Examples with Library org.hl7.fhir.r5.model.Library used on opensource projects

Example 71 with Library

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

the class DefaultVT method testMeasureEvaluationByMeasureIdentifier.

// to tag a specific test to be part of DVT (deployment verification test)
@Category(DVT.class)
@Test
public /**
 * Test a successful measure evaluation using identifier and version as the lookup key
 */
void testMeasureEvaluationByMeasureIdentifier() throws Exception {
    // You want -Denabled.dark.features=all in your Liberty jvm.options
    Assume.assumeTrue(isServiceDarkFeatureEnabled(CohortEngineRestConstants.DARK_LAUNCHED_MEASURE_EVALUATION));
    final String RESOURCE = getUrlBase() + CohortServiceAPISpec.CREATE_DELETE_EVALUATION_PATH;
    FhirContext fhirContext = FhirContext.forR4();
    IParser parser = fhirContext.newJsonParser().setPrettyPrint(true);
    Library library = TestHelper.getTemplateLibrary();
    Identifier identifier = new Identifier().setValue("measure-identifier").setSystem("http://ibm.com/health/test");
    Measure measure = TestHelper.getTemplateMeasure(library);
    measure.setIdentifier(Arrays.asList(identifier));
    ByteArrayOutputStream baos = new ByteArrayOutputStream();
    TestHelper.createMeasureArtifact(baos, parser, measure, library);
    // Files.write( baos.toByteArray(), new File("target/test_measure_v1_0_0.zip"));
    Map<String, Parameter> parameterOverrides = new HashMap<>();
    parameterOverrides.put("Measurement Period", new IntervalParameter(new DateParameter("2019-07-04"), true, new DateParameter("2020-07-04"), true));
    MeasureEvaluation requestData = new MeasureEvaluation();
    requestData.setDataServerConfig(dataServerConfig);
    requestData.setTerminologyServerConfig(termServerConfig);
    // This is a patient ID that is assumed to exist in the target FHIR server
    requestData.setPatientId(VALID_PATIENT_ID);
    requestData.setMeasureContext(new MeasureContext(null, parameterOverrides, new com.ibm.cohort.engine.measure.Identifier(identifier.getSystem(), identifier.getValue()), measure.getVersion()));
    requestData.setEvidenceOptions(new MeasureEvidenceOptions(false, MeasureEvidenceOptions.DefineReturnOptions.NONE));
    ObjectMapper om = new ObjectMapper();
    System.out.println(om.writeValueAsString(requestData));
    RequestSpecification request = buildBaseRequest(new Headers()).queryParam(CohortEngineRestHandler.VERSION, ServiceBuildConstants.DATE).multiPart(CohortEngineRestHandler.REQUEST_DATA_PART, requestData, "application/json").multiPart(CohortEngineRestHandler.MEASURE_PART, "test_measure_v1_0_0.zip", new ByteArrayInputStream(baos.toByteArray()));
    ValidatableResponse response = request.post(RESOURCE, getServiceVersion()).then();
    ValidatableResponse vr = runSuccessValidation(response, ContentType.JSON, HttpStatus.SC_OK);
    String expected = getJsonFromFile(ServiceAPIGlobalSpec.EXP_FOLDER_TYPE, "measure_evaluation_exp.json");
    String actual = vr.extract().asString();
    assertMeasureReportEquals(parser, expected, actual, false);
}

Example 72 with Library

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

the class SparkCqlEvaluator method getFilteredRequests.

/**
 * @param requests     Request object to filter.
 * @param libraries    Map of library id to version used for filtering
 *                     down request based on library id. If this argument
 *                     is null or empty, then no library id filtering
 *                     is performed.
 * @param expressions  Used to optionally override which expressions will
 *                     run for each individual CqlEvaluationRequest. If this
 *                     argument is null or empty, no expressions are overwritten.
 *
 * @return CqlEvaluationRequests with the original requests optionally filtered
 *         based on the library ids the.
 *         Requests will optionally have their expressions overridden
 *         by args.expressions. if any are provided.
 *         Individual requests will also will also have any global
 *         parameters set on each individual CqlEvaluationRequest.
 */
protected CqlEvaluationRequests getFilteredRequests(CqlEvaluationRequests requests, Map<String, String> libraries, Collection<String> expressions) {
    if (requests != null) {
        List<CqlEvaluationRequest> evaluations = requests.getEvaluations();
        if (libraries != null && !libraries.isEmpty()) {
            evaluations = evaluations.stream().filter(r -> libraries.keySet().contains(r.getDescriptor().getLibraryId())).collect(Collectors.toList());
        }
        if (expressions != null && !expressions.isEmpty()) {
            evaluations.forEach(x -> x.setExpressions(x.getExpressions().stream().filter(e -> expressions.contains(e.getName())).collect(Collectors.toSet())));
        }
        if (requests.getGlobalParameters() != null) {
            for (CqlEvaluationRequest evaluation : evaluations) {
                for (Map.Entry<String, Parameter> globalParameter : requests.getGlobalParameters().entrySet()) {
                    Map<String, Parameter> parameters = evaluation.getParameters();
                    if (parameters == null) {
                        evaluation.setParameters(new HashMap<>());
                        parameters = evaluation.getParameters();
                    }
                    parameters.putIfAbsent(globalParameter.getKey(), globalParameter.getValue());
                }
            }
        }
        requests.setEvaluations(evaluations);
        jobSpecification.set(requests);
    }
    return requests;
}

Example 73 with Library

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

the class R4LibraryDependencyGatherer method gatherForLibraryId.

public List<Library> gatherForLibraryId(String rootLibraryId) {
    List<Library> retVal = Collections.emptyList();
    Library rootLibrary = resolveLibrary(rootLibraryId);
    if (rootLibrary != null) {
        retVal = recurse(rootLibrary, new HashSet<>());
    }
    return retVal;
}

Example 74 with Library

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

the class R4FhirBundleExtractorTest method extractAll.

@Test
public void extractAll() {
    String firstVersion = "1.0.0";
    String secondVersion = "2.0.0";
    String thirdVersion = "3.0.0";
    String fourthVersion = "4.0.0";
    Library library1 = new Library().setVersion(firstVersion);
    Library library2 = new Library().setVersion(secondVersion);
    Measure measure = new Measure().setVersion(thirdVersion);
    Library library3 = new Library().setVersion(fourthVersion);
    Bundle bundle = new Bundle();
    addToBundle(library1, bundle);
    addToBundle(library2, bundle);
    addToBundle(measure, bundle);
    addToBundle(library3, bundle);
    R4FhirBundleExtractor<Library> extractor = getExtractor();
    List<Library> libraries = extractor.extractAll(bundle);
    List<String> actual = libraries.stream().map(Library::getVersion).collect(Collectors.toList());
    List<String> expected = Arrays.asList(firstVersion, secondVersion, fourthVersion);
    Assert.assertEquals(expected, actual);
}

Example 75 with Library

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

the class R4LibraryDependencyGathererTest method withCodelessType.

private void withCodelessType(Library library) {
    CodeableConcept type = new CodeableConcept();
    type.setText("text");
    library.setType(type);
}