Examples with CommonAnalysisType com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType used on opensource projects

Example 1 with CommonAnalysisType

use of com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType in project ArachneCentralAPI by OHDSI.

the class BaseAnalysisController method addCommonEntityToAnalysis.

@ApiOperation("Add common entity to analysis")
@RequestMapping(value = "/api/v1/analysis-management/analyses/{analysisId}/entities", method = POST)
public JsonResult addCommonEntityToAnalysis(@PathVariable("analysisId") Long analysisId, @RequestBody @Valid DataReferenceDTO entityReference, @RequestParam(value = "type", required = false, defaultValue = "COHORT") CommonAnalysisType analysisType, Principal principal) throws NotExistException, JMSException, IOException, PermissionDeniedException, URISyntaxException {
    if (!analysisModificationLock.add(analysisId)) {
        throw new ValidationRuntimeException("Analysis import rejected", Collections.singletonMap(entityReference.getEntityGuid(), Collections.singletonList("Another import into this analysis is in progress")));
    }
    try {
        LOGGER.debug("Started import into analysis {}", analysisId);
        final IUser user = getUser(principal);
        final DataNode dataNode = dataNodeService.getById(entityReference.getDataNodeId());
        final T analysis = analysisService.getById(analysisId);
        final DataReference dataReference = dataReferenceService.addOrUpdate(entityReference.getEntityGuid(), dataNode);
        final List<MultipartFile> entityFiles = getEntityFiles(entityReference, dataNode, analysisType);
        String description = doAddCommonEntityToAnalysis(analysis, dataReference, user, analysisType, entityFiles);
        return new JsonResult(NO_ERROR, description);
    } finally {
        analysisModificationLock.remove(analysisId);
        LOGGER.debug("Completed import into analysis {}", analysisId);
    }
}

Example 2 with CommonAnalysisType

use of com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType in project ArachneCentralAPI by OHDSI.

the class BaseAnalysisController method getEntityFiles.

public List<MultipartFile> getEntityFiles(DataReferenceDTO entityReference, DataNode dataNode, CommonAnalysisType entityType) throws JMSException, IOException, URISyntaxException {
    Long waitForResponse = datanodeImportTimeout;
    Long messageLifeTime = datanodeImportTimeout;
    String baseQueue = MessagingUtils.Entities.getBaseQueue(dataNode);
    CommonEntityRequestDTO request = new CommonEntityRequestDTO(entityReference.getEntityGuid(), entityType);
    ProducerConsumerTemplate exchangeTpl = new ProducerConsumerTemplate(destinationResolver, request, baseQueue, waitForResponse, messageLifeTime);
    final ObjectMessage responseMessage = jmsTemplate.execute(exchangeTpl, true);
    if (responseMessage == null) {
        String message = String.format(ENTITY_IS_NOT_AVAILABLE, entityType.getTitle(), entityReference.getEntityGuid(), entityReference.getDataNodeId());
        throw new ServiceNotAvailableException(message);
    }
    final List<ImportedFile> importedFiles = (List<ImportedFile>) responseMessage.getObject();
    boolean hasAnalysisRunner = hasAnalysisRunner(importedFiles);
    if (entityType.equals(CommonAnalysisType.ESTIMATION) && !hasAnalysisRunner) {
        return importService.processEstimation(importedFiles);
    }
    List<MultipartFile> files = importedFiles.stream().map(file -> conversionService.convert(file, MockMultipartFile.class)).collect(Collectors.toList());
    if (!hasAnalysisRunner) {
        files.addAll(generateAnalysisFiles(entityType));
    }
    return files;
}

Example 3 with CommonAnalysisType

use of com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType in project ArachneCentralAPI by OHDSI.

the class BaseDataNodeCommonAnalysisController method listCohorts.

/**
 * Returns list of cohorts defined in Atlas connected to the Data node
 * (for Central's UI)
 */
@ApiOperation("Returns list of cohorts defined in Atlas connected to the Data node")
@RequestMapping(value = "/api/v1/data-nodes/{dataNodeId}/{type}", method = GET)
public List<CommonCohortShortDTO> listCohorts(@PathVariable("dataNodeId") Long dataNodeId, @PathVariable("type") String type) throws JMSException, NotExistException {
    DN dataNode = baseDataNodeService.getById(dataNodeId);
    CommonAnalysisType analysisType = analysisTypeMap.getOrDefault(type, CommonAnalysisType.COHORT);
    return dataNodeMessageService.getDataList(dataNode, analysisType);
}

Example 4 with CommonAnalysisType

use of com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType in project ArachneCentralAPI by OHDSI.

the class BaseDataNodeMessageServiceImpl method getDataList.

@Override
@PreAuthorize("hasPermission(#dataNode, " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).IMPORT_FROM_DATANODE)")
public <T extends CommonEntityDTO> List<T> getDataList(DN dataNode, CommonAnalysisType analysisType) throws JMSException {
    Long waitForResponse = messagingTimeout;
    Long messageLifeTime = messagingTimeout;
    // Get all Atlases available in user's tenant
    List<IAtlas> atlasList = atlasService.findAll().stream().filter(a -> a.getVersion() != null).collect(Collectors.toList());
    String baseQueue = MessagingUtils.EntitiesList.getBaseQueue(dataNode);
    ProducerConsumerTemplate exchangeTpl = new ProducerConsumerTemplate(destinationResolver, new CommonEntityRequestObject(atlasList.stream().map(IAtlas::getId).collect(Collectors.toList()), analysisType), baseQueue, waitForResponse, messageLifeTime);
    ObjectMessage responseMessage = jmsTemplate.execute(exchangeTpl, true);
    List<T> entityList = (List<T>) responseMessage.getObject();
    Map<Long, IAtlas> atlasMap = atlasList.stream().collect(Collectors.toMap(IAtlas::getId, a -> a));
    entityList.forEach(e -> e.setName(atlasMap.get(e.getOriginId()).getName() + ": " + e.getName()));
    return entityList;
}

Example 5 with CommonAnalysisType

use of com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType in project ArachneCentralAPI by OHDSI.

the class BaseAnalysisCreateDTOToAnalysisConverter method convert.

@Override
public A convert(DTO dto) {
    A analysis = newAnalysis();
    analysis.setTitle(dto.getTitle());
    analysis.setDescription(dto.getDescription());
    final CommonAnalysisType analysisType = CommonAnalysisType.valueOf(dto.getTypeId());
    analysis.setType(analysisType);
    S study = newStudy();
    study.setId(dto.getStudyId());
    analysis.setStudy(study);
    return analysis;
}