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Example 56 with Parameters

use of org.hl7.fhir.r5.model.Parameters in project quality-measure-and-cohort-service by Alvearie.

the class CohortEngineRestHandler method getMeasureParametersById.

@POST
@Path("/fhir/measure/{measure_id}/parameters")
@Produces(MediaType.APPLICATION_JSON)
@Consumes(MediaType.MULTIPART_FORM_DATA)
@ApiOperation(value = "Get measure parameters by id", notes = CohortEngineRestHandler.MEASURE_API_NOTES, response = MeasureParameterInfoList.class, nickname = "get_measure_parameters_by_id", tags = { "FHIR Measures" })
@ApiImplicitParams({ @ApiImplicitParam(name = FHIR_DATA_SERVER_CONFIG_PART, value = CohortEngineRestHandler.EXAMPLE_DATA_SERVER_CONFIG_JSON, dataTypeClass = FhirServerConfig.class, required = true, paramType = "form", type = "file") })
@ApiResponses(value = { @ApiResponse(code = 200, message = "Successful Operation", response = MeasureParameterInfoList.class), @ApiResponse(code = 400, message = "Bad Request", response = ServiceErrorList.class), @ApiResponse(code = 500, message = "Server Error", response = ServiceErrorList.class) })
public Response getMeasureParametersById(@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, @ApiParam(value = CohortEngineRestHandler.MEASURE_ID_DESC, required = true) @PathParam(CohortEngineRestHandler.MEASURE_ID) String measureId) {
    final String methodName = MethodNames.GET_MEASURE_PARAMETERS_BY_ID.getName();
    Response response = null;
    try {
        // Perform api setup
        Response errorResponse = ServiceBaseUtility.apiSetup(version, logger, methodName);
        if (errorResponse != null) {
            return errorResponse;
        }
        IAttachment dataSourceAttachment = multipartBody.getAttachment(FHIR_DATA_SERVER_CONFIG_PART);
        if (dataSourceAttachment == null) {
            throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", FHIR_DATA_SERVER_CONFIG_PART));
        }
        // deserialize the MeasuresEvaluation request
        ObjectMapper om = new ObjectMapper();
        FhirServerConfig fhirServerConfig = om.readValue(dataSourceAttachment.getDataHandler().getInputStream(), FhirServerConfig.class);
        // validate the contents of the fhirServerConfig
        validateBean(fhirServerConfig);
        // get the fhir client object used to call to FHIR
        FhirClientBuilder clientBuilder = FhirClientBuilderFactory.newInstance().newFhirClientBuilder();
        IGenericClient measureClient = clientBuilder.createFhirClient(fhirServerConfig);
        // resolve the measure, and return the parameter info for all the libraries linked to by the measure
        FhirResourceResolver<Measure> measureResolver = R4FhirServerResourceResolverFactory.createMeasureResolver(measureClient);
        List<MeasureParameterInfo> parameterInfoList = FHIRRestUtils.getParametersForMeasureId(measureResolver, measureId);
        // return the results
        MeasureParameterInfoList status = new MeasureParameterInfoList().measureParameterInfoList(parameterInfoList);
        response = Response.ok(status).build();
    } catch (Throwable e) {
        // map any exceptions caught into the proper REST error response objects
        return new CohortServiceExceptionMapper().toResponse(e);
    } finally {
        // Perform api cleanup
        Response errorResponse = ServiceBaseUtility.apiCleanup(logger, methodName);
        if (errorResponse != null) {
            response = errorResponse;
        }
    }
    return response;
}
Also used : MeasureParameterInfo(com.ibm.cohort.engine.api.service.model.MeasureParameterInfo) FhirClientBuilder(com.ibm.cohort.fhir.client.config.FhirClientBuilder) IGenericClient(ca.uhn.fhir.rest.client.api.IGenericClient) IAttachment(com.ibm.websphere.jaxrs20.multipart.IAttachment) Response(javax.ws.rs.core.Response) ApiResponse(io.swagger.annotations.ApiResponse) Measure(org.hl7.fhir.r4.model.Measure) MeasureParameterInfoList(com.ibm.cohort.engine.api.service.model.MeasureParameterInfoList) FhirServerConfig(com.ibm.cohort.fhir.client.config.FhirServerConfig) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) Path(javax.ws.rs.Path) ApiImplicitParams(io.swagger.annotations.ApiImplicitParams) POST(javax.ws.rs.POST) Produces(javax.ws.rs.Produces) Consumes(javax.ws.rs.Consumes) ApiOperation(io.swagger.annotations.ApiOperation) ApiResponses(io.swagger.annotations.ApiResponses)

Example 57 with Parameters

use of org.hl7.fhir.r5.model.Parameters in project quality-measure-and-cohort-service by Alvearie.

the class CohortEngineRestHandler method getMeasureParameters.

@POST
@Path("/fhir/measure/identifier/{measure_identifier_value}/parameters")
@Produces(MediaType.APPLICATION_JSON)
@Consumes(MediaType.MULTIPART_FORM_DATA)
@ApiOperation(value = "Get measure parameters", notes = CohortEngineRestHandler.MEASURE_API_NOTES, response = MeasureParameterInfoList.class, authorizations = { @Authorization(value = "BasicAuth") }, responseContainer = "List", tags = { "FHIR Measures" })
@ApiImplicitParams({ @ApiImplicitParam(name = FHIR_DATA_SERVER_CONFIG_PART, value = CohortEngineRestHandler.EXAMPLE_DATA_SERVER_CONFIG_JSON, dataTypeClass = FhirServerConfig.class, required = true, paramType = "form", type = "file") })
@ApiResponses(value = { @ApiResponse(code = 200, message = "Successful Operation", response = MeasureParameterInfoList.class), @ApiResponse(code = 400, message = "Bad Request", response = ServiceErrorList.class), @ApiResponse(code = 500, message = "Server Error", response = ServiceErrorList.class) })
public Response getMeasureParameters(@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, @ApiParam(value = CohortEngineRestHandler.MEASURE_IDENTIFIER_VALUE_DESC, required = true) @PathParam(CohortEngineRestHandler.MEASURE_IDENTIFIER_VALUE) String measureIdentifierValue, @ApiParam(value = CohortEngineRestHandler.MEASURE_IDENTIFIER_SYSTEM_DESC, required = false) @QueryParam(CohortEngineRestHandler.MEASURE_IDENTIFIER_SYSTEM) String measureIdentifierSystem, @ApiParam(value = CohortEngineRestHandler.MEASURE_VERSION_DESC, required = false) @QueryParam(CohortEngineRestHandler.MEASURE_VERSION) String measureVersion) {
    final String methodName = MethodNames.GET_MEASURE_PARAMETERS.getName();
    Response response = null;
    try {
        // Perform api setup
        Response errorResponse = ServiceBaseUtility.apiSetup(version, logger, methodName);
        if (errorResponse != null) {
            return errorResponse;
        }
        IAttachment dataSourceAttachment = multipartBody.getAttachment(FHIR_DATA_SERVER_CONFIG_PART);
        if (dataSourceAttachment == null) {
            throw new IllegalArgumentException(String.format("Missing '%s' MIME attachment", FHIR_DATA_SERVER_CONFIG_PART));
        }
        // deserialize the MeasuresEvaluation request
        ObjectMapper om = new ObjectMapper();
        FhirServerConfig fhirServerConfig = om.readValue(dataSourceAttachment.getDataHandler().getInputStream(), FhirServerConfig.class);
        // validate the contents of the fhirServerConfig
        validateBean(fhirServerConfig);
        // get the fhir client object used to call to FHIR
        FhirClientBuilder clientBuilder = FhirClientBuilderFactory.newInstance().newFhirClientBuilder();
        IGenericClient measureClient = clientBuilder.createFhirClient(fhirServerConfig);
        // build the identifier object which is used by the fhir client
        // to find the measure
        Identifier identifier = new Identifier().setValue(measureIdentifierValue).setSystem(measureIdentifierSystem);
        // resolve the measure, and return the parameter info for all the libraries linked to by the measure
        FhirResourceResolver<Measure> measureResolver = R4FhirServerResourceResolverFactory.createMeasureResolver(measureClient);
        List<MeasureParameterInfo> parameterInfoList = FHIRRestUtils.getParametersForMeasureIdentifier(measureResolver, identifier, measureVersion);
        // return the results
        MeasureParameterInfoList status = new MeasureParameterInfoList().measureParameterInfoList(parameterInfoList);
        response = Response.ok(status).build();
    } catch (Throwable e) {
        // map any exceptions caught into the proper REST error response objects
        return new CohortServiceExceptionMapper().toResponse(e);
    } finally {
        // Perform api cleanup
        Response errorResponse = ServiceBaseUtility.apiCleanup(logger, methodName);
        if (errorResponse != null) {
            response = errorResponse;
        }
    }
    return response;
}
Also used : MeasureParameterInfo(com.ibm.cohort.engine.api.service.model.MeasureParameterInfo) FhirClientBuilder(com.ibm.cohort.fhir.client.config.FhirClientBuilder) IGenericClient(ca.uhn.fhir.rest.client.api.IGenericClient) IAttachment(com.ibm.websphere.jaxrs20.multipart.IAttachment) Response(javax.ws.rs.core.Response) ApiResponse(io.swagger.annotations.ApiResponse) Identifier(org.hl7.fhir.r4.model.Identifier) Measure(org.hl7.fhir.r4.model.Measure) MeasureParameterInfoList(com.ibm.cohort.engine.api.service.model.MeasureParameterInfoList) FhirServerConfig(com.ibm.cohort.fhir.client.config.FhirServerConfig) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) Path(javax.ws.rs.Path) ApiImplicitParams(io.swagger.annotations.ApiImplicitParams) POST(javax.ws.rs.POST) Produces(javax.ws.rs.Produces) Consumes(javax.ws.rs.Consumes) ApiOperation(io.swagger.annotations.ApiOperation) ApiResponses(io.swagger.annotations.ApiResponses)

Example 58 with Parameters

use of org.hl7.fhir.r5.model.Parameters in project quality-measure-and-cohort-service by Alvearie.

the class MeasureEvaluatorTest method measure_report_generated___FHIR_measure_parameters_on_measure_report.

@Test
public void measure_report_generated___FHIR_measure_parameters_on_measure_report() throws Exception {
    CapabilityStatement metadata = getCapabilityStatement();
    mockFhirResourceRetrieval("/metadata?_format=json", metadata);
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1970-10-10");
    mockFhirResourceRetrieval(patient);
    Library library = mockLibraryRetrieval("TestDummyPopulations", DEFAULT_VERSION, "cql/fhir-measure/test-dummy-populations.xml", ELM_MIME_TYPE);
    Measure measure = getCohortMeasure("CohortMeasureName", library, INITIAL_POPULATION);
    Map<String, Type> measureParameters = new HashMap<>();
    measureParameters.put("base64Param", new Base64BinaryType("AAA"));
    measureParameters.put("booleanParam", new BooleanType(false));
    measureParameters.put("dateParam", new DateType("2020-01-01"));
    measureParameters.put("dateTimeParam", new DateTimeType("2020-01-01T12:00:00"));
    measureParameters.put("decimalParam", new DecimalType(12.0));
    measureParameters.put("instantParam", new InstantType("2020-01-01T12:00:00-04:00"));
    measureParameters.put("integerParam", new IntegerType(1));
    measureParameters.put("stringParam", new StringType("str"));
    measureParameters.put("timeParam", new TimeType("05:30:00"));
    measureParameters.put("uriParam", new UriType("abcde"));
    measureParameters.put("codeableConceptParam", new CodeableConcept().setText("display").addCoding(new Coding().setCode("val").setSystem("sys").setDisplay("display")));
    measureParameters.put("codingParam", new Coding().setCode("v").setSystem("s").setDisplay("d"));
    measureParameters.put("periodParam", new Period().setStart(new Date(1)).setEnd(new Date(2)));
    measureParameters.put("quantityParam", new Quantity().setValue(1).setUnit("g"));
    measureParameters.put("rangeParam", new Range().setLow(new Quantity().setUnit("g").setValue(1)).setHigh(new Quantity().setUnit("g").setValue(5)));
    measureParameters.put("ratioParam", new Ratio().setNumerator(new Quantity().setUnit("g").setValue(1)).setDenominator(new Quantity().setUnit("g").setValue(5)));
    List<Extension> parameterExtensions = measureParameters.entrySet().stream().map(x -> createMeasureParameter(x.getKey(), x.getValue())).collect(Collectors.toList());
    measure.setExtension(parameterExtensions);
    mockFhirResourceRetrieval(measure);
    MeasureReport report = evaluator.evaluatePatientMeasure(measure.getId(), patient.getId(), null);
    assertNotNull(report);
    List<String> parameterNames = report.getExtension().stream().filter(x -> x.getUrl().equals(MEASURE_PARAMETER_VALUE_URL)).map(x -> (ParameterDefinition) x.getValue()).map(ParameterDefinition::getName).collect(Collectors.toList());
    // Expected parameters are the ones listed above, plus the special parameters
    // measurement period and product line
    assertEquals(measureParameters.size() + 2, parameterNames.size());
    assertTrue(parameterNames.containsAll(measureParameters.keySet()));
    assertTrue(parameterNames.contains(CDMConstants.MEASUREMENT_PERIOD));
    assertTrue(parameterNames.contains(CDMConstants.PRODUCT_LINE));
}
Also used : Arrays(java.util.Arrays) Date(java.util.Date) PARAMETER_VALUE_URL(com.ibm.cohort.engine.cdm.CDMConstants.PARAMETER_VALUE_URL) Range(org.hl7.fhir.r4.model.Range) StringUtils(org.apache.commons.lang3.StringUtils) ConceptParameter(com.ibm.cohort.cql.evaluation.parameters.ConceptParameter) InvalidOperatorArgument(org.opencds.cqf.cql.engine.exception.InvalidOperatorArgument) CapabilityStatement(org.hl7.fhir.r4.model.CapabilityStatement) HumanName(org.hl7.fhir.r4.model.HumanName) RatioParameter(com.ibm.cohort.cql.evaluation.parameters.RatioParameter) Map(java.util.Map) StringType(org.hl7.fhir.r4.model.StringType) Assert.fail(org.junit.Assert.fail) ParseException(java.text.ParseException) IntegerType(org.hl7.fhir.r4.model.IntegerType) Patient(org.hl7.fhir.r4.model.Patient) DefineReturnOptions(com.ibm.cohort.engine.measure.evidence.MeasureEvidenceOptions.DefineReturnOptions) IntegerParameter(com.ibm.cohort.cql.evaluation.parameters.IntegerParameter) 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Example 59 with Parameters

use of org.hl7.fhir.r5.model.Parameters in project quality-measure-and-cohort-service by Alvearie.

the class MeasureEvaluatorTest method runCareGapTest.

private void runCareGapTest(Map<String, Parameter> parameters, Map<String, Integer> careGapExpectations) throws ParseException, Exception {
    CapabilityStatement metadata = getCapabilityStatement();
    mockFhirResourceRetrieval("/metadata?_format=json", metadata);
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1970-10-10");
    mockFhirResourceRetrieval(patient);
    Library library = mockLibraryRetrieval("TestDummyPopulations", DEFAULT_VERSION, "cql/fhir-measure/test-dummy-populations.cql");
    Measure measure = getCareGapMeasure("ProportionMeasureName", library, expressionsByPopulationType, "CareGap1", "CareGap2");
    mockFhirResourceRetrieval(measure);
    MeasureReport report = evaluator.evaluatePatientMeasure(measure.getId(), patient.getId(), parameters);
    assertNotNull(report);
    assertPopulationExpectations(measure, report, careGapExpectations);
}
Also used : CapabilityStatement(org.hl7.fhir.r4.model.CapabilityStatement) Measure(org.hl7.fhir.r4.model.Measure) Patient(org.hl7.fhir.r4.model.Patient) MeasureReport(org.hl7.fhir.r4.model.MeasureReport) Library(org.hl7.fhir.r4.model.Library)

Example 60 with Parameters

use of org.hl7.fhir.r5.model.Parameters in project quality-measure-and-cohort-service by Alvearie.

the class R4RestFhirTerminologyProvider method lookup.

/**
 * This is a small patch to the OSS implementation to use named-parameter lookup on
 * the operation response instead of just assuming a positional location.
 */
@Override
public Code lookup(Code code, CodeSystemInfo codeSystem) throws ResourceNotFoundException {
    Parameters respParam = fhirClient.operation().onType(CodeSystem.class).named("lookup").withParameter(Parameters.class, "code", new CodeType(code.getCode())).andParameter("system", new UriType(codeSystem.getId())).execute();
    StringType display = (StringType) respParam.getParameter("display");
    if (display != null) {
        code.withDisplay(display.getValue());
    }
    return code.withSystem(codeSystem.getId());
}
Also used : Parameters(org.hl7.fhir.r4.model.Parameters) StringType(org.hl7.fhir.r4.model.StringType) CodeType(org.hl7.fhir.r4.model.CodeType) UriType(org.hl7.fhir.r4.model.UriType)

Aggregations

Parameters (org.hl7.fhir.r4.model.Parameters)105 Test (org.junit.jupiter.api.Test)96 SpringBootTest (org.springframework.boot.test.context.SpringBootTest)71 StringType (org.hl7.fhir.r4.model.StringType)68 RestIntegrationTest (org.opencds.cqf.ruler.test.RestIntegrationTest)61 HashMap (java.util.HashMap)58 ArrayList (java.util.ArrayList)53 FHIRException (org.hl7.fhir.exceptions.FHIRException)48 IOException (java.io.IOException)44 Parameters (org.hl7.fhir.dstu3.model.Parameters)41 Bundle (org.hl7.fhir.r4.model.Bundle)34 Measure (org.hl7.fhir.r4.model.Measure)31 Path (javax.ws.rs.Path)25 Produces (javax.ws.rs.Produces)25 Patient (org.hl7.fhir.r4.model.Patient)25 FileNotFoundException (java.io.FileNotFoundException)24 List (java.util.List)24 JsonObject (javax.json.JsonObject)23 GET (javax.ws.rs.GET)23 ExtraParameters (org.apache.camel.component.fhir.api.ExtraParameters)23