use of com.ibm.cohort.engine.api.service.model.CohortEvaluation in project quality-measure-and-cohort-service by Alvearie.
the class CohortEngineRestHandler method evaluateCohort.
@POST
@Path("/cohort-evaluation")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces({ MediaType.APPLICATION_JSON })
@ApiOperation(value = "Evaluates a specific define within a CQL for a set of patients", notes = COHORT_EVALUATION_API_NOTES, response = String.class, tags = { "Cohort Evaluation" }, nickname = "evaluate_cohort", extensions = { @Extension(properties = { @ExtensionProperty(name = DarkFeatureSwaggerFilter.DARK_FEATURE_NAME, value = CohortEngineRestConstants.DARK_LAUNCHED_COHORT_EVALUATION) }) })
@ApiImplicitParams({ // This is necessary for the dark launch feature
@ApiImplicitParam(access = DarkFeatureSwaggerFilter.DARK_FEATURE_CONTROLLED, paramType = "header", dataType = "string"), @ApiImplicitParam(name = REQUEST_DATA_PART, value = EXAMPLE_COHORT_REQUEST_DATA_JSON, dataTypeClass = CohortEvaluation.class, required = true, paramType = "form", type = "file"), @ApiImplicitParam(name = CQL_DEFINITION, value = CQL_REQUIREMENTS, dataTypeClass = File.class, required = true, paramType = "form", type = "file") })
@ApiResponses(value = { @ApiResponse(code = 200, message = "Successful Operation", response = CohortResult.class), @ApiResponse(code = 400, message = "Bad Request", response = ServiceErrorList.class), @ApiResponse(code = 500, message = "Server Error", response = ServiceErrorList.class) })
public Response evaluateCohort(@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_COHORT.getName();
Response response = null;
// Error out if feature is not enabled
ServiceBaseUtility.isDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_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));
}
// deserialize the MeasuresEvaluation request
ObjectMapper om = new ObjectMapper();
CohortEvaluation evaluationRequest = om.readValue(metadataAttachment.getDataHandler().getInputStream(), CohortEvaluation.class);
FhirServerConfig dataServerConfig = evaluationRequest.getDataServerConfig();
FhirServerConfig terminologyServerConfig = evaluationRequest.getTerminologyServerConfig() == null ? evaluationRequest.getDataServerConfig() : evaluationRequest.getTerminologyServerConfig();
IAttachment cqlAttachment = multipartBody.getAttachment(CQL_DEFINITION);
if (cqlAttachment == null) {
throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", CQL_DEFINITION));
}
// validate the contents of the fhirServerConfig
validateBean(dataServerConfig);
validateBean(terminologyServerConfig);
FhirClientBuilderFactory clientBuilderFactory = FhirClientBuilderFactory.newInstance();
FhirClientBuilder clientBuilder = clientBuilderFactory.newFhirClientBuilder();
CqlLibraryProvider libraryProvider;
try (InputStream is = cqlAttachment.getDataHandler().getInputStream()) {
ZipInputStream zis = new ZipInputStream(is);
MapCqlLibraryProviderFactory libraryProviderFactory = new MapCqlLibraryProviderFactory();
String[] attachmentHeaders = cqlAttachment.getHeader("Content-Disposition").split(";");
String filename = null;
for (String header : attachmentHeaders) {
if (header.contains("filename")) {
filename = FilenameUtils.removeExtension(header.split("=")[1].replaceAll("\"", ""));
}
}
String[] searchPaths = new String[] { "cql", filename + "/cql" };
libraryProvider = libraryProviderFactory.fromZipStream(zis, searchPaths);
}
CqlLibraryProvider fhirClasspathProvider = new ClasspathCqlLibraryProvider();
libraryProvider = new PriorityCqlLibraryProvider(libraryProvider, fhirClasspathProvider);
CqlToElmTranslator translator = new CqlToElmTranslator();
libraryProvider = new TranslatingCqlLibraryProvider(libraryProvider, translator);
IGenericClient dataClient = clientBuilder.createFhirClient(dataServerConfig);
IGenericClient termClient = clientBuilder.createFhirClient(terminologyServerConfig);
CqlTerminologyProvider termProvider = new R4RestFhirTerminologyProvider(termClient);
List<String> passingPatients;
try (RetrieveCacheContext retrieveCacheContext = new DefaultRetrieveCacheContext()) {
passingPatients = evaluateCohort(dataClient, termProvider, libraryProvider, retrieveCacheContext, evaluationRequest);
}
response = Response.status(Response.Status.OK).header("Content-Type", "application/json").entity(new CohortResult(passingPatients)).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;
}
use of com.ibm.cohort.engine.api.service.model.CohortEvaluation in project quality-measure-and-cohort-service by Alvearie.
the class CohortEngineRestHandlerTest method testCohortMultipleDependencies.
@PrepareForTest({ Response.class, FHIRRestUtils.class })
@Test
public void testCohortMultipleDependencies() throws Exception {
prepMocks();
mockResponseClasses();
mockFhirResourceRetrieval("/metadata?_format=json", 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 baseFile = new File("src/test/resources/cql/dependency_test-1.0.0/DependencyTest-1.0.0.cql");
ZipEntry firstEntry = new ZipEntry("cql/DependencyTest-1.0.0.cql");
zos.putNextEntry(firstEntry);
byte[] x = new byte[(int) baseFile.length()];
new FileInputStream(baseFile).read(x);
zos.write(x);
File additionalFile = new File("src/test/resources/cql/dependency_test-1.0.0/ImportantDependency-1.1.1.cql");
ZipEntry secondEntry = new ZipEntry("cql/ImportantDependency-1.1.1.cql");
zos.putNextEntry(secondEntry);
byte[] y = new byte[(int) additionalFile.length()];
new FileInputStream(additionalFile).read(y);
zos.write(y);
zos.closeEntry();
}
CohortEvaluation requestData = new CohortEvaluation();
FhirServerConfig serverConfig = getFhirServerConfig();
requestData.setDataServerConfig(serverConfig);
requestData.setTerminologyServerConfig(serverConfig);
requestData.setDefineToRun("DependentFemale");
requestData.setEntrypoint("DependencyTest-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);
ByteArrayInputStream zipIs = new ByteArrayInputStream(baos.toByteArray());
IAttachment measurePart = mockAttachment(zipIs);
// 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("dependency_test-1.0.0.zip");
when(measurePart.getHeader("Content-Disposition")).thenReturn("dependency_test-1.0.0.zip");
Response loadResponse = restHandler.evaluateCohort(mockRequestContext, null, body);
assertNotNull(loadResponse);
PowerMockito.verifyStatic(Response.class);
Response.status(Status.OK);
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.engine.api.service.model.CohortEvaluation in project quality-measure-and-cohort-service by Alvearie.
the class CohortEngineRestHandlerTest method testCohortBadDefine.
@PrepareForTest({ Response.class, FHIRRestUtils.class })
@Test
public void testCohortBadDefine() throws Exception {
prepMocks();
mockResponseClasses();
// 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-1.0.0.cql");
ZipEntry entry = new ZipEntry("cql/Test-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(null);
requestData.setLoggingLevel(CqlDebug.TRACE);
requestData.setEntrypoint("Test-1.0.0.cql");
requestData.setPatientIds("123");
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("cql/basic/Test-1.0.0.cql");
when(measurePart.getHeader("Content-Disposition")).thenReturn("cql/basic/Test-1.0.0.cql");
Response loadResponse = restHandler.evaluateCohort(mockRequestContext, null, body);
assertNotNull(loadResponse);
PowerMockito.verifyStatic(Response.class);
Response.status(400);
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.engine.api.service.model.CohortEvaluation in project quality-measure-and-cohort-service by Alvearie.
the class CohortEngineRestHandlerTest method testCohortEvaluation.
@PrepareForTest({ Response.class, FHIRRestUtils.class })
@Test
public void testCohortEvaluation() throws Exception {
prepMocks();
mockResponseClasses();
mockFhirResourceRetrieval("/metadata?_format=json", 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-1.0.0.cql");
ZipEntry entry = new ZipEntry("cql/Test-1.0.0.cql");
zos.putNextEntry(entry);
byte[] x = new byte[(int) tempFile.length()];
new FileInputStream(tempFile).read(x);
zos.write(x);
zos.closeEntry();
}
CohortEvaluation requestData = new CohortEvaluation();
FhirServerConfig serverConfig = getFhirServerConfig();
requestData.setDataServerConfig(serverConfig);
requestData.setTerminologyServerConfig(serverConfig);
requestData.setDefineToRun("Female");
requestData.setEntrypoint("Test-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);
ByteArrayInputStream zipIs = new ByteArrayInputStream(baos.toByteArray());
IAttachment measurePart = mockAttachment(zipIs);
// 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_1.0.0.zip");
when(measurePart.getHeader("Content-Disposition")).thenReturn("Test_1.0.0.zip");
Response loadResponse = restHandler.evaluateCohort(mockRequestContext, null, body);
assertNotNull(loadResponse);
PowerMockito.verifyStatic(Response.class);
Response.status(Status.OK);
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.engine.api.service.model.CohortEvaluation in project quality-measure-and-cohort-service by Alvearie.
the class DefaultVT method testCohortEvaluationWithLogging.
@Test
public void testCohortEvaluationWithLogging() {
final String RESOURCE = getUrlBase() + "/{version}/cohort-evaluation";
Assume.assumeTrue(isServiceDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_VALUE_SET_UPLOAD));
// Create the metadata part of the request
CohortEvaluation requestData = new CohortEvaluation();
requestData.setDataServerConfig(dataServerConfig);
requestData.setTerminologyServerConfig(dataServerConfig);
requestData.setDefineToRun("Male");
requestData.setEntrypoint("cql/basic/Test-1.0.0.cql");
requestData.setPatientIds(VALID_PATIENT_ID);
requestData.setLoggingLevel(CqlDebug.TRACE);
RequestSpecification request = buildBaseRequest(new Headers()).queryParam(CohortEngineRestHandler.VERSION, ServiceBuildConstants.DATE).multiPart(CohortEngineRestHandler.REQUEST_DATA_PART, requestData, "application/json").multiPart(CohortEngineRestHandler.CQL_DEFINITION, new File("src/test/resources/cql/zip/Test-1.0.0.zip"));
ValidatableResponse response = request.post(RESOURCE, getServiceVersion()).then();
ValidatableResponse vr = runSuccessValidation(response, ContentType.JSON, HttpStatus.SC_OK);
String actual = vr.extract().response().getBody().prettyPrint();
String expected = "{\n \"result\": [\n \n ]\n}";
assertEquals(expected, actual);
}
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