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

Example 1 with DataReference

use of com.odysseusinc.arachne.portal.model.DataReference 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 DataReference

use of com.odysseusinc.arachne.portal.model.DataReference 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 3 with DataReference

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

the class AnalysisFilesSavingServiceImpl method saveFiles.

@PreAuthorize("hasPermission(#analysis, " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).UPLOAD_ANALYSIS_FILES)")
protected List<AnalysisFile> saveFiles(List<MultipartFile> multipartFiles, IUser user, A analysis, DataReference dataReference, BiPredicate<String, CommonAnalysisType> checkFileExecutabilityPredicate) {
    List<MultipartFile> filteredFiles = multipartFiles.stream().filter(file -> !(CommonAnalysisType.COHORT.equals(analysis.getType()) && file.getName().endsWith(OHDSI_JSON_EXT))).filter(file -> !file.getName().startsWith(ANALYSIS_INFO_FILE_DESCRIPTION)).collect(Collectors.toList());
    List<AnalysisFile> savedFiles = new ArrayList<>();
    List<String> errorFileMessages = new ArrayList<>();
    for (MultipartFile file : filteredFiles) {
        try {
            final boolean isExecutable = checkFileExecutabilityPredicate.test(file.getOriginalFilename(), analysis.getType());
            savedFiles.add(saveFile(file, user, analysis, file.getName(), isExecutable, dataReference));
        } catch (AlreadyExistException e) {
            errorFileMessages.add(e.getMessage());
        }
    }
    if (!errorFileMessages.isEmpty()) {
        throw new ValidationRuntimeException("Failed to save files", ImmutableMap.of(dataReference.getGuid(), errorFileMessages));
    }
    return savedFiles;
}

Example 4 with DataReference

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

the class AnalysisFilesSavingServiceImpl method saveCohortAnalysisArchive.

@PreAuthorize("hasPermission(#analysis, " + "T(com.odysseusinc.arachne.portal.security.ArachnePermission).UPLOAD_ANALYSIS_FILES)")
public void saveCohortAnalysisArchive(A analysis, DataReference dataReference, IUser user, List<MultipartFile> files) {
    MultipartFile genericSqlFile = files.stream().filter(file -> file.getName().endsWith(OHDSI_SQL_EXT)).findAny().orElseThrow(() -> new ArachneSystemRuntimeException(String.format("There is no sql file for %s analysis.", analysis.getId())));
    Collection<MultipartFile> filesForArchive = files.stream().filter(file -> ObjectUtils.notEqual(file, genericSqlFile)).filter(file -> !StringUtils.equals(ANALYSIS_INFO_FILE_DESCRIPTION, file.getName())).collect(Collectors.toList());
    ByteArrayOutputStream out = new ByteArrayOutputStream();
    try (ZipOutputStream zos = new ZipOutputStream(out)) {
        generateFilesForEachDialectAndAddToZip(zos, genericSqlFile);
        ZipUtil.addZipEntries(zos, filesForArchive);
    } catch (IOException e) {
        log.error("Failed to create zip file for {} analysis", analysis.getId(), e);
        throw new ArachneSystemRuntimeException(e);
    }
    String fileName = AnalysisArchiveUtils.getArchiveFileName(CommonAnalysisType.COHORT, getAnalysisName(genericSqlFile));
    MultipartFile sqlArchive = new MockMultipartFile(fileName, fileName, "application/zip", out.toByteArray());
    try {
        saveFile(sqlArchive, user, analysis, fileName, false, dataReference);
    } catch (Exception e) {
        log.error("Failed to save zip file for {} analysis", analysis.getId(), e);
        throw new ArachneSystemRuntimeException(e);
    }
}

Example 5 with DataReference

use of com.odysseusinc.arachne.portal.model.DataReference 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(existingAnalysisFile -> {
        analysisService.deleteAnalysisFile(analysis, existingAnalysisFile);
        analysis.getFiles().remove(existingAnalysisFile);
    });
    final String description = doAddCommonEntityToAnalysis(analysis, dataReference, user, analysisType, entityFiles);
    return new JsonResult(NO_ERROR, description);
}