Examples with PatientListMeasureEvaluation com.ibm.cohort.engine.api.service.model.PatientListMeasureEvaluation used on opensource projects

Example 1 with PatientListMeasureEvaluation

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

the class CohortEngineRestHandlerTest method testEvaluatePatientListMeasureMissingPatient.

@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class })
@Test
public void testEvaluatePatientListMeasureMissingPatient() throws Exception {
    prepMocks();
    PowerMockito.mockStatic(ServiceBaseUtility.class);
    PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, MethodNames.EVALUATE_PATIENT_LIST_MEASURE.getName())).thenReturn(null);
    mockResponseClasses();
    Library library = TestHelper.getTemplateLibrary();
    Measure measure = TestHelper.getTemplateMeasure(library);
    Patient patient = getPatient("patientId", AdministrativeGender.MALE, 40);
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    mockNotFound("/Patient/" + patient.getId() + "\\?_format=json");
    FhirServerConfig clientConfig = getFhirServerConfig();
    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 measureContext = new MeasureContext(measure.getId(), parameterOverrides);
    PatientListMeasureEvaluation request = new PatientListMeasureEvaluation();
    request.setDataServerConfig(clientConfig);
    request.setPatientIds(Collections.singletonList(patient.getId()));
    request.setMeasureContext(measureContext);
    FhirContext fhirContext = FhirContext.forR4();
    IParser parser = fhirContext.newJsonParser().setPrettyPrint(true);
    // Create the metadata part of the request
    ObjectMapper om = new ObjectMapper();
    String json = om.writeValueAsString(request);
    ByteArrayInputStream jsonIs = new ByteArrayInputStream(json.getBytes());
    IAttachment rootPart = mockAttachment(jsonIs);
    // Create the ZIP part of the request
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    TestHelper.createMeasureArtifact(baos, parser, measure, library);
    ByteArrayInputStream zipIs = new ByteArrayInputStream(baos.toByteArray());
    IAttachment measurePart = mockAttachment(zipIs);
    // Assemble them together into a reasonable facsimile of the real request
    IMultipartBody body = mock(IMultipartBody.class);
    when(body.getAttachment(CohortEngineRestHandler.REQUEST_DATA_PART)).thenReturn(rootPart);
    when(body.getAttachment(CohortEngineRestHandler.MEASURE_PART)).thenReturn(measurePart);
    Response loadResponse = restHandler.evaluatePatientListMeasure(mockRequestContext, VERSION, body);
    assertNotNull(loadResponse);
    PowerMockito.verifyStatic(Response.class);
    Response.status(400);
}

Example 2 with PatientListMeasureEvaluation

use of com.ibm.cohort.engine.api.service.model.PatientListMeasureEvaluation 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);
}

Example 3 with PatientListMeasureEvaluation

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

the class CohortEngineRestHandlerTest method testEvaluatePatientListMeasureSuccess.

@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class })
@Test
public void testEvaluatePatientListMeasureSuccess() throws Exception {
    prepMocks();
    PowerMockito.mockStatic(ServiceBaseUtility.class);
    PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, MethodNames.EVALUATE_PATIENT_LIST_MEASURE.getName())).thenReturn(null);
    mockResponseClasses();
    Library library = TestHelper.getTemplateLibrary();
    Measure measure = TestHelper.getTemplateMeasure(library);
    Patient patient1 = getPatient("patientId1", AdministrativeGender.MALE, 40);
    Patient patient2 = getPatient("patientId2", AdministrativeGender.FEMALE, 40);
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    mockFhirResourceRetrieval(patient1);
    mockFhirResourceRetrieval(patient2);
    FhirServerConfig clientConfig = getFhirServerConfig();
    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 measureContext = new MeasureContext(measure.getId(), parameterOverrides);
    PatientListMeasureEvaluation request = new PatientListMeasureEvaluation();
    request.setDataServerConfig(clientConfig);
    ArrayList<String> patientIds = new ArrayList<>();
    patientIds.add(patient1.getId());
    patientIds.add(patient2.getId());
    request.setPatientIds(patientIds);
    request.setMeasureContext(measureContext);
    request.setExpandValueSets(true);
    request.setSearchPageSize(500);
    FhirContext fhirContext = FhirContext.forR4();
    IParser parser = fhirContext.newJsonParser().setPrettyPrint(true);
    // Create the metadata part of the request
    ObjectMapper om = new ObjectMapper();
    String json = om.writeValueAsString(request);
    ByteArrayInputStream jsonIs = new ByteArrayInputStream(json.getBytes());
    IAttachment rootPart = mockAttachment(jsonIs);
    // Create the ZIP part of the request
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    TestHelper.createMeasureArtifact(baos, parser, measure, library);
    ByteArrayInputStream zipIs = new ByteArrayInputStream(baos.toByteArray());
    IAttachment measurePart = mockAttachment(zipIs);
    // Assemble them together into a reasonable facsimile of the real request
    IMultipartBody body = mock(IMultipartBody.class);
    when(body.getAttachment(CohortEngineRestHandler.REQUEST_DATA_PART)).thenReturn(rootPart);
    when(body.getAttachment(CohortEngineRestHandler.MEASURE_PART)).thenReturn(measurePart);
    Response loadResponse = restHandler.evaluatePatientListMeasure(mockRequestContext, VERSION, body);
    assertEquals(mockResponse, loadResponse);
    PowerMockito.verifyStatic(Response.class);
    Response.status(Response.Status.OK);
}

Example 4 with PatientListMeasureEvaluation

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

the class CohortEngineRestHandler method evaluatePatientListMeasure.

@POST
@Path("/evaluation-patient-list")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces({ MediaType.APPLICATION_JSON })
@ApiOperation(value = "Evaluates a measure bundle for a list of patients", notes = EVALUATION_API_NOTES, response = String.class, tags = { "Measure Evaluation" }, extensions = { @Extension(properties = { @ExtensionProperty(name = DarkFeatureSwaggerFilter.DARK_FEATURE_NAME, value = CohortEngineRestConstants.DARK_LAUNCHED_PATIENT_LIST_MEASURE_EVALUATION) }) })
@ApiImplicitParams({ // This is necessary for the dark launch feature
@ApiImplicitParam(access = DarkFeatureSwaggerFilter.DARK_FEATURE_CONTROLLED, paramType = "header", dataType = "string"), // These are necessary to create a proper view of the request body that is all wrapped up in the Liberty IMultipartBody parameter
@ApiImplicitParam(name = REQUEST_DATA_PART, value = EXAMPLE_PATIENT_LIST_MEASURE_REQUEST_DATA_JSON, dataTypeClass = PatientListMeasureEvaluation.class, required = true, paramType = "form", type = "file"), @ApiImplicitParam(name = MEASURE_PART, value = EXAMPLE_MEASURE_ZIP, dataTypeClass = File.class, required = true, paramType = "form", type = "file") })
@ApiResponses(value = { @ApiResponse(code = 200, message = "Successful Operation: This API returns the JSON representation of a FHIR MeasureReport. A full example can be found at https://www.hl7.org/fhir/measurereport-cms146-cat2-example.html"), @ApiResponse(code = 400, message = "Bad Request", response = ServiceErrorList.class), @ApiResponse(code = 500, message = "Server Error", response = ServiceErrorList.class) })
public Response evaluatePatientListMeasure(@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_PATIENT_LIST_MEASURE.getName();
    Response response = null;
    // Error out if feature is not enabled
    ServiceBaseUtility.isDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_PATIENT_LIST_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));
        }
        IAttachment measureAttachment = multipartBody.getAttachment(MEASURE_PART);
        if (measureAttachment == null) {
            throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", MEASURE_PART));
        }
        // deserialize the PatientListMeasureEvaluation request
        ObjectMapper om = new ObjectMapper();
        PatientListMeasureEvaluation evaluationRequest = om.readValue(metadataAttachment.getDataHandler().getInputStream(), PatientListMeasureEvaluation.class);
        // validate the contents of the evaluationRequest
        validateBean(evaluationRequest);
        FhirContext fhirContext = FhirContext.forR4();
        try (InputStream is = measureAttachment.getDataHandler().getInputStream();
            RetrieveCacheContext retrieveCacheContext = new DefaultRetrieveCacheContext()) {
            MeasureEvaluator evaluator = createMeasureEvaluator(is, evaluationRequest.getDataServerConfig(), evaluationRequest.getTerminologyServerConfig(), evaluationRequest.isExpandValueSets(), evaluationRequest.getSearchPageSize(), retrieveCacheContext, fhirContext);
            MeasureReport report = evaluator.evaluatePatientListMeasure(evaluationRequest.getPatientIds(), evaluationRequest.getMeasureContext(), evaluationRequest.getEvidenceOptions());
            // The default serializer gets into an infinite loop when trying to serialize MeasureReport, so we use the
            // HAPI encoder instead.
            IParser parser = fhirContext.newJsonParser();
            ResponseBuilder responseBuilder = Response.status(Response.Status.OK).header("Content-Type", "application/json").entity(parser.encodeResourceToString(report));
            response = responseBuilder.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;
}