Examples with Library org.hl7.fhir.r5.model.Library used on opensource projects

Example 31 with Library

use of org.hl7.fhir.r5.model.Library in project cqf-ruler by DBCG.

the class CqlExecutionProviderIT method testDataBundleCqlExecutionProvider.

@Test
public void testDataBundleCqlExecutionProvider() throws Exception {
    Parameters params = new Parameters();
    Parameters libraryParameter = new Parameters();
    libraryParameter.addParameter().setName("url").setValue(new StringType(this.getClient().getServerBase() + "Library/SimpleDstu3Library"));
    libraryParameter.addParameter().setName("name").setValue(new StringType("SimpleDstu3Library"));
    params.addParameter().setName("library").setResource(libraryParameter);
    params.addParameter().setName("expression").setValue(new StringType("SimpleDstu3Library.\"observationRetrieve\""));
    String packagePrefix = "org/opencds/cqf/ruler/cpg/dstu3/provider/";
    loadResource(packagePrefix + "SimpleDstu3Library.json");
    loadResource(packagePrefix + "SimplePatient.json");
    Bundle data = (Bundle) loadResource(packagePrefix + "SimpleDataBundle.json");
    params.addParameter().setName("data").setResource(data);
    params.addParameter().setName("useServerData").setValue(new BooleanType(false));
    Parameters results = getClient().operation().onServer().named("$cql").withParameters(params).execute();
    assertTrue(results.getParameter().get(0).getResource() instanceof Bundle);
    assertTrue(((Bundle) results.getParameter().get(0).getResource()).getEntry().get(0).getResource() instanceof Observation);
    assertTrue(results.getParameter().get(1).getValue() instanceof StringType);
    assertTrue(((StringType) results.getParameter().get(1).getValue()).asStringValue().equals("List"));
    logger.debug("Results: ", results);
}

Example 32 with Library

use of org.hl7.fhir.r5.model.Library in project cqf-ruler by DBCG.

the class CqlExecutionProviderIT method testReferencedLibraryCqlExecutionProvider.

@Test
public void testReferencedLibraryCqlExecutionProvider() throws Exception {
    Parameters params = new Parameters();
    params.addParameter().setName("subject").setValue(new StringType("Patient/SimplePatient"));
    Parameters libraryParameter = new Parameters();
    libraryParameter.addParameter().setName("url").setValue(new StringType(this.getClient().getServerBase() + "Library/SimpleDstu3Library"));
    libraryParameter.addParameter().setName("name").setValue(new StringType("SimpleDstu3Library"));
    params.addParameter().setName("library").setResource(libraryParameter);
    params.addParameter().setName("expression").setValue(new StringType("SimpleDstu3Library.\"simpleBooleanExpression\""));
    String packagePrefix = "org/opencds/cqf/ruler/cpg/dstu3/provider/";
    loadResource(packagePrefix + "SimpleDstu3Library.json");
    loadResource(packagePrefix + "SimplePatient.json");
    Parameters results = getClient().operation().onServer().named("$cql").withParameters(params).execute();
    assertTrue(results.getParameter().get(0).getValue() instanceof StringType);
    assertTrue(((StringType) results.getParameter().get(0).getValue()).asStringValue().equals("true"));
    assertTrue(results.getParameter().get(1).getValue() instanceof StringType);
    assertTrue(((StringType) results.getParameter().get(1).getValue()).asStringValue().equals("Boolean"));
    logger.debug("Results: ", results);
}

Example 33 with Library

use of org.hl7.fhir.r5.model.Library in project cqf-ruler by DBCG.

the class LibraryEvaluationProviderIT method testLibraryEvaluationValidationThrows.

@Test
public void testLibraryEvaluationValidationThrows() throws IOException {
    Parameters params = new Parameters();
    params.addParameter().setName("periodStart").setValue(new StringType("2021-01-01"));
    params.addParameter().setName("periodEnd").setValue(new StringType("2021-12-31"));
    params.addParameter().setName("patientId").setValue(null);
    params.addParameter().setName("context").setValue(new StringType("Patient"));
    String packagePrefix = "org/opencds/cqf/ruler/cpg/r4/provider/";
    loadResource(packagePrefix + "ColorectalCancerScreeningsFHIR.json");
    Library lib = getClient().read().resource(Library.class).withId("ColorectalCancerScreeningsFHIR").execute();
    assertNotNull(lib);
    assertThrows(InternalErrorException.class, () -> {
        getClient().operation().onInstance(new IdType("Library", "ColorectalCancerScreeningsFHIR")).named("$evaluate").withParameters(params).returnResourceType(Bundle.class).execute();
    });
}

Example 34 with Library

use of org.hl7.fhir.r5.model.Library in project quality-measure-and-cohort-service by Alvearie.

the class CohortEngineRestHandler method createMeasureEvaluator.

private MeasureEvaluator createMeasureEvaluator(InputStream inputStream, FhirServerConfig dataServerConfig, FhirServerConfig terminologyServerConfig, Boolean expandValueSets, Integer searchPageSize, RetrieveCacheContext retrieveCacheContext, FhirContext fhirContext) throws IOException {
    FhirClientBuilder clientBuilder = FhirClientBuilderFactory.newInstance().newFhirClientBuilder(fhirContext);
    IGenericClient dataClient = clientBuilder.createFhirClient(dataServerConfig);
    IGenericClient terminologyClient = dataClient;
    if (terminologyServerConfig != null) {
        terminologyClient = clientBuilder.createFhirClient(terminologyServerConfig);
    }
    IParser parser = dataClient.getFhirContext().newJsonParser();
    String[] searchPaths = new String[] { "fhirResources", "fhirResources/libraries" };
    R4QualityMeasureResolverFactory resolverFactory = new R4QualityMeasureResolverFactory(parser);
    R4QualityMeasureResolvers resolvers = resolverFactory.fromZipStream(new ZipInputStream(inputStream), searchPaths);
    FhirResourceResolver<Library> libraryResolver = resolvers.getLibraryResolver();
    FhirResourceResolver<Measure> measureResolver = resolvers.getMeasureResolver();
    R4LibraryDependencyGatherer libraryDependencyGatherer = new R4LibraryDependencyGatherer(libraryResolver);
    CqlTerminologyProvider terminologyProvider = new R4RestFhirTerminologyProvider(terminologyClient);
    if (expandValueSets == null) {
        expandValueSets = R4DataProviderFactory.DEFAULT_IS_EXPAND_VALUE_SETS;
    }
    if (searchPageSize == null) {
        searchPageSize = R4DataProviderFactory.DEFAULT_PAGE_SIZE;
    }
    Map<String, CqlDataProvider> dataProviders = R4DataProviderFactory.createDataProviderMap(dataClient, terminologyProvider, retrieveCacheContext, R4FhirModelResolverFactory.createCachingResolver(), expandValueSets, searchPageSize);
    return new MeasureEvaluator(measureResolver, libraryResolver, libraryDependencyGatherer, terminologyProvider, dataProviders);
}

Example 35 with Library

use of org.hl7.fhir.r5.model.Library in project quality-measure-and-cohort-service by Alvearie.

the class CohortCLITest method testCQLTranslationCustomIGWithTargetUrl.

@Test
public void testCQLTranslationCustomIGWithTargetUrl() throws Exception {
    FhirServerConfig fhirConfig = getFhirServerConfig();
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient = getPatient("123", Enumerations.AdministrativeGender.FEMALE, "1978-05-06");
    patient.addExtension(new Extension("http://fakeIg.com/fake-extension", new StringType("fakeValue")));
    mockFhirResourceRetrieval(patient);
    Library root = getLibrary("test", DEFAULT_RESOURCE_VERSION, "cql/ig-test/Test-1.0.0.cql");
    Library helpers = getLibrary("FHIRHelpers", "4.0.0", "cql/fhir-helpers/FHIRHelpers.cql", "text/cql", "cql/fhir-helpers/FHIRHelpers.xml", "application/elm+json");
    RelatedArtifact related = new RelatedArtifact();
    related.setType(RelatedArtifactType.DEPENDSON);
    related.setResource("/Library/" + helpers.getId());
    root.addRelatedArtifact(related);
    mockFhirResourceRetrieval(root);
    mockFhirSingletonBundleRetrieval(helpers);
    File tmpFile = new File("target/fhir-stub.json");
    ObjectMapper om = new ObjectMapper();
    try (Writer w = new FileWriter(tmpFile)) {
        w.write(om.writeValueAsString(fhirConfig));
    }
    try {
        PrintStream originalOut = System.out;
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        try (PrintStream captureOut = new PrintStream(baos)) {
            System.setOut(captureOut);
            CohortCLI.main(new String[] { "-d", tmpFile.getAbsolutePath(), "-f", root.getId(), "-l", root.getName(), "-v", root.getVersion(), "-c", patient.getId(), "-s", "CQL", "-i", "src/test/resources/modelinfo/ig-with-target-modelinfo-0.0.1.xml" });
        } finally {
            System.setOut(originalOut);
        }
        String output = new String(baos.toByteArray());
        System.out.println(output);
        verify(1, getRequestedFor(urlEqualTo("/Patient/" + patient.getId() + "?_format=json")));
        verify(1, getRequestedFor(urlEqualTo("/Library/" + root.getId() + "?_format=json")));
        verify(1, getRequestedFor(urlEqualTo("/Library?url=%2FLibrary%2F" + helpers.getId() + "&_format=json")));
    } finally {
        tmpFile.delete();
    }
}