Examples with ResultFile com.odysseusinc.arachne.portal.model.ResultFile used on opensource projects

Example 6 with ResultFile

use of com.odysseusinc.arachne.portal.model.ResultFile in project ArachneCentralAPI by OHDSI.

the class BaseSubmissionInsightServiceImpl method createSubmissionInsight.

@Override
@PreAuthorize("hasPermission(#submissionId,  'Submission', " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).EDIT_ANALYSIS)")
public SubmissionInsight createSubmissionInsight(Long submissionId, SubmissionInsight insight) throws AlreadyExistException, NotExistException {
    LOGGER.info(CREATING_INSIGHT_LOG, submissionId);
    final SubmissionInsight submissionInsight = submissionInsightRepository.findOneBySubmissionId(submissionId);
    if (submissionInsight != null) {
        final String message = String.format(INSIGHT_ALREADY_EXISTS_EXCEPTION, submissionId);
        throw new AlreadyExistException(message);
    }
    final List<SubmissionStatus> allowedStatuses = Arrays.asList(EXECUTED_PUBLISHED, FAILED_PUBLISHED);
    final Submission submission = submissionService.getSubmissionByIdAndStatus(submissionId, allowedStatuses);
    throwNotExistExceptionIfNull(submission, submissionId);
    insight.setId(null);
    insight.setCreated(new Date());
    insight.setSubmission(submission);
    final SubmissionInsight savedInsight = submissionInsightRepository.save(insight);
    final List<SubmissionInsightSubmissionFile> submissionInsightSubmissionFiles = submission.getSubmissionGroup().getFiles().stream().map(sf -> new SubmissionInsightSubmissionFile(savedInsight, sf, new CommentTopic())).collect(Collectors.toList());
    submissionInsightSubmissionFileRepository.save(submissionInsightSubmissionFiles);
    final List<ResultFile> resultFiles = submission.getResultFiles();
    resultFiles.forEach(resultFile -> resultFile.setCommentTopic(new CommentTopic()));
    submissionResultFileRepository.save(resultFiles);
    return savedInsight;
}

Example 7 with ResultFile

use of com.odysseusinc.arachne.portal.model.ResultFile 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 8 with ResultFile

use of com.odysseusinc.arachne.portal.model.ResultFile in project ArachneCentralAPI by OHDSI.

the class BaseSubmissionServiceImpl method getSubmissionResultAllFiles.

@Override
public void getSubmissionResultAllFiles(IUser user, Long analysisId, Long submissionId, String archiveName, OutputStream os) throws IOException, PermissionDeniedException {
    Submission submission = submissionRepository.findOne(submissionId);
    checkSubmissionPermission(user, submission);
    Path resultFilesPath = Paths.get(contentStorageHelper.getResultFilesDir(submission));
    try (ZipOutputStream zos = new ZipOutputStream(os)) {
        for (ResultFile resultFile : submission.getResultFiles()) {
            Path relativePath = resultFilesPath.relativize(Paths.get(resultFile.getPath()));
            ZipUtil.addZipEntry(zos, relativePath.toString(), contentStorageService.getContentByFilepath(resultFile.getPath()));
        }
    }
}

Example 9 with ResultFile

use of com.odysseusinc.arachne.portal.model.ResultFile 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;
}

Example 10 with ResultFile

use of com.odysseusinc.arachne.portal.model.ResultFile in project ArachneCentralAPI by OHDSI.

the class BaseSubmissionServiceImpl method createResultFile.

@Override
@Transactional
public ResultFile createResultFile(Path filePath, String name, Submission submission, Long createById) throws IOException {
    ResultFile resultFile = new ResultFile();
    resultFile.setSubmission(submission);
    ArachneFileMeta fileMeta = contentStorageService.saveFile(filePath.toFile(), contentStorageHelper.getResultFilesDir(submission, name), createById);
    resultFile.setPath(fileMeta.getPath());
    return resultFile;
}