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

Example 16 with Analysis

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

the class BaseSubmissionServiceImpl method getSubmissionGroups.

@Override
@PreAuthorize("hasPermission(#submissoinGroupSearch.analysisId,  'Analysis', " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).ACCESS_STUDY)")
@PostAuthorize("@ArachnePermissionEvaluator.addPermissionsToSubmissions(principal, returnObject )")
public Page<SubmissionGroup> getSubmissionGroups(SubmissionGroupSearch submissoinGroupSearch) {
    final SubmissionGroupSpecification submissionGroupSpecification = new SubmissionGroupSpecification(submissoinGroupSearch);
    final Integer page = submissoinGroupSearch.getPage();
    final PageRequest pageRequest = new PageRequest(page == null ? 0 : page - 1, submissoinGroupSearch.getPageSize(), new Sort(Sort.Direction.DESC, "created"));
    final Page<SubmissionGroup> submissionGroups = submissionGroupRepository.findAll(submissionGroupSpecification, pageRequest);
    final List<SubmissionGroup> content = submissionGroups.getContent();
    final Map<Long, SubmissionGroup> submissionGroupMap = content.stream().collect(Collectors.toMap(SubmissionGroup::getId, sg -> {
        sg.setSubmissions(new ArrayList<>());
        return sg;
    }));
    final Set<Long> submissionGroupIds = submissionGroupMap.keySet();
    if (!CollectionUtils.isEmpty(submissionGroupIds)) {
        final SubmissionSpecification<T> submissionSpecification = SubmissionSpecification.<T>builder(submissionGroupIds).withStatuses(submissoinGroupSearch.getSubmissionStatuses()).withDataSourceIds(submissoinGroupSearch.getDataSourceIds()).hasInsight(submissoinGroupSearch.getHasInsight()).showHidden(submissoinGroupSearch.getShowHidden()).build();
        submissionRepository.findAll(submissionSpecification).forEach(s -> submissionGroupMap.get(s.getSubmissionGroup().getId()).getSubmissions().add(s));
    }
    return submissionGroups;
}

Example 17 with Analysis

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

the class BaseSubmissionController method getResultFiles.

@ApiOperation("Get result files of the submission.")
@RequestMapping(value = "/api/v1/analysis-management/submissions/{submissionId}/results", method = GET)
public List<ResultFileDTO> getResultFiles(Principal principal, @PathVariable("submissionId") Long submissionId, @RequestParam(value = "path", required = false, defaultValue = "") String path, @RequestParam(value = "real-name", required = false) String realName) throws PermissionDeniedException, IOException {
    IUser user = userService.getByEmail(principal.getName());
    ResultFileSearch resultFileSearch = new ResultFileSearch();
    resultFileSearch.setPath(path);
    resultFileSearch.setRealName(realName);
    List<? extends ArachneFileMeta> resultFileList = submissionService.getResultFiles(user, submissionId, resultFileSearch);
    String resultFilesPath = contentStorageHelper.getResultFilesDir(Submission.class, submissionId, null);
    return resultFileList.stream().map(rf -> {
        ResultFileDTO rfDto = conversionService.convert(rf, ResultFileDTO.class);
        rfDto.setSubmissionId(submissionId);
        rfDto.setRelativePath(contentStorageHelper.getRelativePath(resultFilesPath, rfDto.getPath()));
        return rfDto;
    }).collect(Collectors.toList());
}

Example 18 with Analysis

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

the class InvitationableToInvitationDTOConverter method convert.

@Override
public InvitationDTO convert(Invitationable source) {
    final InvitationDTO invitationDTO = new InvitationDTO();
    final List<ActionDTO> actionList = Arrays.asList(new ActionDTO("Accept", "accept", "success"), new ActionDTO("Decline", "decline", "cancel"));
    invitationDTO.setActionList(actionList);
    invitationDTO.setType(source.getInvitationType());
    invitationDTO.setId(source.getId());
    invitationDTO.setActionType(source.getActionType());
    invitationDTO.setDate(source.getCreated());
    invitationDTO.setUser(conversionService.convert(source.getAuthor(), ShortUserDTO.class));
    final Object entity = source.getEntity();
    String title = "";
    Long id = null;
    if (entity instanceof Study) {
        final Study study = (Study) entity;
        title = study.getTitle();
        id = study.getId();
    } else if (entity instanceof Paper) {
        final Paper paper = (Paper) entity;
        title = paper.getStudy().getDescription();
        id = paper.getId();
    } else if (entity instanceof Analysis) {
        final Analysis analysis = (Analysis) entity;
        title = analysis.getTitle();
        id = analysis.getId();
    }
    final InvitationEntityDTO studyShortDTO = getInvitationEntityDTO(title, id);
    invitationDTO.setEntity(studyShortDTO);
    return invitationDTO;
}

Example 19 with Analysis

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

the class BaseStudyToStudyDTOConverter method convert.

@Override
public DTO convert(final S source) {
    final DTO studyDTO = createResultObject();
    studyDTO.setStatus(conversionService.convert(source.getStatus(), StudyStatusDTO.class));
    studyDTO.setTitle(source.getTitle());
    studyDTO.setType(conversionService.convert(source.getType(), StudyTypeDTO.class));
    studyDTO.setEndDate(source.getEndDate());
    studyDTO.setStartDate(source.getStartDate());
    studyDTO.setDescription(source.getDescription());
    if (!CollectionUtils.isEmpty(source.getParticipants())) {
        studyDTO.setParticipants(source.getParticipants().stream().map(link -> conversionService.convert(link, ParticipantDTO.class)).collect(Collectors.toList()));
    }
    final List<StudyDataSourceLink> foundLinks = studyService.getLinksByStudyId(source.getId(), EntityUtils.fromAttributePaths("dataSource.dataNode.dataNodeUsers.user"));
    for (final StudyDataSourceLink studyDataSourceLink : foundLinks) {
        final DataSourceDTO dataSourceDTO = conversionService.convert(studyDataSourceLink, DataSourceDTO.class);
        studyDTO.getDataSources().add(dataSourceDTO);
    }
    List<Analysis> analyses = getAnalyses(source);
    for (final Analysis analysis : analyses) {
        studyDTO.getAnalyses().add(conversionService.convert(analysis, BaseAnalysisDTO.class));
    }
    List<StudyFile> files = studyService.getFilesByStudyId(source.getId(), EntityUtils.fromAttributePaths("author"));
    for (final StudyFile studyFile : files) {
        studyDTO.getFiles().add(conversionService.convert(studyFile, StudyFileDTO.class));
    }
    studyDTO.setCreated(source.getCreated());
    studyDTO.setUpdated(source.getUpdated());
    studyDTO.setId(source.getId());
    studyDTO.setPermissions(conversionService.convert(source, PermissionsDTO.class));
    studyDTO.setPaperId(source.getPaper() == null ? null : source.getPaper().getId());
    studyDTO.setPrivacy(source.getPrivacy());
    proceedAdditionalFields(studyDTO, source);
    return studyDTO;
}

Example 20 with Analysis

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

the class AnalysisHelperTest method createSubmission.

@Test
@WithUserDetails("admin@odysseusinc.com")
public void createSubmission() throws Exception {
    DataSource dataSource = prepareDataSource();
    when(dataSourceService.getByIdUnsecured(1L)).thenReturn(dataSource);
    IUser user = prepareUser();
    Study study = prepareStudy(user);
    Analysis analysis = prepareAnalysis(user, study);
    List<Submission> submissions = AnalysisHelper.createSubmission(submissionService, Collections.<Long>singletonList(1L), user, analysis);
    try {
        assertThat(submissions, is(not(empty())));
        assertThat(submissions, contains(hasProperty("status", notNullValue())));
        assertThat(submissions, contains(hasProperty("submissionGroup", notNullValue())));
    } finally {
        cleanup(submissions, analysis, study);
    }
}