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

Example 1 with Analysis

use of com.odysseusinc.arachne.portal.model.Analysis 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);
            });
        }
    }
    return true;
}

Example 2 with Analysis

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

the class BaseSubmissionController method createSubmission.

@ApiOperation("Create and send submission.")
@RequestMapping(value = "/api/v1/analysis-management/{analysisId}/submissions", method = POST)
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.getByEmail(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 3 with Analysis

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

the class BaseSubmissionToCommonAnalysisDTOConverter method convert.

@Override
public CommonAnalysisDTO convert(T source) {
    final CommonAnalysisDTO dto = createResultObject();
    dto.setId(source.getId());
    final Analysis analysis = source.getSubmissionGroup().getAnalysis();
    if (analysis != null) {
        dto.setName(analysis.getTitle());
        dto.setType(analysis.getType());
        Study study = analysis.getStudy();
        if (study != null && conversionService.canConvert(study.getClass(), CommonStudyDTO.class)) {
            dto.setStudy(conversionService.convert(study, CommonStudyDTO.class));
        }
    }
    IUser author = source.getSubmissionGroup().getAuthor();
    if (author != null && conversionService.canConvert(author.getClass(), CommonArachneUserDTO.class)) {
        CommonArachneUserDTO userDTO = conversionService.convert(author, CommonArachneUserDTO.class);
        dto.setOwner(userDTO);
    }
    dto.setUpdateSubmissionStatusPassword(source.getUpdatePassword());
    dto.setCentralDataSourceId(source.getDataSource().getId());
    for (SubmissionFile submissionFile : source.getSubmissionGroup().getFiles()) {
        if (submissionFile.getExecutable() && StringUtils.isEmpty(dto.getExecutableFileName())) {
            dto.setExecutableFileName(submissionFile.getRealName());
            dto.setInnerExecutableFilename(submissionFile.getEntryPoint());
        }
    }
    dto.setAnalysisFiles(source.getSubmissionGroup().getFiles().stream().map(file -> conversionService.convert(file, CommonAnalysisFileDTO.class)).collect(Collectors.toList()));
    proceedAdditionalFields(dto, source);
    return dto;
}

Example 4 with Analysis

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

the class StudyStateMachineTest method testAnalysisListDiscriminatorChangingInfo.

@Test
public void testAnalysisListDiscriminatorChangingInfo() {
    Study activeStudy = createStudy(ACTIVE);
    activeStudy.getAnalyses().add(new Analysis());
    // now study has one analysis and transitions from Active to Initiate should have Info status
    List<StudyTransition> availableStates = stateMachine.getAvailableStates(activeStudy);
    assertEquals(2, availableStates.size());
    assertTrue(availableStates.get(0).isInfo());
    assertFalse(availableStates.get(1).isInfo());
}

Example 5 with Analysis

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

the class AnalysisHelperTest method prepareAnalysis.

private Analysis prepareAnalysis(IUser author, Study study) throws Exception {
    List<Analysis> exists = analysisRepository.findByTitleAndStudyId("AnalysisHelperTest#test", study.getId());
    if (!exists.isEmpty()) {
        analysisRepository.delete(exists);
    }
    Analysis analysis = new Analysis();
    analysis.setTitle("AnalysisHelperTest#test");
    analysis.setFiles(new ArrayList<>());
    analysis.setAuthor(author);
    analysis.setStudy(study);
    analysis.setType(CommonAnalysisType.COHORT_CHARACTERIZATION);
    Set<ArachnePermission> permissions = new HashSet<>();
    permissions.add(ArachnePermission.CREATE_SUBMISSION);
    permissions.add(ArachnePermission.CREATE_ANALYSIS);
    analysis.setPermissions(permissions);
    analysis = analysisService.create(analysis);
    AnalysisFile file = new AnalysisFile();
    file.setUuid(UUID.randomUUID().toString());
    file.setAnalysis(analysis);
    file.setContentType("text/plain");
    file.setLabel("");
    file.setAuthor(author);
    file.setUpdatedBy(author);
    file.setExecutable(Boolean.TRUE);
    file.setRealName("test.sql");
    Date created = new Date();
    file.setCreated(created);
    file.setUpdated(created);
    file.setVersion(1);
    file = analysisFileRepository.save(file);
    analysis.getFiles().add(file);
    Path dir = Paths.get(analysisHelper.getStoreFilesPath(), study.getId().toString(), analysis.getId().toString());
    Files.createDirectories(dir);
    Path path = dir.resolve(file.getUuid());
    Files.write(path, "test".getBytes());
    return analysis;
}