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Example 16 with IParser

use of org.hl7.fhir.dstu3.formats.IParser in project BridgeServer2 by Sage-Bionetworks.

the class CRCControllerTest method makeObservation.

private String makeObservation(String json) {
    IParser parser = FHIR_CONTEXT.newJsonParser();
    Observation observation = parser.parseResource(Observation.class, json);
    return FHIR_CONTEXT.newJsonParser().encodeResourceToString(observation);
}
Also used : Observation(org.hl7.fhir.dstu3.model.Observation) IParser(ca.uhn.fhir.parser.IParser)

Example 17 with IParser

use of org.hl7.fhir.dstu3.formats.IParser in project quality-measure-and-cohort-service by Alvearie.

the class CohortEngineRestHandler method evaluateMeasure.

@POST
@Path("/evaluation")
@Consumes(MediaType.MULTIPART_FORM_DATA)
@Produces({ MediaType.APPLICATION_JSON })
@ApiOperation(value = "Evaluates a measure bundle for a single patient", notes = EVALUATION_API_NOTES, response = String.class, tags = { "Measure Evaluation" }, nickname = "evaluate_measure", extensions = { @Extension(properties = { @ExtensionProperty(name = DarkFeatureSwaggerFilter.DARK_FEATURE_NAME, value = CohortEngineRestConstants.DARK_LAUNCHED_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_REQUEST_DATA_JSON, dataTypeClass = MeasureEvaluation.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-cat1-example.html"), @ApiResponse(code = 400, message = "Bad Request", response = ServiceErrorList.class), @ApiResponse(code = 500, message = "Server Error", response = ServiceErrorList.class) })
public Response evaluateMeasure(@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_MEASURE.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));
        }
        IAttachment measureAttachment = multipartBody.getAttachment(MEASURE_PART);
        if (measureAttachment == null) {
            throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", MEASURE_PART));
        }
        // deserialize the MeasuresEvaluation request
        ObjectMapper om = new ObjectMapper();
        MeasureEvaluation evaluationRequest = om.readValue(metadataAttachment.getDataHandler().getInputStream(), MeasureEvaluation.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.evaluatePatientMeasure(evaluationRequest.getPatientId(), 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;
}
Also used : FhirContext(ca.uhn.fhir.context.FhirContext) MeasureEvaluation(com.ibm.cohort.engine.api.service.model.MeasureEvaluation) PatientListMeasureEvaluation(com.ibm.cohort.engine.api.service.model.PatientListMeasureEvaluation) ZipInputStream(java.util.zip.ZipInputStream) InputStream(java.io.InputStream) DefaultRetrieveCacheContext(com.ibm.cohort.engine.measure.cache.DefaultRetrieveCacheContext) RetrieveCacheContext(com.ibm.cohort.engine.measure.cache.RetrieveCacheContext) MeasureReport(org.hl7.fhir.r4.model.MeasureReport) DefaultRetrieveCacheContext(com.ibm.cohort.engine.measure.cache.DefaultRetrieveCacheContext) MeasureEvaluator(com.ibm.cohort.engine.measure.MeasureEvaluator) IAttachment(com.ibm.websphere.jaxrs20.multipart.IAttachment) Response(javax.ws.rs.core.Response) ApiResponse(io.swagger.annotations.ApiResponse) ResponseBuilder(javax.ws.rs.core.Response.ResponseBuilder) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) IParser(ca.uhn.fhir.parser.IParser) Path(javax.ws.rs.Path) ApiImplicitParams(io.swagger.annotations.ApiImplicitParams) POST(javax.ws.rs.POST) Consumes(javax.ws.rs.Consumes) Produces(javax.ws.rs.Produces) ApiOperation(io.swagger.annotations.ApiOperation) ApiResponses(io.swagger.annotations.ApiResponses)

Example 18 with IParser

use of org.hl7.fhir.dstu3.formats.IParser in project quality-measure-and-cohort-service by Alvearie.

the class CohortEngineRestHandler method createMeasureEvaluator.

private MeasureEvaluator createMeasureEvaluator(InputStream inputStream, FhirServerConfig dataServerConfig, FhirServerConfig terminologyServerConfig, Boolean expandValueSets, Integer searchPageSize, RetrieveCacheContext retrieveCacheContext, FhirContext fhirContext) throws IOException {
    FhirClientBuilder clientBuilder = FhirClientBuilderFactory.newInstance().newFhirClientBuilder(fhirContext);
    IGenericClient dataClient = clientBuilder.createFhirClient(dataServerConfig);
    IGenericClient terminologyClient = dataClient;
    if (terminologyServerConfig != null) {
        terminologyClient = clientBuilder.createFhirClient(terminologyServerConfig);
    }
    IParser parser = dataClient.getFhirContext().newJsonParser();
    String[] searchPaths = new String[] { "fhirResources", "fhirResources/libraries" };
    R4QualityMeasureResolverFactory resolverFactory = new R4QualityMeasureResolverFactory(parser);
    R4QualityMeasureResolvers resolvers = resolverFactory.fromZipStream(new ZipInputStream(inputStream), searchPaths);
    FhirResourceResolver<Library> libraryResolver = resolvers.getLibraryResolver();
    FhirResourceResolver<Measure> measureResolver = resolvers.getMeasureResolver();
    R4LibraryDependencyGatherer libraryDependencyGatherer = new R4LibraryDependencyGatherer(libraryResolver);
    CqlTerminologyProvider terminologyProvider = new R4RestFhirTerminologyProvider(terminologyClient);
    if (expandValueSets == null) {
        expandValueSets = R4DataProviderFactory.DEFAULT_IS_EXPAND_VALUE_SETS;
    }
    if (searchPageSize == null) {
        searchPageSize = R4DataProviderFactory.DEFAULT_PAGE_SIZE;
    }
    Map<String, CqlDataProvider> dataProviders = R4DataProviderFactory.createDataProviderMap(dataClient, terminologyProvider, retrieveCacheContext, R4FhirModelResolverFactory.createCachingResolver(), expandValueSets, searchPageSize);
    return new MeasureEvaluator(measureResolver, libraryResolver, libraryDependencyGatherer, terminologyProvider, dataProviders);
}
Also used : FhirClientBuilder(com.ibm.cohort.fhir.client.config.FhirClientBuilder) IGenericClient(ca.uhn.fhir.rest.client.api.IGenericClient) R4QualityMeasureResolverFactory(com.ibm.cohort.cql.hapi.resolver.R4QualityMeasureResolverFactory) R4RestFhirTerminologyProvider(com.ibm.cohort.engine.terminology.R4RestFhirTerminologyProvider) MeasureEvaluator(com.ibm.cohort.engine.measure.MeasureEvaluator) ZipInputStream(java.util.zip.ZipInputStream) Measure(org.hl7.fhir.r4.model.Measure) R4QualityMeasureResolvers(com.ibm.cohort.cql.hapi.resolver.R4QualityMeasureResolvers) R4LibraryDependencyGatherer(com.ibm.cohort.cql.hapi.R4LibraryDependencyGatherer) Library(org.hl7.fhir.r4.model.Library) CqlTerminologyProvider(com.ibm.cohort.cql.terminology.CqlTerminologyProvider) CqlDataProvider(com.ibm.cohort.cql.data.CqlDataProvider) IParser(ca.uhn.fhir.parser.IParser)

Example 19 with IParser

use of org.hl7.fhir.dstu3.formats.IParser in project quality-measure-and-cohort-service by Alvearie.

the class CohortCLITest method testMainZippedLibrariesMultiFolderWithExtraEntries.

@Test
public void testMainZippedLibrariesMultiFolderWithExtraEntries() throws Exception {
    FhirServerConfig fhirConfig = getFhirServerConfig();
    IParser encoder = getFhirParser();
    mockFhirResourceRetrieval("/metadata?_format=json", encoder, getCapabilityStatement(), fhirConfig);
    Patient patient = getPatient("123", Enumerations.AdministrativeGender.FEMALE, "1978-05-06");
    mockFhirResourceRetrieval(patient);
    File tmpFile = new File("target/fhir-stub.json");
    ObjectMapper om = new ObjectMapper();
    try (Writer w = new FileWriter(tmpFile)) {
        w.write(om.writeValueAsString(fhirConfig));
    }
    try {
        PrintStream originalOut = System.out;
        ByteArrayOutputStream baos = new ByteArrayOutputStream();
        try (PrintStream captureOut = new PrintStream(baos)) {
            System.setOut(captureOut);
            CohortCLI.main(new String[] { "-d", tmpFile.getAbsolutePath(), "-t", tmpFile.getAbsolutePath(), "-f", "src/test/resources/cql/zip-with-folders/cohorts.zip", "-l", "Breast-Cancer", "-v", "Screening", "-e", "Female", "-e", "Ages 40 to 75", "-e", "MeetsInclusionCriteria", "-c", "123", "-s", "CQL" });
        } finally {
            System.setOut(originalOut);
        }
        String output = new String(baos.toByteArray());
        String[] lines = output.split("\r?\n");
        assertEquals(output, 6, lines.length);
        System.out.println(output);
        verify(1, getRequestedFor(urlEqualTo("/Patient/123?_format=json")));
    } finally {
        tmpFile.delete();
    }
}
Also used : PrintStream(java.io.PrintStream) FileWriter(java.io.FileWriter) Patient(org.hl7.fhir.r4.model.Patient) FhirServerConfig(com.ibm.cohort.fhir.client.config.FhirServerConfig) ByteArrayOutputStream(java.io.ByteArrayOutputStream) File(java.io.File) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) FileWriter(java.io.FileWriter) Writer(java.io.Writer) IParser(ca.uhn.fhir.parser.IParser) Test(org.junit.Test)

Example 20 with IParser

use of org.hl7.fhir.dstu3.formats.IParser 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);
}
Also used : FhirContext(ca.uhn.fhir.context.FhirContext) HashMap(java.util.HashMap) MeasureEvaluation(com.ibm.cohort.engine.api.service.model.MeasureEvaluation) PatientListMeasureEvaluation(com.ibm.cohort.engine.api.service.model.PatientListMeasureEvaluation) Patient(org.hl7.fhir.r4.model.Patient) ByteArrayOutputStream(java.io.ByteArrayOutputStream) IAttachment(com.ibm.websphere.jaxrs20.multipart.IAttachment) Response(javax.ws.rs.core.Response) MeasureContext(com.ibm.cohort.engine.measure.MeasureContext) IMultipartBody(com.ibm.websphere.jaxrs20.multipart.IMultipartBody) DateParameter(com.ibm.cohort.cql.evaluation.parameters.DateParameter) ByteArrayInputStream(java.io.ByteArrayInputStream) Measure(org.hl7.fhir.r4.model.Measure) DateParameter(com.ibm.cohort.cql.evaluation.parameters.DateParameter) Parameter(com.ibm.cohort.cql.evaluation.parameters.Parameter) IntervalParameter(com.ibm.cohort.cql.evaluation.parameters.IntervalParameter) FhirServerConfig(com.ibm.cohort.fhir.client.config.FhirServerConfig) Library(org.hl7.fhir.r4.model.Library) IntervalParameter(com.ibm.cohort.cql.evaluation.parameters.IntervalParameter) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) IParser(ca.uhn.fhir.parser.IParser) PrepareForTest(org.powermock.core.classloader.annotations.PrepareForTest) Test(org.junit.Test) PrepareForTest(org.powermock.core.classloader.annotations.PrepareForTest)

Aggregations

IParser (ca.uhn.fhir.parser.IParser)89 FhirContext (ca.uhn.fhir.context.FhirContext)43 IOException (java.io.IOException)35 ByteArrayOutputStream (java.io.ByteArrayOutputStream)30 Test (org.junit.Test)24 InputStream (java.io.InputStream)22 IParser (org.hl7.fhir.r5.formats.IParser)19 JsonParser (org.hl7.fhir.r5.formats.JsonParser)18 Test (org.junit.jupiter.api.Test)18 FHIRException (org.hl7.fhir.exceptions.FHIRException)17 ByteArrayInputStream (java.io.ByteArrayInputStream)16 File (java.io.File)16 FileInputStream (java.io.FileInputStream)16 ObjectMapper (com.fasterxml.jackson.databind.ObjectMapper)15 Bundle (org.hl7.fhir.r4.model.Bundle)14 FileOutputStream (java.io.FileOutputStream)12 Bundle (org.hl7.fhir.dstu3.model.Bundle)12 IBaseResource (org.hl7.fhir.instance.model.api.IBaseResource)12 XmlParser (org.hl7.fhir.r5.formats.XmlParser)12 ArrayList (java.util.ArrayList)11