use of com.ibm.cohort.fhir.client.config.FhirServerConfig in project quality-measure-and-cohort-service by Alvearie.
the class CohortEngineRestHandlerTest method testCohortBadCQLDefinition.
@PrepareForTest({ Response.class, FHIRRestUtils.class })
@Test
public void testCohortBadCQLDefinition() throws Exception {
prepMocks();
mockResponseClasses();
mockFhirResourceRetrieval("/metadata", getCapabilityStatement());
Patient patient = getPatient("123", AdministrativeGender.FEMALE, 40);
mockFhirResourceRetrieval(patient);
PowerMockito.mockStatic(ServiceBaseUtility.class);
PowerMockito.mockStatic(FHIRRestUtils.class);
PowerMockito.mockStatic(DefaultFhirClientBuilder.class);
PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, MethodNames.EVALUATE_COHORT.getName())).thenReturn(null);
PowerMockito.whenNew(DefaultFhirClientBuilder.class).withArguments(Mockito.any()).thenReturn(mockDefaultFhirClientBuilder);
// Create the ZIP part of the request
ByteArrayOutputStream baos = new ByteArrayOutputStream();
try (ZipOutputStream zos = new ZipOutputStream(baos)) {
File tempFile = new File("src/test/resources/cql/basic/Test-bad-1.0.0.cql");
ZipEntry entry = new ZipEntry("cql/Test-bad-1.0.0.cql");
zos.putNextEntry(entry);
byte[] x = new byte[(int) tempFile.length()];
new FileInputStream(tempFile).read(x);
zos.write(x);
zos.closeEntry();
}
ByteArrayInputStream zipIs = new ByteArrayInputStream(baos.toByteArray());
IAttachment measurePart = mockAttachment(zipIs);
CohortEvaluation requestData = new CohortEvaluation();
FhirServerConfig serverConfig = getFhirServerConfig();
requestData.setDataServerConfig(serverConfig);
requestData.setTerminologyServerConfig(serverConfig);
requestData.setDefineToRun("Female");
requestData.setEntrypoint("Test-bad-1.0.0.cql");
requestData.setPatientIds("123");
requestData.setLoggingLevel(CqlDebug.TRACE);
ObjectMapper om = new ObjectMapper();
String json = om.writeValueAsString(requestData);
ByteArrayInputStream jsonIs = new ByteArrayInputStream(json.getBytes());
IAttachment request = mockAttachment(jsonIs);
// Assemble them together into a reasonable facsimile of the real request
IMultipartBody body = getFhirConfigFileBody();
when(body.getAttachment(CohortEngineRestHandler.CQL_DEFINITION)).thenReturn(measurePart);
when(body.getAttachment(CohortEngineRestHandler.REQUEST_DATA_PART)).thenReturn(request);
when(measurePart.getDataHandler().getName()).thenReturn("Test-bad_1.0.0_cql.zip");
when(measurePart.getHeader("Content-Disposition")).thenReturn("Test-bad_1.0.0_cql.zip");
Response loadResponse = restHandler.evaluateCohort(mockRequestContext, null, body);
assertNotNull(loadResponse);
PowerMockito.verifyStatic(Response.class);
Response.status(500);
PowerMockito.verifyStatic(ServiceBaseUtility.class);
ServiceBaseUtility.apiSetup(Mockito.isNull(), Mockito.any(), Mockito.anyString());
// verifyStatic must be called before each verification
PowerMockito.verifyStatic(ServiceBaseUtility.class);
ServiceBaseUtility.apiCleanup(Mockito.any(), Mockito.eq(MethodNames.EVALUATE_COHORT.getName()));
}
use of com.ibm.cohort.fhir.client.config.FhirServerConfig in project quality-measure-and-cohort-service by Alvearie.
the class CohortEngineRestHandlerTest method testEvaluateMeasureMoreThanOneFormOfId.
@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class })
@Test
public void testEvaluateMeasureMoreThanOneFormOfId() 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", 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, new Identifier().setValue("identifier"));
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);
}
use of com.ibm.cohort.fhir.client.config.FhirServerConfig in project quality-measure-and-cohort-service by Alvearie.
the class CohortEngineRestHandlerTest method testEvaluateMeasureMissingMeasureId.
@PrepareForTest({ Response.class, TenantManager.class, ServiceBaseUtility.class })
@Test
public void testEvaluateMeasureMissingMeasureId() throws Exception {
prepMocks();
PowerMockito.mockStatic(ServiceBaseUtility.class);
PowerMockito.when(ServiceBaseUtility.apiSetup(VERSION, logger, MethodNames.EVALUATE_MEASURE.getName())).thenReturn(null);
mockResponseClasses();
Patient patient = getPatient("patientId", AdministrativeGender.MALE, 40);
mockFhirResourceRetrieval("/metadata", getCapabilityStatement());
mockFhirResourceRetrieval(patient);
FhirServerConfig clientConfig = getFhirServerConfig();
MeasureContext measureContext = new MeasureContext("unknown");
MeasureEvaluation evaluationRequest = new MeasureEvaluation();
evaluationRequest.setDataServerConfig(clientConfig);
evaluationRequest.setPatientId(patient.getId());
evaluationRequest.setMeasureContext(measureContext);
// evaluationRequest.setEvidenceOptions(evidenceOptions);
// 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
ByteArrayInputStream zipIs = TestHelper.emptyZip();
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);
}
use of com.ibm.cohort.fhir.client.config.FhirServerConfig 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);
}
use of com.ibm.cohort.fhir.client.config.FhirServerConfig in project quality-measure-and-cohort-service by Alvearie.
the class CqlEvaluatorIntegrationTest method testCannotConnectToFHIRDataServer.
// @Test
// @Ignore // uncomment when JSON ELMs start working -
// // https://github.com/DBCG/cql_engine/issues/405
// public void testJsonCQLWithIncludes() throws Exception {
// Patient patient = getPatient("123", Enumerations.AdministrativeGender.FEMALE, "1978-05-06");
//
// CqlEvaluator wrapper = setupTestFor(patient, "cql/includes/Breast-Cancer-Screening.json");
//
// final AtomicBoolean found = new AtomicBoolean(false);
// final AtomicInteger count = new AtomicInteger(0);
// wrapper.evaluate("Breast-Cancer-Screening", "1", /* parameters= */null, null, Arrays.asList("123"),
// (p, e, r) -> {
// count.incrementAndGet();
// if (e.equals("MeetsInclusionCriteria")) {
// assertEquals("Unexpected value for expression result", Boolean.TRUE, r);
// found.set(true);
// }
// });
// assertEquals("Missing expression result", true, found.get());
// verify(1, getRequestedFor(urlEqualTo("/Patient/123?_format=json")));
// }
@Test(expected = CqlException.class)
public void testCannotConnectToFHIRDataServer() throws Exception {
Patient patient = new Patient();
patient.setGender(Enumerations.AdministrativeGender.FEMALE);
FhirServerConfig fhirConfig = new FhirServerConfig();
fhirConfig.setEndpoint("http://its.not.me");
CqlEvaluator evaluator = setupTestFor(patient, fhirConfig, "cql.basic");
evaluator.evaluate(new CqlVersionedIdentifier("Test", "1.0.0"), null, newPatientContext("123"), Collections.singleton("Female"));
}
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