Examples with ArachneFileMeta com.odysseusinc.arachne.storage.model.ArachneFileMeta used on opensource projects

Example 11 with ArachneFileMeta

use of com.odysseusinc.arachne.storage.model.ArachneFileMeta in project ArachneCentralAPI by OHDSI.

the class BaseSubmissionServiceImpl method storeExtractedFiles.

private void storeExtractedFiles(Submission submission, Path unzipDir, long uploadedBy) {
    List<ResultFile> resultFiles = new ArrayList<>();
    for (File extractedFile : CommonFileUtils.getFiles(unzipDir.toFile())) {
        String relativeFilepath = unzipDir.relativize(extractedFile.toPath()).toString().replace('\\', '/');
        String destinationPath = contentStorageHelper.getResultFilesDir(submission, relativeFilepath);
        ArachneFileMeta arachneFileMeta = contentStorageService.saveFile(extractedFile, destinationPath, uploadedBy);
        ResultFile resultFile = new ResultFile();
        resultFile.setSubmission(submission);
        resultFile.setPath(arachneFileMeta.getPath());
        resultFiles.add(resultFile);
    }
    submissionResultFileRepository.saveAll(resultFiles);
}

Example 12 with ArachneFileMeta

use of com.odysseusinc.arachne.storage.model.ArachneFileMeta in project ArachneCentralAPI by OHDSI.

the class BaseSubmissionServiceImpl method createResultFilesBatch.

@Override
@Transactional
public List<ResultFile> createResultFilesBatch(List<FileSaveRequest> fileSaveRequests, Submission submission, Long createById) throws IOException {
    fileSaveRequests.forEach(entry -> entry.setDestinationFilepath(contentStorageHelper.getResultFilesDir(submission, entry.getDestinationFilepath())));
    List<ArachneFileMeta> metaList = contentStorageService.saveBatch(fileSaveRequests, createById);
    return metaList.stream().map(fm -> {
        ResultFile resultFile = new ResultFile();
        resultFile.setSubmission(submission);
        resultFile.setPath(fm.getPath());
        return resultFile;
    }).collect(Collectors.toList());
}

Example 13 with ArachneFileMeta

use of com.odysseusinc.arachne.storage.model.ArachneFileMeta in project ArachneCentralAPI by OHDSI.

the class BaseSubmissionServiceImpl method getResultFileAndCheckPermission.

@Override
public ArachneFileMeta getResultFileAndCheckPermission(IUser user, Submission submission, Long analysisId, String fileUuid) throws PermissionDeniedException {
    ArachneFileMeta byFileUuid = contentStorageService.getFileByIdentifier(fileUuid);
    checkSubmissionPermission(user, submission);
    return byFileUuid;
}

Example 14 with ArachneFileMeta

use of com.odysseusinc.arachne.storage.model.ArachneFileMeta in project ArachneCentralAPI by OHDSI.

the class BaseSubmissionServiceImpl method deleteSubmissionResultFile.

@Override
public boolean deleteSubmissionResultFile(Long submissionId, ResultFile resultFile) throws NotExistException, ValidationException {
    final T submission = submissionRepository.findByIdAndStatusIn(submissionId, Collections.singletonList(IN_PROGRESS.name()));
    throwNotExistExceptionIfNull(submission, submissionId);
    Optional.ofNullable(resultFile).orElseThrow(() -> new NotExistException(String.format(RESULT_FILE_NOT_EXISTS_EXCEPTION, resultFile.getId(), submission.getId()), ResultFile.class));
    ArachneFileMeta fileMeta = contentStorageService.getFileByPath(resultFile.getPath());
    if (fileMeta.getCreatedBy() == null) {
        // not manually uploaded
        throw new ValidationException(String.format(FILE_NOT_UPLOADED_MANUALLY_EXCEPTION, resultFile.getId()));
    }
    deleteSubmissionResultFile(resultFile);
    submission.getResultFiles().remove(resultFile);
    submission.setUpdated(new Date());
    saveSubmission(submission);
    return true;
}