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Example 91 with Extension

use of org.hl7.fhir.r4.model.Extension 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));
    }
}
Also used : Meta(org.hl7.fhir.r4.model.Meta) Reference(org.hl7.fhir.r4.model.Reference) IIdType(org.hl7.fhir.instance.model.api.IIdType)

Example 92 with Extension

use of org.hl7.fhir.r4.model.Extension in project ipf by oehf.

the class Iti67ResourceProvider method documentReferenceSearch.

@SuppressWarnings("unused")
@Search(type = DocumentReference.class)
public IBundleProvider documentReferenceSearch(@RequiredParam(name = DocumentReference.SP_PATIENT, chainWhitelist = { "", Patient.SP_IDENTIFIER }) ReferenceParam patient, @OptionalParam(name = DocumentReference.SP_STATUS) TokenOrListParam status, @OptionalParam(name = DocumentReference.SP_IDENTIFIER) TokenParam identifier, @OptionalParam(name = DocumentReference.SP_DATE) DateRangeParam date, @OptionalParam(name = STU3_INDEXED) DateRangeParam indexed, @OptionalParam(name = DocumentReference.SP_AUTHOR, chainWhitelist = { Practitioner.SP_FAMILY, Practitioner.SP_GIVEN }) ReferenceAndListParam author, @OptionalParam(name = DocumentReference.SP_CATEGORY) TokenOrListParam category, @OptionalParam(name = STU3_CLASS) TokenOrListParam class_, @OptionalParam(name = DocumentReference.SP_TYPE) TokenOrListParam type, @OptionalParam(name = DocumentReference.SP_SETTING) TokenOrListParam setting, @OptionalParam(name = DocumentReference.SP_PERIOD) DateRangeParam period, @OptionalParam(name = DocumentReference.SP_FACILITY) TokenOrListParam facility, @OptionalParam(name = DocumentReference.SP_EVENT) TokenOrListParam event, @OptionalParam(name = DocumentReference.SP_SECURITY_LABEL) TokenOrListParam securityLabel, @OptionalParam(name = STU3_SECURITY_LABEL) TokenOrListParam label, @OptionalParam(name = DocumentReference.SP_FORMAT) TokenOrListParam format, @OptionalParam(name = DocumentReference.SP_RELATED, chainWhitelist = { "", DocumentReference.SP_IDENTIFIER }) ReferenceOrListParam related, // -> related.identifier
@OptionalParam(name = STU3_RELATED_ID) TokenOrListParam relatedId, // -> related
@OptionalParam(name = STU3_RELATED_REF) ReferenceOrListParam relatedRef, // Extension to ITI-67
@OptionalParam(name = IAnyResource.SP_RES_ID) TokenParam resourceId, @Sort SortSpec sortSpec, @IncludeParam Set<Include> includeSpec, RequestDetails requestDetails, HttpServletRequest httpServletRequest, HttpServletResponse httpServletResponse) {
    // Be graceful and accept STU3 parameters as well
    var dateParam = date != null ? date : indexed;
    var categoryParam = category != null ? category : class_;
    var securityLabelParam = securityLabel != null ? securityLabel : label;
    // Handle "related" parameters
    ReferenceOrListParam relatedParam = new ReferenceOrListParam();
    TokenOrListParam relatedIdParam = new TokenOrListParam();
    if (relatedRef != null) {
        relatedParam = relatedRef;
    } else if (relatedId != null) {
        relatedIdParam = relatedId;
    } else if (related != null) {
        related.getValuesAsQueryTokens().stream().filter(referenceParam -> !DocumentReference.SP_IDENTIFIER.equals(referenceParam.getChain())).forEach(relatedParam::addOr);
        related.getValuesAsQueryTokens().stream().filter(referenceParam -> DocumentReference.SP_IDENTIFIER.equals(referenceParam.getChain())).map(referenceParam -> referenceParam.toTokenParam(getFhirContext())).forEach(relatedIdParam::addOr);
    }
    var searchParameters = Iti67SearchParameters.builder().status(status).identifier(identifier).date(dateParam).category(categoryParam).type(type).setting(setting).period(period).facility(facility).event(event).securityLabel(securityLabelParam).format(format).related(relatedParam).relatedId(relatedIdParam)._id(resourceId).sortSpec(sortSpec).includeSpec(includeSpec).fhirContext(getFhirContext()).build();
    searchParameters.setAuthor(author);
    var patientChain = patient.getChain();
    if (Patient.SP_IDENTIFIER.equals(patientChain)) {
        searchParameters.setPatientIdentifier(patient.toTokenParam(getFhirContext()));
    } else if (patientChain == null || patientChain.isEmpty()) {
        searchParameters.setPatientReference(patient);
    }
    // Run down the route
    return requestBundleProvider(null, searchParameters, ResourceType.DocumentReference.name(), httpServletRequest, httpServletResponse, requestDetails);
}
Also used : IdParam(ca.uhn.fhir.rest.annotation.IdParam) IncludeParam(ca.uhn.fhir.rest.annotation.IncludeParam) AbstractPlainProvider(org.openehealth.ipf.commons.ihe.fhir.AbstractPlainProvider) IBundleProvider(ca.uhn.fhir.rest.api.server.IBundleProvider) IAnyResource(org.hl7.fhir.instance.model.api.IAnyResource) RequiredParam(ca.uhn.fhir.rest.annotation.RequiredParam) HttpServletRequest(javax.servlet.http.HttpServletRequest) RequestDetails(ca.uhn.fhir.rest.api.server.RequestDetails) DateRangeParam(ca.uhn.fhir.rest.param.DateRangeParam) Search(ca.uhn.fhir.rest.annotation.Search) ReferenceParam(ca.uhn.fhir.rest.param.ReferenceParam) Patient(org.hl7.fhir.r4.model.Patient) Read(ca.uhn.fhir.rest.annotation.Read) Practitioner(org.hl7.fhir.r4.model.Practitioner) ReferenceOrListParam(ca.uhn.fhir.rest.param.ReferenceOrListParam) DocumentReference(org.hl7.fhir.r4.model.DocumentReference) Sort(ca.uhn.fhir.rest.annotation.Sort) InvalidRequestException(ca.uhn.fhir.rest.server.exceptions.InvalidRequestException) HttpServletResponse(javax.servlet.http.HttpServletResponse) Set(java.util.Set) ReferenceAndListParam(ca.uhn.fhir.rest.param.ReferenceAndListParam) Include(ca.uhn.fhir.model.api.Include) IdType(org.hl7.fhir.r4.model.IdType) TokenParam(ca.uhn.fhir.rest.param.TokenParam) ResourceType(org.hl7.fhir.r4.model.ResourceType) SortSpec(ca.uhn.fhir.rest.api.SortSpec) TokenOrListParam(ca.uhn.fhir.rest.param.TokenOrListParam) OptionalParam(ca.uhn.fhir.rest.annotation.OptionalParam) TokenOrListParam(ca.uhn.fhir.rest.param.TokenOrListParam) ReferenceOrListParam(ca.uhn.fhir.rest.param.ReferenceOrListParam) Search(ca.uhn.fhir.rest.annotation.Search)

Example 93 with Extension

use of org.hl7.fhir.r4.model.Extension 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 94 with Extension

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

the class CohortCLITest method testCQLTranslationCustomIGWithTargetUrl.

@Test
public void testCQLTranslationCustomIGWithTargetUrl() throws Exception {
    FhirServerConfig fhirConfig = getFhirServerConfig();
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient = getPatient("123", Enumerations.AdministrativeGender.FEMALE, "1978-05-06");
    patient.addExtension(new Extension("http://fakeIg.com/fake-extension", new StringType("fakeValue")));
    mockFhirResourceRetrieval(patient);
    Library root = getLibrary("test", DEFAULT_RESOURCE_VERSION, "cql/ig-test/Test-1.0.0.cql");
    Library helpers = getLibrary("FHIRHelpers", "4.0.0", "cql/fhir-helpers/FHIRHelpers.cql", "text/cql", "cql/fhir-helpers/FHIRHelpers.xml", "application/elm+json");
    RelatedArtifact related = new RelatedArtifact();
    related.setType(RelatedArtifactType.DEPENDSON);
    related.setResource("/Library/" + helpers.getId());
    root.addRelatedArtifact(related);
    mockFhirResourceRetrieval(root);
    mockFhirSingletonBundleRetrieval(helpers);
    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(), "-f", root.getId(), "-l", root.getName(), "-v", root.getVersion(), "-c", patient.getId(), "-s", "CQL", "-i", "src/test/resources/modelinfo/ig-with-target-modelinfo-0.0.1.xml" });
        } finally {
            System.setOut(originalOut);
        }
        String output = new String(baos.toByteArray());
        System.out.println(output);
        verify(1, getRequestedFor(urlEqualTo("/Patient/" + patient.getId() + "?_format=json")));
        verify(1, getRequestedFor(urlEqualTo("/Library/" + root.getId() + "?_format=json")));
        verify(1, getRequestedFor(urlEqualTo("/Library?url=%2FLibrary%2F" + helpers.getId() + "&_format=json")));
    } finally {
        tmpFile.delete();
    }
}
Also used : PrintStream(java.io.PrintStream) StringType(org.hl7.fhir.r4.model.StringType) FileWriter(java.io.FileWriter) Patient(org.hl7.fhir.r4.model.Patient) ByteArrayOutputStream(java.io.ByteArrayOutputStream) RelatedArtifact(org.hl7.fhir.r4.model.RelatedArtifact) Extension(org.hl7.fhir.r4.model.Extension) FhirServerConfig(com.ibm.cohort.fhir.client.config.FhirServerConfig) Library(org.hl7.fhir.r4.model.Library) File(java.io.File) ObjectMapper(com.fasterxml.jackson.databind.ObjectMapper) FileWriter(java.io.FileWriter) Writer(java.io.Writer) Test(org.junit.Test)

Example 95 with Extension

use of org.hl7.fhir.r4.model.Extension 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());
}
Also used : Extension(org.hl7.fhir.r4.model.Extension) Observation(org.hl7.fhir.r4.model.Observation) Patient(org.hl7.fhir.r4.model.Patient) MeasureReport(org.hl7.fhir.r4.model.MeasureReport) Code(org.opencds.cqf.cql.engine.runtime.Code) HashMap(java.util.HashMap) Map(java.util.Map) CodeableConcept(org.hl7.fhir.r4.model.CodeableConcept) Test(org.junit.Test)

Aggregations

Extension (org.hl7.fhir.r4.model.Extension)154 ArrayList (java.util.ArrayList)104 Coding (org.hl7.fhir.r4.model.Coding)69 Test (org.junit.jupiter.api.Test)69 Extension (org.hl7.fhir.dstu3.model.Extension)67 FHIRException (org.hl7.fhir.exceptions.FHIRException)55 StructureDefinition (org.hl7.fhir.r5.model.StructureDefinition)46 ElementDefinition (org.hl7.fhir.r5.model.ElementDefinition)42 Extension (org.hl7.fhir.r5.model.Extension)41 XhtmlNode (org.hl7.fhir.utilities.xhtml.XhtmlNode)39 Test (org.junit.Test)36 Cell (org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Cell)35 List (java.util.List)34 CodeableConcept (org.hl7.fhir.r4.model.CodeableConcept)34 Date (java.util.Date)30 Coding (org.hl7.fhir.dstu3.model.Coding)29 Piece (org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Piece)27 Row (org.hl7.fhir.utilities.xhtml.HierarchicalTableGenerator.Row)27 Reference (org.hl7.fhir.dstu3.model.Reference)26 Patient (org.hl7.fhir.r4.model.Patient)26