Examples with CqlToElmTranslator com.ibm.cohort.cql.translation.CqlToElmTranslator used on opensource projects

Example 1 with CqlToElmTranslator

use of com.ibm.cohort.cql.translation.CqlToElmTranslator in project quality-measure-and-cohort-service by Alvearie.

the class CohortEngineRestHandler method evaluateCohort.

@POST
@Path("/cohort-evaluation")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces({ MediaType.APPLICATION_JSON })
@ApiOperation(value = "Evaluates a specific define within a CQL for a set of patients", notes = COHORT_EVALUATION_API_NOTES, response = String.class, tags = { "Cohort Evaluation" }, nickname = "evaluate_cohort", extensions = { @Extension(properties = { @ExtensionProperty(name = DarkFeatureSwaggerFilter.DARK_FEATURE_NAME, value = CohortEngineRestConstants.DARK_LAUNCHED_COHORT_EVALUATION) }) })
@ApiImplicitParams({ // This is necessary for the dark launch feature
@ApiImplicitParam(access = DarkFeatureSwaggerFilter.DARK_FEATURE_CONTROLLED, paramType = "header", dataType = "string"), @ApiImplicitParam(name = REQUEST_DATA_PART, value = EXAMPLE_COHORT_REQUEST_DATA_JSON, dataTypeClass = CohortEvaluation.class, required = true, paramType = "form", type = "file"), @ApiImplicitParam(name = CQL_DEFINITION, value = CQL_REQUIREMENTS, dataTypeClass = File.class, required = true, paramType = "form", type = "file") })
@ApiResponses(value = { @ApiResponse(code = 200, message = "Successful Operation", response = CohortResult.class), @ApiResponse(code = 400, message = "Bad Request", response = ServiceErrorList.class), @ApiResponse(code = 500, message = "Server Error", response = ServiceErrorList.class) })
public Response evaluateCohort(@Context HttpServletRequest request, @ApiParam(value = ServiceBaseConstants.MINOR_VERSION_DESCRIPTION, required = true, defaultValue = ServiceBuildConstants.DATE) @QueryParam(CohortEngineRestHandler.VERSION) String version, @ApiParam(hidden = true, type = "file", required = true) IMultipartBody multipartBody) {
    final String methodName = MethodNames.EVALUATE_COHORT.getName();
    Response response = null;
    // Error out if feature is not enabled
    ServiceBaseUtility.isDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_MEASURE_EVALUATION);
    try {
        // Perform api setup
        Response errorResponse = ServiceBaseUtility.apiSetup(version, logger, methodName);
        if (errorResponse != null) {
            return errorResponse;
        }
        if (multipartBody == null) {
            throw new IllegalArgumentException("A multipart/form-data body is required");
        }
        IAttachment metadataAttachment = multipartBody.getAttachment(REQUEST_DATA_PART);
        if (metadataAttachment == null) {
            throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", REQUEST_DATA_PART));
        }
        // deserialize the MeasuresEvaluation request
        ObjectMapper om = new ObjectMapper();
        CohortEvaluation evaluationRequest = om.readValue(metadataAttachment.getDataHandler().getInputStream(), CohortEvaluation.class);
        FhirServerConfig dataServerConfig = evaluationRequest.getDataServerConfig();
        FhirServerConfig terminologyServerConfig = evaluationRequest.getTerminologyServerConfig() == null ? evaluationRequest.getDataServerConfig() : evaluationRequest.getTerminologyServerConfig();
        IAttachment cqlAttachment = multipartBody.getAttachment(CQL_DEFINITION);
        if (cqlAttachment == null) {
            throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", CQL_DEFINITION));
        }
        // validate the contents of the fhirServerConfig
        validateBean(dataServerConfig);
        validateBean(terminologyServerConfig);
        FhirClientBuilderFactory clientBuilderFactory = FhirClientBuilderFactory.newInstance();
        FhirClientBuilder clientBuilder = clientBuilderFactory.newFhirClientBuilder();
        CqlLibraryProvider libraryProvider;
        try (InputStream is = cqlAttachment.getDataHandler().getInputStream()) {
            ZipInputStream zis = new ZipInputStream(is);
            MapCqlLibraryProviderFactory libraryProviderFactory = new MapCqlLibraryProviderFactory();
            String[] attachmentHeaders = cqlAttachment.getHeader("Content-Disposition").split(";");
            String filename = null;
            for (String header : attachmentHeaders) {
                if (header.contains("filename")) {
                    filename = FilenameUtils.removeExtension(header.split("=")[1].replaceAll("\"", ""));
                }
            }
            String[] searchPaths = new String[] { "cql", filename + "/cql" };
            libraryProvider = libraryProviderFactory.fromZipStream(zis, searchPaths);
        }
        CqlLibraryProvider fhirClasspathProvider = new ClasspathCqlLibraryProvider();
        libraryProvider = new PriorityCqlLibraryProvider(libraryProvider, fhirClasspathProvider);
        CqlToElmTranslator translator = new CqlToElmTranslator();
        libraryProvider = new TranslatingCqlLibraryProvider(libraryProvider, translator);
        IGenericClient dataClient = clientBuilder.createFhirClient(dataServerConfig);
        IGenericClient termClient = clientBuilder.createFhirClient(terminologyServerConfig);
        CqlTerminologyProvider termProvider = new R4RestFhirTerminologyProvider(termClient);
        List<String> passingPatients;
        try (RetrieveCacheContext retrieveCacheContext = new DefaultRetrieveCacheContext()) {
            passingPatients = evaluateCohort(dataClient, termProvider, libraryProvider, retrieveCacheContext, evaluationRequest);
        }
        response = Response.status(Response.Status.OK).header("Content-Type", "application/json").entity(new CohortResult(passingPatients)).build();
    } catch (Throwable e) {
        // map any exceptions caught into the proper REST error response objects
        response = new CohortServiceExceptionMapper().toResponse(e);
    } finally {
        // Perform api cleanup
        Response errorResponse = ServiceBaseUtility.apiCleanup(logger, methodName);
        if (errorResponse != null) {
            response = errorResponse;
        }
    }
    return response;
}

Example 2 with CqlToElmTranslator

use of com.ibm.cohort.cql.translation.CqlToElmTranslator in project quality-measure-and-cohort-service by Alvearie.

the class TranslationCLI method runWithArgs.

public void runWithArgs(TranslationOptions options, PrintStream out) throws Exception {
    CqlLibraryProvider libraryProvider;
    if (options.directory != null && options.directory.exists()) {
        MapCqlLibraryProviderFactory libraryProviderFactory = new MapCqlLibraryProviderFactory();
        libraryProvider = libraryProviderFactory.fromDirectory(options.directory.toPath());
    } else {
        libraryProvider = new MapCqlLibraryProvider(Collections.emptyMap());
    }
    CqlLibraryProvider fhirClasspathProvider = new ClasspathCqlLibraryProvider();
    libraryProvider = new PriorityCqlLibraryProvider(libraryProvider, fhirClasspathProvider);
    CqlToElmTranslator translator = new CqlToElmTranslator();
    if (options.modelInfoFile != null && options.modelInfoFile.exists()) {
        translator.registerModelInfo(options.modelInfoFile);
    }
    String content;
    try (InputStream is = new FileInputStream(options.cqlPath)) {
        content = IOUtils.toString(is, StandardCharsets.UTF_8);
    }
    // The values in the descriptor are not relevant for the translation CLI.
    CqlLibraryDescriptor descriptor = new CqlLibraryDescriptor().setFormat(Format.CQL).setLibraryId("TranslationCLI").setVersion("TranslationCLI");
    CqlLibrary library = new CqlLibrary().setDescriptor(descriptor).setContent(content);
    CqlTranslationResult result = translator.translate(library, new ProviderBasedCqlLibrarySourceProvider(libraryProvider));
    out.println("Translated Library: ");
    out.println(result.getMainLibrary().getContent());
}

Example 3 with CqlToElmTranslator

use of com.ibm.cohort.cql.translation.CqlToElmTranslator in project quality-measure-and-cohort-service by Alvearie.

the class PatientTestBase method setupTestFor.

protected CqlEvaluator setupTestFor(DomainResource resource, FhirServerConfig fhirConfig, String firstPackage, String... packages) {
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    mockFhirResourceRetrieval(resource);
    CqlEvaluator evaluator = null;
    if (firstPackage != null) {
        FhirClientBuilderFactory factory = FhirClientBuilderFactory.newInstance();
        FhirClientBuilder fhirClientBuilder = factory.newFhirClientBuilder();
        CqlLibraryProvider classpathCqlLibraryProvider = new ClasspathCqlLibraryProvider(firstPackage, packages);
        CqlToElmTranslator translator = new CqlToElmTranslator();
        CqlLibraryProvider libraryProvider = new TranslatingCqlLibraryProvider(classpathCqlLibraryProvider, translator);
        IGenericClient testClient = fhirClientBuilder.createFhirClient(fhirConfig);
        CqlTerminologyProvider termProvider = new R4RestFhirTerminologyProvider(testClient);
        CqlDataProvider dataProvider = R4DataProviderFactory.createDataProvider(testClient, termProvider, null, R4FhirModelResolverFactory.createCachingResolver(), true, null);
        evaluator = new CqlEvaluator().setLibraryProvider(libraryProvider).setDataProvider(dataProvider).setTerminologyProvider(termProvider).setCacheContexts(false);
    }
    return evaluator;
}

Example 4 with CqlToElmTranslator

use of com.ibm.cohort.cql.translation.CqlToElmTranslator in project quality-measure-and-cohort-service by Alvearie.

the class SparkCqlEvaluator method createDataTypeAliases.

private Map<String, String> createDataTypeAliases(List<ContextDefinition> filteredContexts, CqlToElmTranslator translator) {
    Set<String> dataTypes = filteredContexts.stream().map(ContextDefinition::getPrimaryDataType).collect(Collectors.toSet());
    Collection<ModelInfo> modelInfos = translator.getRegisteredModelInfos().values();
    Map<String, String> dataTypeAliases = new HashMap<>();
    for (ModelInfo modelInfo : modelInfos) {
        modelInfo.getTypeInfo().stream().filter(ClassInfo.class::isInstance).map(ClassInfo.class::cast).filter(classInfo -> dataTypes.contains(classInfo.getName())).forEach(info -> {
            String dataType = info.getName();
            QName baseType = ModelUtils.getBaseTypeName(modelInfo, info);
            if (baseType != null) {
                // for inheritance types
                dataTypeAliases.put(dataType, baseType.getLocalPart());
            }
            Collection<String> choiceTypes = ModelUtils.getChoiceTypeNames(info);
            // for choice types
            choiceTypes.forEach(choiceType -> dataTypeAliases.put(dataType, choiceType));
        });
    }
    return dataTypeAliases;
}

Example 5 with CqlToElmTranslator

use of com.ibm.cohort.cql.translation.CqlToElmTranslator in project quality-measure-and-cohort-service by Alvearie.

the class SparkCqlEvaluator method getCqlTranslator.

protected CqlToElmTranslator getCqlTranslator() throws IOException {
    // TODO - replace with cohort shared translation component
    final CqlToElmTranslator translator = new CqlToElmTranslator();
    if (args.modelInfoPaths != null && !args.modelInfoPaths.isEmpty()) {
        for (String path : args.modelInfoPaths) {
            Path filePath = new Path(path);
            FileSystem modelInfoFilesystem = filePath.getFileSystem(this.hadoopConfiguration.value());
            try (Reader r = new InputStreamReader(modelInfoFilesystem.open(filePath))) {
                translator.registerModelInfo(r);
            }
        }
    }
    return translator;
}