Examples with MeasureContext com.ibm.cohort.engine.measure.MeasureContext used on opensource projects

Example 6 with MeasureContext

use of com.ibm.cohort.engine.measure.MeasureContext in project quality-measure-and-cohort-service by Alvearie.

the class PatientListMeasureEvaluationTest method when_serialize_deserialize___properties_are_unchanged.

@Test
public void when_serialize_deserialize___properties_are_unchanged() throws Exception {
    FhirServerConfig dataServerConfig = new FhirServerConfig();
    dataServerConfig.setEndpoint("dataserver");
    FhirServerConfig termServerConfig = new FhirServerConfig();
    termServerConfig.setEndpoint("termserver");
    Map<String, Parameter> parameterOverrides = new HashMap<>();
    parameterOverrides.put("Measurement Period", new IntervalParameter(new DateParameter("2019-07-04"), true, new DateParameter("2020-07-04"), true));
    MeasureContext ctx = new MeasureContext("measureId", parameterOverrides);
    PatientListMeasureEvaluation evaluation = new PatientListMeasureEvaluation();
    evaluation.setDataServerConfig(dataServerConfig);
    evaluation.setTerminologyServerConfig(termServerConfig);
    List<String> patientIds = new ArrayList<>();
    patientIds.add("patientId1");
    patientIds.add("patientId2");
    evaluation.setPatientIds(patientIds);
    evaluation.setMeasureContext(ctx);
    evaluation.setEvidenceOptions(new MeasureEvidenceOptions(false, MeasureEvidenceOptions.DefineReturnOptions.ALL));
    ObjectMapper om = new ObjectMapper();
    String serialized = om.writeValueAsString(evaluation);
    PatientListMeasureEvaluation deserialized = om.readValue(serialized, PatientListMeasureEvaluation.class);
    assertEquals(evaluation, deserialized);
}

Example 7 with MeasureContext

use of com.ibm.cohort.engine.measure.MeasureContext in project quality-measure-and-cohort-service by Alvearie.

the class DefaultVT method testMeasureEvaluationByMeasureIdentifier.

// to tag a specific test to be part of DVT (deployment verification test)
@Category(DVT.class)
@Test
public /**
 * Test a successful measure evaluation using identifier and version as the lookup key
 */
void testMeasureEvaluationByMeasureIdentifier() throws Exception {
    // You want -Denabled.dark.features=all in your Liberty jvm.options
    Assume.assumeTrue(isServiceDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_MEASURE_EVALUATION));
    final String RESOURCE = getUrlBase() + CohortServiceAPISpec.CREATE_DELETE_EVALUATION_PATH;
    FhirContext fhirContext = FhirContext.forR4();
    IParser parser = fhirContext.newJsonParser().setPrettyPrint(true);
    Library library = TestHelper.getTemplateLibrary();
    Identifier identifier = new Identifier().setValue("measure-identifier").setSystem("http://ibm.com/health/test");
    Measure measure = TestHelper.getTemplateMeasure(library);
    measure.setIdentifier(Arrays.asList(identifier));
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    TestHelper.createMeasureArtifact(baos, parser, measure, library);
    // Files.write( baos.toByteArray(), new File("target/test_measure_v1_0_0.zip"));
    Map<String, Parameter> parameterOverrides = new HashMap<>();
    parameterOverrides.put("Measurement Period", new IntervalParameter(new DateParameter("2019-07-04"), true, new DateParameter("2020-07-04"), true));
    MeasureEvaluation requestData = new MeasureEvaluation();
    requestData.setDataServerConfig(dataServerConfig);
    requestData.setTerminologyServerConfig(termServerConfig);
    // This is a patient ID that is assumed to exist in the target FHIR server
    requestData.setPatientId(VALID_PATIENT_ID);
    requestData.setMeasureContext(new MeasureContext(null, parameterOverrides, new com.ibm.cohort.engine.measure.Identifier(identifier.getSystem(), identifier.getValue()), measure.getVersion()));
    requestData.setEvidenceOptions(new MeasureEvidenceOptions(false, MeasureEvidenceOptions.DefineReturnOptions.NONE));
    ObjectMapper om = new ObjectMapper();
    System.out.println(om.writeValueAsString(requestData));
    RequestSpecification request = buildBaseRequest(new Headers()).queryParam(CohortEngineRestHandler.VERSION, ServiceBuildConstants.DATE).multiPart(CohortEngineRestHandler.REQUEST_DATA_PART, requestData, "application/json").multiPart(CohortEngineRestHandler.MEASURE_PART, "test_measure_v1_0_0.zip", new ByteArrayInputStream(baos.toByteArray()));
    ValidatableResponse response = request.post(RESOURCE, getServiceVersion()).then();
    ValidatableResponse vr = runSuccessValidation(response, ContentType.JSON, HttpStatus.SC_OK);
    String expected = getJsonFromFile(ServiceAPIGlobalSpec.EXP_FOLDER_TYPE, "measure_evaluation_exp.json");
    String actual = vr.extract().asString();
    assertMeasureReportEquals(parser, expected, actual, false);
}

Example 8 with MeasureContext

use of com.ibm.cohort.engine.measure.MeasureContext 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 9 with MeasureContext

use of com.ibm.cohort.engine.measure.MeasureContext in project quality-measure-and-cohort-service by Alvearie.

the class DefaultVT method testMeasureEvaluationByMeasureID.

// to tag a specific test to be part of DVT (deployment verification test)
@Category(DVT.class)
@Test
public /**
 * Test a successful measure evaluation using Resource.id as the lookup key
 */
void testMeasureEvaluationByMeasureID() throws Exception {
    // You want -Denabled.dark.features=all in your Liberty jvm.options
    Assume.assumeTrue(isServiceDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_MEASURE_EVALUATION));
    final String RESOURCE = getUrlBase() + CohortServiceAPISpec.CREATE_DELETE_EVALUATION_PATH;
    FhirContext fhirContext = FhirContext.forR4();
    IParser parser = fhirContext.newJsonParser().setPrettyPrint(true);
    Library library = TestHelper.getTemplateLibrary();
    Measure measure = TestHelper.getTemplateMeasure(library);
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    TestHelper.createMeasureArtifact(baos, parser, measure, library);
    // Files.write( baos.toByteArray(), new File("target/test_measure_v1_0_0.zip"));
    Map<String, Parameter> parameterOverrides = new HashMap<>();
    parameterOverrides.put("Measurement Period", new IntervalParameter(new DateParameter("2019-07-04"), true, new DateParameter("2020-07-04"), true));
    MeasureEvaluation requestData = new MeasureEvaluation();
    requestData.setDataServerConfig(dataServerConfig);
    requestData.setTerminologyServerConfig(termServerConfig);
    // This is a patient ID that is assumed to exist in the target FHIR server
    requestData.setPatientId(VALID_PATIENT_ID);
    requestData.setMeasureContext(new MeasureContext(measure.getId(), parameterOverrides));
    requestData.setEvidenceOptions(new MeasureEvidenceOptions(false, MeasureEvidenceOptions.DefineReturnOptions.NONE));
    ObjectMapper om = new ObjectMapper();
    System.out.println(om.writeValueAsString(requestData));
    RequestSpecification request = buildBaseRequest(new Headers()).queryParam(CohortEngineRestHandler.VERSION, ServiceBuildConstants.DATE).multiPart(CohortEngineRestHandler.REQUEST_DATA_PART, requestData, "application/json").multiPart(CohortEngineRestHandler.MEASURE_PART, "test_measure_v1_0_0.zip", new ByteArrayInputStream(baos.toByteArray()));
    ValidatableResponse response = request.post(RESOURCE, getServiceVersion()).then();
    ValidatableResponse vr = runSuccessValidation(response, ContentType.JSON, HttpStatus.SC_OK);
    String expected = getJsonFromFile(ServiceAPIGlobalSpec.EXP_FOLDER_TYPE, "measure_evaluation_exp.json");
    String actual = vr.extract().asString();
    assertMeasureReportEquals(parser, expected, actual, false);
}

Example 10 with MeasureContext

use of com.ibm.cohort.engine.measure.MeasureContext in project quality-measure-and-cohort-service by Alvearie.

the class DefaultVT method testPatientListMeasureEvaluation.

// to tag a specific test to be part of DVT (deployment verification test)
@Category(DVT.class)
@Test
public /**
 * Test a successful measure evaluation using Resource.id as the lookup key
 */
void testPatientListMeasureEvaluation() throws Exception {
    // You want -Denabled.dark.features=all in your Liberty jvm.options
    Assume.assumeTrue(isServiceDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_PATIENT_LIST_MEASURE_EVALUATION));
    final String RESOURCE = getUrlBase() + CohortServiceAPISpec.POST_PATIENT_LIST_EVALUATION_PATH;
    FhirContext fhirContext = FhirContext.forR4();
    IParser parser = fhirContext.newJsonParser().setPrettyPrint(true);
    Library library = TestHelper.getTemplateLibrary();
    Measure measure = TestHelper.getTemplateMeasure(library);
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    TestHelper.createMeasureArtifact(baos, parser, measure, library);
    Map<String, Parameter> parameterOverrides = new HashMap<>();
    parameterOverrides.put("Measurement Period", new IntervalParameter(new DateParameter("2019-07-04"), true, new DateParameter("2020-07-04"), true));
    ;
    PatientListMeasureEvaluation requestData = new PatientListMeasureEvaluation();
    requestData.setDataServerConfig(dataServerConfig);
    requestData.setTerminologyServerConfig(termServerConfig);
    // These patients are assumed to exist in the target FHIR server
    List<String> patientIds = new ArrayList<>();
    patientIds.add(VALID_PATIENT_ID);
    patientIds.add(ANOTHER_VALID_PATIENT_ID);
    requestData.setPatientIds(patientIds);
    requestData.setMeasureContext(new MeasureContext(measure.getId(), parameterOverrides));
    requestData.setEvidenceOptions(new MeasureEvidenceOptions(false, MeasureEvidenceOptions.DefineReturnOptions.NONE));
    ObjectMapper om = new ObjectMapper();
    System.out.println(om.writeValueAsString(requestData));
    RequestSpecification request = buildBaseRequest(new Headers()).queryParam(CohortEngineRestHandler.VERSION, ServiceBuildConstants.DATE).multiPart(CohortEngineRestHandler.REQUEST_DATA_PART, requestData, "application/json").multiPart(CohortEngineRestHandler.MEASURE_PART, "test_measure_v1_0_0.zip", new ByteArrayInputStream(baos.toByteArray()));
    ValidatableResponse response = request.post(RESOURCE, getServiceVersion()).then();
    ValidatableResponse vr = runSuccessValidation(response, ContentType.JSON, HttpStatus.SC_OK);
    String expected = getJsonFromFile(ServiceAPIGlobalSpec.EXP_FOLDER_TYPE, "patient_list_measure_evaluation_exp.json");
    String actual = vr.extract().asString();
    assertMeasureReportEquals(parser, expected, actual, true);
}