Examples with PriorityCqlLibraryProvider com.ibm.cohort.cql.library.PriorityCqlLibraryProvider used on opensource projects

Example 1 with PriorityCqlLibraryProvider

use of com.ibm.cohort.cql.library.PriorityCqlLibraryProvider 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 PriorityCqlLibraryProvider

use of com.ibm.cohort.cql.library.PriorityCqlLibraryProvider 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 PriorityCqlLibraryProvider

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

the class CohortCLI method runWithArgs.

/**
 * Simulate main method behavior in a non-static context for use in testing
 * tools. This method is intended to be called only once. Multiple calls for the
 * same library path will attempt duplicate library loading.
 *
 * @param args parameter values
 * @param out  location where contents that would normally go to stdout should
 *             be written
 * @return CQLEvaluator
 * @throws IOException IOException
 */
public CqlEvaluator runWithArgs(String[] args, PrintStream out) throws IOException {
    Arguments arguments = new Arguments();
    Console console = new DefaultConsole(out);
    JCommander jc = JCommander.newBuilder().programName("cql-engine").console(console).addObject(arguments).build();
    jc.parse(args);
    CqlEvaluator wrapper = null;
    if (arguments.isDisplayHelp) {
        jc.usage();
    } else {
        FhirClientBuilderFactory factory = FhirClientBuilderFactory.newInstance();
        FhirClientBuilder fhirClientBuilder = factory.newFhirClientBuilder();
        readConnectionConfiguration(arguments);
        MapCqlLibraryProviderFactory libraryProviderFactory = new MapCqlLibraryProviderFactory();
        String[] filters = null;
        if (arguments.filters != null) {
            filters = arguments.filters.toArray(new String[arguments.filters.size()]);
        }
        CqlLibraryProvider backingLibraryProvider;
        Path libraryFolder = Paths.get(arguments.libraryPath);
        if (libraryFolder.toFile().isDirectory()) {
            out.println(String.format("Loading libraries from folder '%s'", libraryFolder.toString()));
            backingLibraryProvider = libraryProviderFactory.fromDirectory(libraryFolder, filters);
        } else if (FileHelpers.isZip(libraryFolder.toFile())) {
            out.println(String.format("Loading libraries from ZIP '%s'", libraryFolder.toString()));
            backingLibraryProvider = libraryProviderFactory.fromZipFile(libraryFolder, filters);
        } else {
            out.println(String.format("Loading libraries from FHIR Library '%s'", libraryFolder.toString()));
            IGenericClient measureClient = fhirClientBuilder.createFhirClient(measureServerConfig);
            FhirResourceResolver<Library> libraryResolver = R4FhirServerResourceResolverFactory.createLibraryResolver(measureClient);
            R4LibraryDependencyGatherer dependencyGatherer = new R4LibraryDependencyGatherer(libraryResolver);
            List<Library> cqlLibraries = dependencyGatherer.gatherForLibraryId(arguments.libraryPath);
            Map<CqlLibraryDescriptor, CqlLibrary> cqlLibraryMap = toCqlLibraryMap(cqlLibraries);
            backingLibraryProvider = new MapCqlLibraryProvider(cqlLibraryMap);
        }
        CqlLibraryProvider fhirClasspathProvider = new ClasspathCqlLibraryProvider();
        backingLibraryProvider = new PriorityCqlLibraryProvider(backingLibraryProvider, fhirClasspathProvider);
        CqlToElmTranslator translator = new CqlToElmTranslator();
        if (arguments.modelInfoFile != null && arguments.modelInfoFile.exists()) {
            translator.registerModelInfo(arguments.modelInfoFile);
        }
        boolean isForceTranslation = arguments.sourceFormat == Format.CQL;
        CqlLibraryProvider libraryProvider = new TranslatingCqlLibraryProvider(backingLibraryProvider, translator, isForceTranslation);
        IGenericClient dataClient = fhirClientBuilder.createFhirClient(dataServerConfig);
        IGenericClient termClient = fhirClientBuilder.createFhirClient(terminologyServerConfig);
        CqlTerminologyProvider termProvider = new R4RestFhirTerminologyProvider(termClient);
        Map<String, com.ibm.cohort.cql.evaluation.parameters.Parameter> parameters = null;
        if (arguments.parameters != null) {
            parameters = parseParameterArguments(arguments.parameters);
        }
        CqlVersionedIdentifier libraryIdentifier = new CqlVersionedIdentifier(arguments.libraryName, arguments.libraryVersion);
        List<Pair<String, String>> contexts;
        if (arguments.contextIds == null || arguments.contextIds.isEmpty()) {
            // If no context ids are provided, perform one run using a null context
            contexts = Collections.singletonList(null);
        } else {
            contexts = arguments.contextIds.stream().map(x -> new ImmutablePair<>(arguments.contextName, x)).collect(Collectors.toList());
        }
        try (RetrieveCacheContext cacheContext = new DefaultRetrieveCacheContext()) {
            CqlDataProvider dataProvider = R4DataProviderFactory.createDataProvider(dataClient, termProvider, cacheContext, R4FhirModelResolverFactory.createCachingResolver(), !arguments.enableTerminologyOptimization, arguments.searchPageSize);
            wrapper = new CqlEvaluator().setLibraryProvider(libraryProvider).setDataProvider(dataProvider).setTerminologyProvider(termProvider);
            ZonedDateTime evaluationDateTime = ZonedDateTime.now();
            for (Pair<String, String> context : contexts) {
                String contextLabel = context == null ? "null" : context.getRight();
                out.println("Context: " + contextLabel);
                CqlEvaluationResult result = wrapper.evaluate(libraryIdentifier, parameters, context, arguments.expressions, arguments.loggingLevel, evaluationDateTime);
                out.print(prettyPrintResult(result));
                out.println("---");
            }
        }
    }
    return wrapper;
}

Example 4 with PriorityCqlLibraryProvider

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

the class SparkCqlEvaluator method createLibraryProvider.

/**
 * Initialize a library provider that will load resources from the configured path
 * in local storage or from the well-known classpath locations. The library provider
 * comes configured with CQL translation enabled and will use custom modelinfo
 * definitions if provided in the configuration.
 *
 * @return configured library provider
 * @throws IOException when model info cannot be read
 * @throws FileNotFoundException when a specified model info file cannot be found
 */
protected CqlLibraryProvider createLibraryProvider() throws IOException, FileNotFoundException {
    CqlLibraryProvider hadoopBasedLp = new HadoopBasedCqlLibraryProvider(new Path(args.cqlPath), this.hadoopConfiguration.value());
    // we are excluding the pre-compiled FHIRHelpers libraries because they were not compiled
    // with the EnableResultTypes option that is required for some of the features of this program.
    ClasspathCqlLibraryProvider cpBasedLp = new ClasspathCqlLibraryProvider();
    cpBasedLp.setSupportedFormats(Format.CQL);
    CqlLibraryProvider priorityLp = new PriorityCqlLibraryProvider(hadoopBasedLp, cpBasedLp);
    return new TranslatingCqlLibraryProvider(priorityLp, getCqlTranslator());
}

Example 5 with PriorityCqlLibraryProvider

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

the class BaseDataTypeRequirementsProcessorTest method createLibrarySourceProvider.

protected CqlLibraryProvider createLibrarySourceProvider(String cqlPath, CqlToElmTranslator translator) throws IOException {
    ClasspathCqlLibraryProvider cpBasedLp = new ClasspathCqlLibraryProvider();
    cpBasedLp.setSupportedFormats(Format.CQL);
    MapCqlLibraryProviderFactory dirProviderFactory = new MapCqlLibraryProviderFactory();
    CqlLibraryProvider dirBasedLp = dirProviderFactory.fromDirectory(Paths.get(cqlPath));
    PriorityCqlLibraryProvider lsp = new PriorityCqlLibraryProvider(dirBasedLp, cpBasedLp);
    CqlLibraryProvider sourceProvider = new TranslatingCqlLibraryProvider(lsp, translator);
    return sourceProvider;
}