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

Example 1 with MeasureContext

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

the class MeasureContextProvider method getMeasureContexts.

public static List<MeasureContext> getMeasureContexts(File input) throws IOException {
    ObjectMapper objectMapper = new ObjectMapper();
    ExecutionConfiguration parsedInput = objectMapper.readValue(input, ExecutionConfiguration.class);
    // Throws an exception if invalid input is encountered
    parsedInput.validate();
    return parsedInput.getMeasureConfigurations().stream().map(x -> {
        MeasureIdentifier measureIdentifier = x.getIdentifier();
        Identifier identifier = null;
        if (measureIdentifier != null) {
            identifier = new Identifier(measureIdentifier.getSystem(), measureIdentifier.getValue());
        }
        return new MeasureContext(x.getMeasureId(), x.getParameters(), identifier, x.getVersion());
    }).collect(Collectors.toList());
}

Example 2 with MeasureContext

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

the class MeasureCLI method validateMeasureContexts.

private void validateMeasureContexts(List<MeasureContext> measureContexts) {
    StringBuilder sb = new StringBuilder();
    ValidatorFactory factory = Validation.buildDefaultValidatorFactory();
    try {
        Validator validator = factory.getValidator();
        // For some reason the validator doesn't work on the List, so I loop
        // through manually for now.
        MeasureContext context;
        for (int i = 0; i < measureContexts.size(); i++) {
            context = measureContexts.get(i);
            Set<ConstraintViolation<MeasureContext>> violations = validator.validate(context);
            if (!violations.isEmpty()) {
                for (ConstraintViolation<MeasureContext> violation : violations) {
                    sb.append(System.lineSeparator()).append("[").append(i).append("].").append(violation.getPropertyPath().toString()).append(": ").append(violation.getMessage());
                }
            }
        }
    } finally {
        factory.close();
    }
    if (sb.length() > 0) {
        throw new IllegalArgumentException(sb.toString());
    }
}

Example 3 with MeasureContext

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

the class CohortEngineRestHandlerTest method testEvaluateMeasureMissingPatient.

@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class })
@Test
public void testEvaluateMeasureMissingPatient() throws Exception {
    prepMocks();
    PowerMockito.mockStatic(ServiceBaseUtility.class);
    PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, MethodNames.EVALUATE_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);
    MeasureEvaluation evaluationRequest = new MeasureEvaluation();
    evaluationRequest.setDataServerConfig(clientConfig);
    evaluationRequest.setPatientId(patient.getId());
    evaluationRequest.setMeasureContext(measureContext);
    // evaluationRequest.setEvidenceOptions(evidenceOptions);
    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(evaluationRequest);
    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.evaluateMeasure(mockRequestContext, VERSION, body);
    assertNotNull(loadResponse);
    PowerMockito.verifyStatic(Response.class);
    Response.status(400);
}

Example 4 with MeasureContext

use of com.ibm.cohort.engine.measure.MeasureContext 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 5 with MeasureContext

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

the class CohortEngineRestHandlerTest method testEvaluateMeasureSuccess.

/**
 * Test the successful building of a response.
 */
@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class })
@Test
public void testEvaluateMeasureSuccess() throws Exception {
    prepMocks();
    PowerMockito.mockStatic(ServiceBaseUtility.class);
    PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, MethodNames.EVALUATE_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());
    mockFhirResourceRetrieval(patient);
    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);
    MeasureEvaluation evaluationRequest = new MeasureEvaluation();
    evaluationRequest.setDataServerConfig(clientConfig);
    evaluationRequest.setPatientId(patient.getId());
    evaluationRequest.setMeasureContext(measureContext);
    // evaluationRequest.setEvidenceOptions(evidenceOptions);
    evaluationRequest.setExpandValueSets(true);
    evaluationRequest.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(evaluationRequest);
    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.evaluateMeasure(mockRequestContext, VERSION, body);
    assertEquals(mockResponse, loadResponse);
    PowerMockito.verifyStatic(Response.class);
    Response.status(Response.Status.OK);
}