Examples with FhirResourceResolver com.ibm.cohort.cql.fhir.resolver.FhirResourceResolver used on opensource projects

Example 1 with FhirResourceResolver

use of com.ibm.cohort.cql.fhir.resolver.FhirResourceResolver 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;
}