Examples with R4LibraryDependencyGatherer com.ibm.cohort.cql.hapi.R4LibraryDependencyGatherer used on opensource projects

Example 6 with R4LibraryDependencyGatherer

use of com.ibm.cohort.cql.hapi.R4LibraryDependencyGatherer in project quality-measure-and-cohort-service by Alvearie.

the class MeasureCLI method runWithArgs.

public MeasureEvaluator runWithArgs(String[] args, PrintStream out) throws IOException {
    MeasureEvaluator evaluator = null;
    Arguments arguments = new Arguments();
    Console console = new DefaultConsole(out);
    JCommander jc = JCommander.newBuilder().programName("measure-engine").console(console).addObject(arguments).build();
    jc.parse(args);
    if (arguments.isDisplayHelp) {
        jc.usage();
    } else {
        arguments.validate();
        readDataServerConfiguration(arguments);
        readTerminologyServerConfiguration(arguments);
        FhirClientBuilderFactory fhirClientBuilderFactory = getFhirClientBuilderFactory();
        IGenericClient dataServerClient = fhirClientBuilderFactory.newFhirClientBuilder().createFhirClient(dataServerConfig);
        IGenericClient terminologyServerClient = fhirClientBuilderFactory.newFhirClientBuilder().createFhirClient(terminologyServerConfig);
        String[] filters = (arguments.filters != null) ? arguments.filters.toArray(new String[arguments.filters.size()]) : null;
        IParser parser = getFhirContext().newJsonParser().setPrettyPrint(true);
        R4QualityMeasureResolverFactory resolverFactory = new R4QualityMeasureResolverFactory(parser);
        FhirResourceResolver<Library> libraryResolver;
        FhirResourceResolver<Measure> measureResolver;
        if (arguments.measureServerConfigFile != null && FileHelpers.isZip(arguments.measureServerConfigFile)) {
            R4QualityMeasureResolvers resolvers = resolverFactory.fromZipFile(arguments.measureServerConfigFile.toPath(), filters);
            libraryResolver = resolvers.getLibraryResolver();
            measureResolver = resolvers.getMeasureResolver();
        } else if (arguments.measureServerConfigFile != null && arguments.measureServerConfigFile.isDirectory()) {
            R4QualityMeasureResolvers resolvers = resolverFactory.fromDirectory(arguments.measureServerConfigFile.toPath(), filters);
            libraryResolver = resolvers.getLibraryResolver();
            measureResolver = resolvers.getMeasureResolver();
        } else {
            readMeasureServerConfiguration(arguments);
            IGenericClient measureServerClient = fhirClientBuilderFactory.newFhirClientBuilder().createFhirClient(measureServerConfig);
            libraryResolver = R4FhirServerResourceResolverFactory.createLibraryResolver(measureServerClient);
            measureResolver = R4FhirServerResourceResolverFactory.createMeasureResolver(measureServerClient);
        }
        List<MeasureContext> measureContexts;
        if (arguments.measureConfigurationFile != null) {
            measureContexts = MeasureContextProvider.getMeasureContexts(arguments.measureConfigurationFile);
        } else {
            measureContexts = MeasureContextProvider.getMeasureContexts(arguments.resourceId, arguments.parameters);
        }
        validateMeasureContexts(measureContexts);
        R4LibraryDependencyGatherer libraryDependencyGatherer = new R4LibraryDependencyGatherer(libraryResolver);
        CqlTerminologyProvider terminologyProvider = new R4RestFhirTerminologyProvider(terminologyServerClient);
        try (RetrieveCacheContext retrieveCacheContext = arguments.disableRetrieveCache ? null : new DefaultRetrieveCacheContext()) {
            Map<String, CqlDataProvider> dataProviders = R4DataProviderFactory.createDataProviderMap(dataServerClient, terminologyProvider, retrieveCacheContext, R4FhirModelResolverFactory.createCachingResolver(), !arguments.enableTerminologyOptimization, arguments.searchPageSize);
            evaluator = new MeasureEvaluator(measureResolver, libraryResolver, libraryDependencyGatherer, terminologyProvider, dataProviders);
            for (String contextId : arguments.contextIds) {
                out.println("Evaluating: " + contextId);
                // Reports only returned for measures where patient is in initial population
                List<MeasureReport> reports = evaluator.evaluatePatientMeasures(contextId, measureContexts, new MeasureEvidenceOptions(arguments.includeEvaluatedResources, arguments.defineReturnOption));
                for (MeasureReport report : reports) {
                    if (arguments.reportFormat == ReportFormat.TEXT) {
                        out.println("Result for " + report.getMeasure());
                        for (MeasureReport.MeasureReportGroupComponent group : report.getGroup()) {
                            for (MeasureReport.MeasureReportGroupPopulationComponent pop : group.getPopulation()) {
                                String popCode = pop.getCode().getCodingFirstRep().getCode();
                                if (pop.getId() != null) {
                                    popCode += "(" + pop.getId() + ")";
                                }
                                out.println(String.format("Population: %s = %d", popCode, pop.getCount()));
                            }
                        }
                    } else {
                        out.println(parser.encodeResourceToString(report));
                    }
                    out.println("---");
                }
                if (reports.isEmpty()) {
                    out.println("---");
                }
            }
        }
    }
    return evaluator;
}

Example 7 with R4LibraryDependencyGatherer

use of com.ibm.cohort.cql.hapi.R4LibraryDependencyGatherer in project quality-measure-and-cohort-service by Alvearie.

the class R4MeasureEvaluatorBuilder method build.

public MeasureEvaluator build() {
    if (clientContext == null) {
        throw new IllegalArgumentException("Client context not provided");
    }
    CqlTerminologyProvider terminologyProvider = new R4RestFhirTerminologyProvider(clientContext.getTerminologyClient());
    Map<String, CqlDataProvider> dataProviders = R4DataProviderFactory.createDataProviderMap(clientContext.getDataClient(), terminologyProvider, cacheContext, isCachingModelResolver ? new CachingModelResolverDecorator(modelResolver) : modelResolver, isExpandValueSets, pageSize);
    FhirResourceResolver<Measure> measureResolver = R4FhirServerResourceResolverFactory.createMeasureResolver(clientContext.getMeasureClient());
    FhirResourceResolver<Library> libraryResolver = R4FhirServerResourceResolverFactory.createLibraryResolver(clientContext.getLibraryClient());
    R4LibraryDependencyGatherer libraryDependencyGatherer = new R4LibraryDependencyGatherer(libraryResolver);
    return new MeasureEvaluator(measureResolver, libraryResolver, libraryDependencyGatherer, terminologyProvider, dataProviders);
}

Example 8 with R4LibraryDependencyGatherer

use of com.ibm.cohort.cql.hapi.R4LibraryDependencyGatherer in project quality-measure-and-cohort-service by Alvearie.

the class MeasureEvaluationSeederTest method create_libraryWithMultipleModels.

@Test(expected = IllegalArgumentException.class)
public void create_libraryWithMultipleModels() throws IOException {
    Measure measure = createMeasure();
    FhirResourceResolver<Library> libraryResolver = Mockito.mock(FhirResourceResolver.class);
    R4LibraryDependencyGatherer dependencyGatherer = Mockito.mock(R4LibraryDependencyGatherer.class);
    Mockito.when(dependencyGatherer.gatherForMeasure(measure)).thenReturn(Collections.singletonList(createLibrary("/cql/seeder/MultipleUsings-1.0.0.xml")));
    MeasureEvaluationSeeder seeder = new MeasureEvaluationSeeder(null, null, dependencyGatherer, libraryResolver);
    seeder.create(measure, periodStart, periodEnd, null, null);
}