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

Example 16 with Submission

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

the class BaseSubmissionServiceImpl method getSubmissionArchiveChunk.

@Override
public Path getSubmissionArchiveChunk(Long id, String updatePassword, String fileName) throws FileNotFoundException {
    Path file;
    Submission submission = submissionRepository.findByIdAndUpdatePassword(id, updatePassword);
    if (submission != null) {
        file = analysisHelper.getSplittedFolder(submission.getSubmissionGroup()).resolve(fileName);
        if (Files.notExists(file)) {
            throw new FileNotFoundException();
        }
    } else {
        throw new FileNotFoundException();
    }
    return file;
}

Example 17 with Submission

use of com.odysseusinc.arachne.portal.model.Submission 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 18 with Submission

use of com.odysseusinc.arachne.portal.model.Submission 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 19 with Submission

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

the class AnalysisSubmissionControllerTests method getResultFilePath.

/*private void prepareResultFile(Long studyId, Long analysisId, Long submissionGroupId, Long submissionId) throws IOException {

        Path dir = Paths.get(analysisHelper.getStoreFilesPath(), studyId.toString(), analysisId.toString(), "sg_" + submissionGroupId, submissionId.toString(), AnalysisPaths.RESULT_DIR);
        Files.createDirectories(dir);
        Path path = dir.resolve("9934135d-07f0-4c6a-afd2-b705a1c8d948");
        Files.write(path, "SELECT * FROM death LIMIT 10".getBytes());
    }*/
private String getResultFilePath(Long submissionId) {
    Submission submission = new Submission();
    submission.setId(submissionId);
    return contentStorageHelper.getResultFilesDir(submission, "test.sql");
}

Example 20 with Submission

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

the class BaseSubmissionController method getResultFiles.

@ApiOperation("Get result files of the submission.")
@RequestMapping(value = "/api/v1/analysis-management/submissions/{submissionId}/results", method = GET)
public List<ResultFileDTO> getResultFiles(Principal principal, @PathVariable("submissionId") Long submissionId, @RequestParam(value = "path", required = false, defaultValue = "") String path, @RequestParam(value = "real-name", required = false) String realName) throws PermissionDeniedException, IOException {
    IUser user = userService.getByEmail(principal.getName());
    ResultFileSearch resultFileSearch = new ResultFileSearch();
    resultFileSearch.setPath(path);
    resultFileSearch.setRealName(realName);
    List<? extends ArachneFileMeta> resultFileList = submissionService.getResultFiles(user, submissionId, resultFileSearch);
    String resultFilesPath = contentStorageHelper.getResultFilesDir(Submission.class, submissionId, null);
    return resultFileList.stream().map(rf -> {
        ResultFileDTO rfDto = conversionService.convert(rf, ResultFileDTO.class);
        rfDto.setSubmissionId(submissionId);
        rfDto.setRelativePath(contentStorageHelper.getRelativePath(resultFilesPath, rfDto.getPath()));
        return rfDto;
    }).collect(Collectors.toList());
}