tudarmstadt.ukp.clarin.webanno.export.model.ExportedProject in project webanno by webanno.

the class LayerExporterTest method runExportImportAndFetchLayers.

private ArgumentCaptor<AnnotationLayer> runExportImportAndFetchLayers() throws Exception {
    // Export the project
    ProjectExportRequest exportRequest = new ProjectExportRequest();
    ProjectExportTaskMonitor monitor = new ProjectExportTaskMonitor();
    exportRequest.setProject(project);
    ExportedProject exportedProject = new ExportedProject();
    sut.exportData(exportRequest, monitor, exportedProject, workFolder);
    // Import the project again
    ArgumentCaptor<AnnotationLayer> captor = ArgumentCaptor.forClass(AnnotationLayer.class);
    doNothing().when(annotationService).createOrUpdateLayer(captor.capture());
    ProjectImportRequest importRequest = new ProjectImportRequest(true);
    ZipFile zipFile = mock(ZipFile.class);
    sut.importData(importRequest, project, exportedProject, zipFile);
    return captor;
}

Example 5 with ExportedProject

use of de.tudarmstadt.ukp.clarin.webanno.export.model.ExportedProject 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++;
    }
}