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

Example 1 with ResultFile

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

the class BaseSubmissionController method deleteSubmissionResultsByUuid.

@ApiOperation("Delete manually uploaded submission result file")
@RequestMapping(value = "/api/v1/analysis-management/submissions/{submissionId}/result/{fileUuid}", method = DELETE)
public JsonResult<Boolean> deleteSubmissionResultsByUuid(@PathVariable("submissionId") Long id, @PathVariable("fileUuid") String fileUuid) {
    LOGGER.info("deleting result file for submission with id={} having uuid={}", id, fileUuid);
    JsonResult.ErrorCode errorCode;
    Boolean hasResult;
    try {
        ResultFile resultFile = submissionService.getResultFileByPath(contentStorageService.getFileByIdentifier(fileUuid).getPath());
        hasResult = submissionService.deleteSubmissionResultFile(id, resultFile);
        errorCode = JsonResult.ErrorCode.NO_ERROR;
    } catch (NotExistException e) {
        LOGGER.warn("Submission was not found, id: {}", id);
        errorCode = JsonResult.ErrorCode.VALIDATION_ERROR;
        hasResult = false;
    } catch (ValidationException e) {
        LOGGER.warn("Result file was not deleted", e);
        errorCode = JsonResult.ErrorCode.VALIDATION_ERROR;
        hasResult = false;
    }
    JsonResult<Boolean> result = new JsonResult<>(errorCode);
    result.setResult(hasResult);
    return result;
}

Example 2 with ResultFile

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

the class BaseSubmissionInsightServiceImpl method extractCommentTopics.

private Set<CommentTopic> extractCommentTopics(SubmissionInsight insight) {
    final Stream<CommentTopic> submissionFilesTopics = insight.getSubmissionInsightSubmissionFiles().stream().map(SubmissionInsightSubmissionFile::getCommentTopic);
    final Submission submission = insight.getSubmission();
    final Stream<CommentTopic> resultFileTopics = submission.getResultFiles().stream().map(ResultFile::getCommentTopic);
    return Stream.concat(submissionFilesTopics, resultFileTopics).map(commentTopic -> {
        commentTopic.setComments(new LinkedList<>());
        return commentTopic;
    }).collect(Collectors.toSet());
}

Example 3 with ResultFile

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

the class BaseSubmissionInsightServiceImpl method deleteSubmissionInsight.

@Override
@PreAuthorize("hasPermission(#submissionId,  'Submission', " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).EDIT_ANALYSIS)")
public void deleteSubmissionInsight(Long submissionId) throws NotExistException {
    LOGGER.info(DELETING_INSIGHT_LOG, submissionId);
    final Submission submission = submissionService.getSubmissionById(submissionId, EntityUtils.fromAttributePaths("submissionInsight", "resultFiles"));
    throwNotExistExceptionIfNull(submission, submissionId);
    throwNotExistExceptionIfNull(submission.getSubmissionInsight(), submissionId);
    final List<ResultFile> resultFiles = submission.getResultFiles();
    resultFiles.forEach(resultFile -> resultFile.setCommentTopic(null));
    submissionResultFileRepository.save(resultFiles);
    submissionInsightRepository.deleteBySubmissionId(submissionId);
}

Example 4 with ResultFile

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

the class BaseSubmissionServiceImpl method uploadResultsByDataOwner.

@Override
public ResultFile uploadResultsByDataOwner(Long submissionId, String name, MultipartFile file) throws NotExistException, IOException {
    UserDetails userDetails = (UserDetails) SecurityContextHolder.getContext().getAuthentication().getPrincipal();
    IUser user = userService.getByUsername(userDetails.getUsername());
    T submission = submissionRepository.findByIdAndStatusIn(submissionId, Collections.singletonList(IN_PROGRESS.name()));
    throwNotExistExceptionIfNull(submission, submissionId);
    File tempFile = File.createTempFile("manual-upload", name);
    file.transferTo(tempFile);
    ResultFile resultFile = createResultFile(tempFile.toPath(), ObjectUtils.firstNonNull(name, file.getOriginalFilename()), submission, user.getId());
    Date updated = new Date();
    List<ResultFile> resultFiles = submission.getResultFiles();
    resultFiles.add(resultFile);
    submission.setUpdated(updated);
    submissionResultFileRepository.save(resultFiles);
    saveSubmission(submission);
    return resultFile;
}

Example 5 with ResultFile

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

the class BaseArachneSecureServiceImpl method getRolesByCommentTopic.

@Override
public List<ParticipantRole> getRolesByCommentTopic(ArachneUser user, CommentTopic topic) {
    SubmissionInsightSubmissionFile submissionInsightLink = submissionInsightSubmissionFileRepository.findByCommentTopic(topic);
    SubmissionInsight insight;
    if (submissionInsightLink == null) {
        ResultFile resultFile = resultFileRepository.findByCommentTopic(topic);
        insight = resultFile.getSubmission().getSubmissionInsight();
    } else {
        insight = submissionInsightLink.getSubmissionInsight();
    }
    return getRolesByInsight(user, insight);
}