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

Example 6 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 7 with CommonAnalysisType

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

the class BaseAnalysisServiceImpl method update.

@Override
@PreAuthorize("hasPermission(#analysis,  'Analysis', " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).EDIT_ANALYSIS)")
public A update(A analysis) throws NotUniqueException, NotExistException, ValidationException {
    A forUpdate = analysisRepository.findOne(analysis.getId());
    if (forUpdate == null) {
        throw new NotExistException("update: analysis with id=" + analysis.getId() + " not exist", Analysis.class);
    }
    if (analysis.getTitle() != null && !analysis.getTitle().equals(forUpdate.getTitle())) {
        List<A> analyses = analysisRepository.findByTitleAndStudyId(analysis.getTitle(), forUpdate.getStudy().getId());
        if (!analyses.isEmpty()) {
            throw new NotUniqueException("title", "Not unique");
        }
        forUpdate.setTitle(analysis.getTitle());
    }
    if (analysis.getDescription() != null) {
        forUpdate.setDescription(analysis.getDescription());
    }
    final CommonAnalysisType analysisType = analysis.getType();
    if (analysisType != null) {
        forUpdate.setType(analysisType);
    }
    final A saved = super.update(forUpdate);
    solrService.indexBySolr(saved);
    return saved;
}

Example 8 with CommonAnalysisType

use of com.odysseusinc.arachne.commons.api.v1.dto.CommonAnalysisType 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 9 with CommonAnalysisType

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

the class BaseAnalysisController method updateCommonEntityInAnalysis.

@ApiOperation("update common entity in analysis")
@RequestMapping(value = "/api/v1/analysis-management/analyses/{analysisId}/entities/{fileUuid}", method = PUT)
public JsonResult updateCommonEntityInAnalysis(@PathVariable("analysisId") Long analysisId, @PathVariable("fileUuid") String fileUuid, @RequestParam(value = "type", required = false, defaultValue = "COHORT") CommonAnalysisType analysisType, Principal principal) throws IOException, JMSException, PermissionDeniedException, URISyntaxException {
    final IUser user = getUser(principal);
    final AnalysisFile analysisFile = analysisService.getAnalysisFile(analysisId, fileUuid);
    T analysis = (T) analysisFile.getAnalysis();
    final DataReference dataReference = analysisFile.getDataReference();
    final DataReferenceDTO entityReference = new DataReferenceDTO(dataReference.getDataNode().getId(), dataReference.getGuid());
    final List<MultipartFile> entityFiles = getEntityFiles(entityReference, dataReference.getDataNode(), analysisType);
    analysisService.findAnalysisFilesByDataReference(analysis, dataReference).forEach(af -> {
        analysisService.deleteAnalysisFile(analysis, af);
        analysis.getFiles().remove(af);
    });
    doAddCommonEntityToAnalysis(analysis, dataReference, user, analysisType, entityFiles);
    return new JsonResult(NO_ERROR);
}

Example 10 with CommonAnalysisType

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

the class SubmissionHelper method updateSubmissionExtendedInfo.

public void updateSubmissionExtendedInfo(final Submission submission) {
    final CommonAnalysisType analysisType = submission.getSubmissionGroup().getAnalysisType();
    SubmissionExtendInfoAnalyzeStrategy strategy;
    switch(analysisType) {
        case COHORT:
            {
                strategy = new CohortSubmissionExtendInfoStrategy();
                break;
            }
        case COHORT_CHARACTERIZATION:
            {
                strategy = new CohortCharacterizationSubmissionExtendInfoStrategy();
                break;
            }
        case INCIDENCE:
            {
                strategy = new IncidenceSubmissionExtendInfoStrategy();
                break;
            }
        case ESTIMATION:
            {
                strategy = new EstimationSubmissionExtendInfoStrategy();
                break;
            }
        case PREDICTION:
            {
                strategy = new PredictionSubmissionExtendInfoStrategy();
                break;
            }
        default:
            {
                strategy = new DefaultSubmissionExtendInfoStrategy();
            }
    }
    strategy.updateExtendInfo(submission);
}