Examples with MeasureReport org.hl7.fhir.r4.model.MeasureReport used on opensource projects

Example 11 with MeasureReport

use of org.hl7.fhir.r4.model.MeasureReport in project cqf-ruler by DBCG.

the class CareGapsProvider method patientReports.

// warning for greater than 7 parameters
@SuppressWarnings("squid:S00107")
private Parameters.ParametersParameterComponent patientReports(RequestDetails requestDetails, String periodStart, String periodEnd, Patient patient, List<String> status, List<Measure> measures, String organization) {
    // TODO: add organization to report, if it exists.
    Composition composition = getComposition(patient);
    List<DetectedIssue> detectedIssues = new ArrayList<>();
    Map<String, Resource> evaluatedResources = new HashMap<>();
    List<MeasureReport> reports = getReports(requestDetails, periodStart, periodEnd, patient, status, measures, composition, detectedIssues, evaluatedResources);
    if (reports.isEmpty()) {
        return null;
    }
    return initializePatientParameter(patient).setResource(addBundleEntries(requestDetails.getFhirServerBase(), composition, detectedIssues, reports, evaluatedResources));
}

Example 12 with MeasureReport

use of org.hl7.fhir.r4.model.MeasureReport in project cqf-ruler by DBCG.

the class CareGapsProvider method initializeReport.

private void initializeReport(MeasureReport report) {
    if (Strings.isNullOrEmpty(report.getId())) {
        IIdType id = Ids.newId(MeasureReport.class, UUID.randomUUID().toString());
        report.setId(id);
    }
    Reference reporter = new Reference().setReference(crProperties.getMeasureReport().getReporter());
    // TODO: figure out what this extension is for
    // reporter.addExtension(new
    // Extension().setUrl(CARE_GAPS_MEASUREREPORT_REPORTER_EXTENSION));
    report.setReporter(reporter);
    if (report.hasMeta()) {
        report.getMeta().addProfile(CARE_GAPS_REPORT_PROFILE);
    } else {
        report.setMeta(new Meta().addProfile(CARE_GAPS_REPORT_PROFILE));
    }
}

Example 13 with MeasureReport

use of org.hl7.fhir.r4.model.MeasureReport 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;
}

Example 14 with MeasureReport

use of org.hl7.fhir.r4.model.MeasureReport in project quality-measure-and-cohort-service by Alvearie.

the class MeasureCLITest method testJsonFormattedOutput.

@Test
public void testJsonFormattedOutput() throws Exception {
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1592-14-03");
    mockFhirResourceRetrieval(patient);
    Library library = mockLibraryRetrieval("Test", DEFAULT_RESOURCE_VERSION, "cql/basic/Test-1.0.0.cql");
    Measure measure = getCohortMeasure("Test", library, "Male");
    mockFhirResourceRetrieval(measure);
    File tmpFile = new File("target/fhir-stub.json");
    ObjectMapper om = new ObjectMapper();
    try (Writer w = new FileWriter(tmpFile)) {
        w.write(om.writeValueAsString(getFhirServerConfig()));
    }
    File tmpMeasureConfigurationsFile = createTmpConfigurationsFileForSingleMeasure(measure.getId());
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    PrintStream out = new PrintStream(baos);
    try {
        MeasureCLI cli = new MeasureCLI();
        cli.runWithArgs(new String[] { "-d", tmpFile.getAbsolutePath(), "-j", tmpMeasureConfigurationsFile.getAbsolutePath(), "-c", patient.getId(), "-f", "JSON" }, out);
    } finally {
        tmpFile.delete();
        tmpMeasureConfigurationsFile.delete();
    }
    String output = new String(baos.toByteArray());
    System.out.println(output);
    assertTrue(output.contains("\"resourceType\": \"MeasureReport\""));
}

Example 15 with MeasureReport

use of org.hl7.fhir.r4.model.MeasureReport in project quality-measure-and-cohort-service by Alvearie.

the class MeasureSupplementalDataEvaluationTest method testProcessAccumulators_notSDESex.

@Test
public void testProcessAccumulators_notSDESex() {
    /* 
		 * Jill - I don't like how this part of the code works.  The code grabs everything after (and including) the "-", 
		 * and then looks for that to exist as an extension on the Patient resource.  This works for race and ethnicity 
		 * on the US-core patient profile, but since we already calculated this in the populate SDE accumulator method
		 * the only reason it's "recalculating" is because the system and display aren't on the passed in map.
		 * Plus, it's coded assuming there is a list of extensions within the extension (which is how US-Core handles race and eth) 
		 * and it magically grabs the first one... so if you have multiple this doesn't match all of them.
		*/
    Code white = new Code();
    white.setCode(WHITE_CODE);
    Map<String, Map<String, Integer>> sdeAccumulators = getSDEAccumulators(SDE_RACE, null, white, new HashMap<>());
    MeasureReport report = new MeasureReport();
    Patient mockPatient = mockPatient();
    Extension raceExtension = new Extension();
    // This can be anything as long as it includes "-race"
    raceExtension.setUrl("something-race");
    // This example was stolen from https://www.hl7.org/fhir/us/core/Patient-example.xml.html
    Extension valueExtension = new Extension();
    valueExtension.setUrl("ombCategory");
    valueExtension.setValue(getWhiteCoding());
    raceExtension.setExtension(Arrays.asList(valueExtension));
    Mockito.when(mockPatient.getExtension()).thenReturn(Arrays.asList(raceExtension));
    MeasureSupplementalDataEvaluation.processAccumulators(report, sdeAccumulators, true, Arrays.asList(mockPatient));
    assertNotNull(report);
    // EvaluatedResource should contain a reference to an observation record created for supplemental data
    assertEquals(1, report.getEvaluatedResource().size());
    // The observation record mentioned previously should exist within the contained resources of the measure report
    assertEquals(1, report.getContained().size());
    assertTrue(report.getContained().get(0) instanceof Observation);
    Observation obs = (Observation) report.getContained().get(0);
    // For a single patient, the code of the observation should be the supplemental data text
    assertEquals(SDE_RACE, obs.getCode().getText());
    // For a single patient, the value of the observation should be the result of the appropriate define
    assertTrue(obs.getValue() instanceof CodeableConcept);
    assertEquals(WHITE_CODE, ((CodeableConcept) obs.getValue()).getCoding().get(0).getCode());
}