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

Example 41 with Library

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

the class MeasureCLITest method testProportionRatioMultiplePatients.

@Test
public void testProportionRatioMultiplePatients() throws Exception {
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    Patient patient1 = mockPatientRetrieval("123", AdministrativeGender.MALE, 30);
    Patient patient2 = mockPatientRetrieval("456", AdministrativeGender.MALE, 45);
    Patient patient3 = mockPatientRetrieval("789", AdministrativeGender.FEMALE, 45);
    Library library = mockLibraryRetrieval("Test", DEFAULT_RESOURCE_VERSION, "cql/basic/Test-1.0.0.cql");
    expressionsByPopulationType.clear();
    expressionsByPopulationType.put(MeasurePopulationType.INITIALPOPULATION, "Male");
    expressionsByPopulationType.put(MeasurePopulationType.DENOMINATOR, "Male");
    expressionsByPopulationType.put(MeasurePopulationType.NUMERATOR, "Over the hill");
    expectationsByPopulationType.clear();
    expectationsByPopulationType.put(MeasurePopulationType.INITIALPOPULATION, 1);
    expectationsByPopulationType.put(MeasurePopulationType.DENOMINATOR, 1);
    expectationsByPopulationType.put(MeasurePopulationType.NUMERATOR, 0);
    Measure measure = getProportionMeasure("Test", library, expressionsByPopulationType);
    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", patient1.getId(), "-c", patient2.getId(), "-c", patient3.getId() }, out);
    } finally {
        tmpFile.delete();
        tmpMeasureConfigurationsFile.delete();
    }
    String output = new String(baos.toByteArray());
    System.out.println(output);
    String[] lines = output.split(System.getProperty("line.separator"));
    assertEquals(output, 18, lines.length);
}

Example 42 with Library

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

the class FhirTestBase method getLibrary.

protected Library getLibrary(String name, String version, String... attachmentData) throws Exception {
    if (attachmentData == null || attachmentData.length == 0 || (attachmentData.length > 2) && ((attachmentData.length % 2) != 0)) {
        fail("Invalid attachment data. Data must consist of one or more pairs of resource path and content-type strings");
    }
    List<String> pairs = new ArrayList<>(Arrays.asList(attachmentData));
    if (pairs.size() == 1) {
        pairs.add("text/cql");
    }
    List<Attachment> attachments = new ArrayList<>();
    for (int i = 0; i < pairs.size(); i += 2) {
        String resource = pairs.get(i);
        String contentType = pairs.get(i + 1);
        try (InputStream is = ClassLoader.getSystemResourceAsStream(resource)) {
            assertNotNull(String.format("No such resource %s found in classpath", resource), is);
            String text = IOUtils.toString(is, StandardCharsets.UTF_8);
            Attachment attachment = new Attachment();
            attachment.setContentType(contentType);
            attachment.setData(text.getBytes());
            attachments.add(attachment);
        }
    }
    Library library = new Library();
    library.setId("library-" + name + "-" + version);
    library.setName(name);
    library.setUrl(IBM_PREFIX + "/Library/" + name);
    library.setVersion(version);
    library.setContent(attachments);
    return library;
}

Example 43 with Library

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

the class MeasureEvaluatorTest method id_based_library_link___successfully_loaded_and_evaluated.

@Test
public void id_based_library_link___successfully_loaded_and_evaluated() throws Exception {
    mockFhirResourceRetrieval("/metadata?_format=json", getCapabilityStatement());
    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("IDBasedLibraryMeasure", library, expressionsByPopulationType, "CareGap1", "CareGap2");
    measure.setLibrary(Arrays.asList(new CanonicalType("Library/" + library.getId())));
    mockFhirResourceRetrieval(measure);
    Map<String, Parameter> passingParameters = new HashMap<>();
    passingParameters.put("InInitialPopulation", new BooleanParameter(true));
    List<MeasureContext> measureContexts = new ArrayList<>();
    measureContexts.add(new MeasureContext(measure.getId(), passingParameters));
    List<MeasureReport> reports = evaluator.evaluatePatientMeasures(patient.getId(), measureContexts);
    assertEquals(1, reports.size());
    MeasureReport report = reports.get(0);
    verifyStandardPopulationCounts(report);
    verify(1, getRequestedFor(urlEqualTo("/Library/" + library.getId() + "?_format=json")));
}

Example 44 with Library

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

the class MeasureEvaluatorTest method in_populations_evaluated_boolean_define_only_returned.

@Test
public void in_populations_evaluated_boolean_define_only_returned() throws Exception {
    CapabilityStatement metadata = getCapabilityStatement();
    mockFhirResourceRetrieval("/metadata?_format=json", metadata);
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1970-10-10");
    mockFhirResourceRetrieval(patient);
    Library library = setupDefineReturnLibrary();
    expressionsByPopulationType.clear();
    expressionsByPopulationType.put(MeasurePopulationType.INITIALPOPULATION, INITIAL_POPULATION);
    expressionsByPopulationType.put(MeasurePopulationType.DENOMINATOR, DENOMINATOR);
    expressionsByPopulationType.put(MeasurePopulationType.NUMERATOR, NUMERATOR);
    Measure measure = getProportionMeasure("ProportionMeasureName", library, expressionsByPopulationType);
    mockFhirResourceRetrieval(measure);
    MeasureReport report = evaluator.evaluatePatientMeasure(measure.getId(), patient.getId(), null, new MeasureEvidenceOptions(false, DefineReturnOptions.BOOLEAN));
    assertNotNull(report);
    assertTrue(report.getEvaluatedResource().isEmpty());
    assertFalse(report.getExtensionsByUrl(CDMConstants.EVIDENCE_URL).isEmpty());
}

Example 45 with Library

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

the class MeasureEvaluatorTest method in_initial_population_when_engine_run_in_utc__engine_defaults_to_utc.

@Test
public void in_initial_population_when_engine_run_in_utc__engine_defaults_to_utc() throws Exception {
    CapabilityStatement metadata = getCapabilityStatement();
    mockFhirResourceRetrieval("/metadata?_format=json", metadata);
    Patient patient = getPatient("123", AdministrativeGender.MALE, "1970-10-10");
    mockFhirResourceRetrieval(patient);
    // Test CQL written to pass when engine run with a timezone of UTC
    // and should fail otherwise
    Library library = mockLibraryRetrieval("TestDatetimeDefaultTimezones", DEFAULT_VERSION, "cql/fhir-measure/test-datetime-default-timezones.cql", "text/cql");
    Measure measure = getCohortMeasure("CohortMeasureName", library, INITIAL_POPULATION);
    mockFhirResourceRetrieval(measure);
    MeasureReport report = evaluator.evaluatePatientMeasure(measure.getId(), patient.getId(), null, new MeasureEvidenceOptions(false, DefineReturnOptions.BOOLEAN));
    assertNotNull(report);
    report.getExtension().stream().filter(x -> x.getUrl().equals(CDMConstants.EVIDENCE_URL)).forEach(x -> validateBooleanEvidence(x, true));
}