Examples with AlreadyExistException com.odysseusinc.arachne.portal.exception.AlreadyExistException used on opensource projects

Example 6 with AlreadyExistException

use of com.odysseusinc.arachne.portal.exception.AlreadyExistException in project ArachneCentralAPI by OHDSI.

the class AnalysisFilesSavingServiceImpl method saveFiles.

@PreAuthorize("hasPermission(#analysis, " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).UPLOAD_ANALYSIS_FILES)")
protected List<AnalysisFile> saveFiles(List<MultipartFile> multipartFiles, IUser user, A analysis, DataReference dataReference, BiPredicate<String, CommonAnalysisType> checkFileExecutabilityPredicate) {
    List<MultipartFile> filteredFiles = multipartFiles.stream().filter(file -> !(CommonAnalysisType.COHORT.equals(analysis.getType()) && file.getName().endsWith(OHDSI_JSON_EXT))).filter(file -> !file.getName().startsWith(ANALYSIS_INFO_FILE_DESCRIPTION)).collect(Collectors.toList());
    List<AnalysisFile> savedFiles = new ArrayList<>();
    List<String> errorFileMessages = new ArrayList<>();
    for (MultipartFile file : filteredFiles) {
        try {
            final boolean isExecutable = checkFileExecutabilityPredicate.test(file.getOriginalFilename(), analysis.getType());
            savedFiles.add(saveFile(file, user, analysis, file.getName(), isExecutable, dataReference));
        } catch (AlreadyExistException e) {
            errorFileMessages.add(e.getMessage());
        }
    }
    if (!errorFileMessages.isEmpty()) {
        throw new ValidationRuntimeException("Failed to save files", ImmutableMap.of(dataReference.getGuid(), errorFileMessages));
    }
    return savedFiles;
}

Example 7 with AlreadyExistException

use of com.odysseusinc.arachne.portal.exception.AlreadyExistException in project ArachneCentralAPI by OHDSI.

the class BaseStudyServiceImpl method addDataSource.

@Override
// ordering annotations is important to check current participants before method invoke
@PreAuthorize("hasPermission(#studyId, 'Study', " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).INVITE_DATANODE)")
public StudyDataSourceLink addDataSource(IUser createdBy, Long studyId, Long dataSourceId) throws NotExistException, AlreadyExistException {
    T study = studyRepository.getOne(studyId);
    if (study == null) {
        throw new NotExistException("study not exist", Study.class);
    }
    DS dataSource = dataSourceService.getNotDeletedById(dataSourceId);
    if (dataSource == null) {
        throw new NotExistException("dataSource not exist", DataSource.class);
    }
    StudyDataSourceLink studyDataSourceLink = studyDataSourceLinkRepository.findByDataSourceIdAndStudyId(dataSource.getId(), study.getId());
    if (studyDataSourceLink == null) {
        studyDataSourceLink = new StudyDataSourceLink();
    } else if (studyDataSourceLink.getStatus().isPendingOrApproved()) {
        throw new AlreadyExistException();
    }
    studyDataSourceLink.setStudy(study);
    studyDataSourceLink.setDataSource(dataSource);
    studyDataSourceLink.setCreated(new Date());
    studyDataSourceLink.setToken(UUID.randomUUID().toString());
    studyDataSourceLink.setCreatedBy(createdBy);
    studyDataSourceLink.setDeletedAt(null);
    AddDataSourceStrategy<DS> strategy = addDataSourceStrategyFactory.getStrategy(dataSource);
    strategy.addDataSourceToStudy(createdBy, dataSource, studyDataSourceLink);
    return studyDataSourceLink;
}

Example 8 with AlreadyExistException

use of com.odysseusinc.arachne.portal.exception.AlreadyExistException 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.saveAll(submissionInsightSubmissionFiles);
    final List<ResultFile> resultFiles = submission.getResultFiles();
    resultFiles.forEach(resultFile -> resultFile.setCommentTopic(new CommentTopic()));
    submissionResultFileRepository.saveAll(resultFiles);
    return savedInsight;
}

Example 9 with AlreadyExistException

use of com.odysseusinc.arachne.portal.exception.AlreadyExistException in project ArachneCentralAPI by OHDSI.

the class EstimationPreprocessor method attachRunner.

private void attachRunner(Analysis analysis, File file) {
    try {
        String runnerContent = template.apply(prepareParameters(analysis, file));
        final MultipartFile analysisFile = new MockMultipartFile(ANALYSIS_RUNNER_FILENAME, ANALYSIS_RUNNER_FILENAME, "text/x-r-source", runnerContent.getBytes());
        AnalysisFile createdFile = analysisService.saveFile(analysisFile, analysis.getAuthor(), analysis, ANALYSIS_RUNNER_FILENAME, true, null);
        String fileUuid = createdFile.getUuid();
        // Set via service function to unselect all other files
        analysisService.setIsExecutable(fileUuid);
    } catch (IOException e) {
        LOGGER.error("Failed to generate estimation R execution", e);
        throw new UncheckedIOException(e);
    } catch (AlreadyExistException e) {
        LOGGER.error("Failed to save file", e);
    }
}

Example 10 with AlreadyExistException

use of com.odysseusinc.arachne.portal.exception.AlreadyExistException in project ArachneCentralAPI by OHDSI.

the class BaseAnalysisController method sendUnlockRequest.

@ApiOperation("Send analysis unlock request")
@RequestMapping(value = "/api/v1/analysis-management/analyses/{analysisId}/unlock-request", method = POST)
public JsonResult<FileDTO> sendUnlockRequest(Principal principal, @PathVariable("analysisId") Long analysisId, @RequestBody AnalysisUnlockRequestDTO analysisUnlockRequestDTO) throws NotExistException, PermissionDeniedException, AlreadyExistException {
    JsonResult result;
    final IUser user = getUser(principal);
    final AnalysisUnlockRequest unlockRequest = new AnalysisUnlockRequest();
    unlockRequest.setUser(user);
    unlockRequest.setStatus(AnalysisUnlockRequestStatus.PENDING);
    unlockRequest.setCreated(new Date());
    unlockRequest.setToken(UUID.randomUUID().toString().replace("-", ""));
    unlockRequest.setDescription(analysisUnlockRequestDTO.getDescription());
    try {
        final AnalysisUnlockRequest analysisUnlockRequest = analysisService.sendAnalysisUnlockRequest(analysisId, unlockRequest);
        analysisService.findLeads((T) analysisUnlockRequest.getAnalysis()).forEach(lead -> wsTemplate.convertAndSendToUser(lead.getUsername(), "/topic/invitations", new UpdateNotificationDTO()));
        result = new JsonResult<>(NO_ERROR);
    } catch (AlreadyExistException ex) {
        result = new JsonResult<>(VALIDATION_ERROR);
        result.setErrorMessage("Unlock request for the analysis was already created");
    }
    return result;
}