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

Example 11 with Analysis

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

the class BaseAnalysisServiceImpl method setIsExecutable.

/**
 * Updates isExecutable flag in a file with the given uuid and sets entry point
 *
 * @param uuid analysis file uuid
 */
@Override
public void setIsExecutable(String uuid) {
    AnalysisFile analysisFile = analysisFileRepository.findByUuid(uuid);
    Analysis analysis = analysisFile.getAnalysis();
    throwAccessDeniedExceptionIfLocked(analysis);
    setExecutableFileInAnalysis(analysis, uuid);
}

Example 12 with Analysis

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

the class BaseAnalysisServiceImpl method sendAnalysisUnlockRequest.

@Override
public AnalysisUnlockRequest sendAnalysisUnlockRequest(Long analysisId, AnalysisUnlockRequest analysisUnlockRequest) throws NotExistException, AlreadyExistException {
    final Optional<A> analysisOptional = analysisRepository.findByIdAndAndLockedTrue(analysisId);
    final Analysis analysis = analysisOptional.orElseThrow(() -> new NotExistException(ANALYSIS_NOT_FOUND_EXCEPTION, Analysis.class));
    IUser user = analysisUnlockRequest.getUser();
    final AnalysisUnlockRequest existUnlockRequest = analysisUnlockRequestRepository.findByAnalysisAndStatus(analysis, AnalysisUnlockRequestStatus.PENDING);
    if (existUnlockRequest != null) {
        String message = String.format(UNLOCK_REQUEST_ALREADY_EXISTS_EXCEPTION, analysis.getId(), user.getId());
        throw new AlreadyExistException(message);
    }
    analysisUnlockRequest.setAnalysis(analysis);
    final AnalysisUnlockRequest savedUnlockRequest = analysisUnlockRequestRepository.save(analysisUnlockRequest);
    studyService.findLeads((S) savedUnlockRequest.getAnalysis().getStudy()).forEach(lead -> mailSender.send(new UnlockAnalysisRequestMailMessage(WebSecurityConfig.getDefaultPortalURI(), lead, savedUnlockRequest)));
    return savedUnlockRequest;
}

Example 13 with Analysis

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

the class BaseArachneSecureServiceImpl method getRolesBySubmission.

@Override
public List<ParticipantRole> getRolesBySubmission(ArachneUser user, Submission submission) {
    List<ParticipantRole> result = new LinkedList<>();
    if (submission != null) {
        Analysis analysis = submission.getSubmissionGroup().getAnalysis();
        result = getRolesByAnalysis(user, analysis);
        final DataNode dataNode = submission.getDataSource().getDataNode();
        if (!DataNodeUtils.isDataNodeOwner(dataNode, user.getId())) {
            // There can be many DATA_SET_OWNER-s in a single study, owning different data sources
            // But in case of Submission, we are interested, whether current user is owner of the submission's DS
            result.removeIf(ParticipantRole.DATA_SET_OWNER::equals);
        }
    }
    return result;
}

Example 14 with Analysis

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

the class BaseAnalysisController method doAddCommonEntityToAnalysis.

protected void doAddCommonEntityToAnalysis(T analysis, DataReference dataReference, IUser user, CommonAnalysisType analysisType, List<MultipartFile> files) throws IOException {
    files.stream().filter(f -> !CommonAnalysisType.COHORT.equals(analysisType) || !f.getName().endsWith(CommonFileUtils.OHDSI_JSON_EXT)).forEach(f -> {
        try {
            analysisService.saveFile(f, user, analysis, f.getName(), detectExecutable(analysisType, f), dataReference);
        } catch (IOException e) {
            LOGGER.error("Failed to save file", e);
        }
    });
    if (analysisType.equals(CommonAnalysisType.COHORT)) {
        final ByteArrayOutputStream out = new ByteArrayOutputStream();
        class StringContainer {

            String value = CommonAnalysisType.COHORT.getTitle();
        }
        final StringContainer generatedFileName = new StringContainer();
        try (final ZipOutputStream zos = new ZipOutputStream(out)) {
            files.forEach(file -> {
                try {
                    if (file.getName().endsWith(CommonFileUtils.OHDSI_SQL_EXT)) {
                        String statement = org.apache.commons.io.IOUtils.toString(file.getInputStream(), "UTF-8");
                        String renderedSql = SqlRender.renderSql(statement, null, null);
                        DBMSType[] dbTypes = new DBMSType[] { DBMSType.POSTGRESQL, DBMSType.ORACLE, DBMSType.MS_SQL_SERVER, DBMSType.REDSHIFT, DBMSType.PDW };
                        String baseName = FilenameUtils.getBaseName(file.getOriginalFilename());
                        String extension = FilenameUtils.getExtension(file.getOriginalFilename());
                        for (final DBMSType dialect : dbTypes) {
                            final String sql = SqlTranslate.translateSql(renderedSql, DBMSType.MS_SQL_SERVER.getOhdsiDB(), dialect.getOhdsiDB());
                            final String fileName = baseName + "." + dialect.getLabel().replaceAll(" ", "-") + "." + extension;
                            ZipUtil.addZipEntry(zos, fileName, new ByteArrayInputStream(sql.getBytes("UTF-8")));
                        }
                        final String shortBaseName = baseName.replaceAll("\\.ohdsi", "");
                        if (!generatedFileName.value.contains(shortBaseName)) {
                            generatedFileName.value += "_" + shortBaseName;
                        }
                    } else {
                        String fileName = file.getName();
                        ZipUtil.addZipEntry(zos, fileName, file.getInputStream());
                    }
                } catch (IOException e) {
                    LOGGER.error("Failed to add file to archive", e);
                    throw new RuntimeIOException(e.getMessage(), e);
                }
            });
        }
        String fileName = generatedFileName.value + ".zip";
        final MultipartFile sqlArchive = new MockMultipartFile(fileName, fileName, "application/zip", out.toByteArray());
        analysisService.saveFile(sqlArchive, user, analysis, fileName, false, dataReference);
    }
}

Example 15 with Analysis

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

the class BaseAnalysisController method list.

@ApiOperation("List analyses.")
@RequestMapping(value = "/api/v1/analysis-management/analyses", method = GET)
public JsonResult<List<D>> list(Principal principal, @RequestParam("study-id") Long studyId) throws PermissionDeniedException, NotExistException {
    JsonResult<List<D>> result;
    IUser user = userService.getByEmail(principal.getName());
    if (user == null) {
        result = new JsonResult<>(PERMISSION_DENIED);
        return result;
    }
    Iterable<T> analyses = analysisService.list(user, studyId);
    result = new JsonResult<>(NO_ERROR);
    List<D> analysisDTOs = StreamSupport.stream(analyses.spliterator(), false).map(analysis -> conversionService.convert(analysis, getAnalysisDTOClass())).collect(Collectors.toList());
    result.setResult(analysisDTOs);
    return result;
}