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

Example 1 with Submission

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

the class BaseSubmissionController method getStatusHistory.

@ApiOperation("Get status history of the submission")
@GetMapping("/api/v1/analysis-management/submissions/{submissionId}/status-history")
public JsonResult<List<SubmissionStatusHistoryElementDTO>> getStatusHistory(@PathVariable("submissionId") Long submissionId) throws NotExistException {
    Submission submission = submissionService.getSubmissionById(submissionId);
    List<SubmissionStatusHistoryElement> submissionStatusHistory = submissionService.getSubmissionStatusHistory(submission.getSubmissionGroup().getAnalysis().getId(), submissionId);
    List<SubmissionStatusHistoryElementDTO> convert = new LinkedList<>();
    for (SubmissionStatusHistoryElement submissionStatusHistoryElement : submissionStatusHistory) {
        convert.add(conversionService.convert(submissionStatusHistoryElement, SubmissionStatusHistoryElementDTO.class));
    }
    JsonResult<List<SubmissionStatusHistoryElementDTO>> result = new JsonResult<>(NO_ERROR);
    result.setResult(convert);
    return result;
}

Example 2 with Submission

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

the class BaseSubmissionController method getResultFile.

private ArachneFileMeta getResultFile(Principal principal, Long submissionId, String fileUuid) throws NotExistException, PermissionDeniedException {
    Submission submission = submissionService.getSubmissionById(submissionId);
    IUser user = userService.getByUsername(principal.getName());
    return submissionService.getResultFileAndCheckPermission(user, submission, submission.getSubmissionGroup().getAnalysis().getId(), fileUuid);
}

Example 3 with Submission

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

the class BaseSubmissionController method createSubmission.

@ApiOperation("Create and send submission.")
@PostMapping("/api/v1/analysis-management/{analysisId}/submissions")
public JsonResult<List<DTO>> createSubmission(Principal principal, @RequestBody @Validated CreateSubmissionsDTO createSubmissionsDTO, @PathVariable("analysisId") Long analysisId) throws PermissionDeniedException, NotExistException, IOException, NoExecutableFileException, ValidationException {
    final JsonResult<List<DTO>> result;
    if (principal == null) {
        throw new PermissionDeniedException();
    }
    IUser user = userService.getByUsername(principal.getName());
    if (user == null) {
        throw new PermissionDeniedException();
    }
    Analysis analysis = analysisService.getById(analysisId);
    final List<Submission> submissions = AnalysisHelper.createSubmission(submissionService, createSubmissionsDTO.getDataSources(), user, analysis);
    final List<DTO> submissionDTOs = submissions.stream().map(s -> conversionService.convert(s, getSubmissionDTOClass())).collect(Collectors.toList());
    result = new JsonResult<>(NO_ERROR);
    result.setResult(submissionDTOs);
    return result;
}

Example 4 with Submission

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

the class ArachnePermissionEvaluator method addPermissions.

public boolean addPermissions(ArachneUser user, HasArachnePermissions hasPermissionsObj) {
    Set<ArachnePermission> allPermissions = getAllPermissions(hasPermissionsObj, user);
    hasPermissionsObj.setPermissions(allPermissions);
    if (hasPermissionsObj instanceof Analysis) {
        final Analysis analysis = (Analysis) hasPermissionsObj;
        final List<SubmissionGroup> submissionGroups = analysis.getSubmissionGroups();
        if (!CollectionUtils.isEmpty(submissionGroups)) {
            submissionGroups.forEach(submissionGroup -> submissionGroup.getSubmissions().forEach(submission -> {
                final Set<ArachnePermission> submissionPermissions = getAllPermissions(submission, user);
                submission.setPermissions(submissionPermissions);
            }));
        }
        final List<AnalysisFile> files = analysis.getFiles();
        if (!CollectionUtils.isEmpty(files)) {
            files.forEach(file -> {
                final Set<ArachnePermission> filePermissions = getAllPermissions(file, user);
                file.setPermissions(filePermissions);
            });
        }
    } else if (hasPermissionsObj instanceof Study) {
        final Study study = (Study) hasPermissionsObj;
        for (final Analysis analysis : study.getAnalyses()) {
            analysis.setPermissions(getAllPermissions(analysis, user));
        }
    }
    return true;
}

Example 5 with Submission

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

the class BaseSubmissionServiceImpl method getResultFiles.

@Override
public List<ArachneFileMeta> getResultFiles(IUser user, Long submissionId, ResultFileSearch resultFileSearch) throws PermissionDeniedException {
    Submission submission = submissionRepository.findById(submissionId, EntityUtils.fromAttributePaths("dataSource", "dataSource.dataNode")).get();
    checkSubmissionPermission(user, submission);
    String resultFilesPath = contentStorageHelper.getResultFilesDir(submission, resultFileSearch.getPath());
    QuerySpec querySpec = new QuerySpec();
    querySpec.setName(resultFileSearch.getRealName());
    querySpec.setPath(resultFilesPath);
    return contentStorageService.searchFiles(querySpec);
}