Examples with Range org.molgenis.api.metadata.v3.model.Range used on opensource projects

Example 1 with Range

use of org.molgenis.api.metadata.v3.model.Range in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7MedicationRequestFHIRConversionTest method dosageInstructionTestDoseRangeRXO.

@Test
void dosageInstructionTestDoseRangeRXO() {
    // Test dosageInstruction.DoseRange using RXO segment WITH a range (RXO.2 exists and RXO.3 exists)
    String hl7message = "MSH|^~\\\\&|||||20210101000000||OMP^O09|MSGID|T|2.6\n" + "PID|||1234||DOE^JANE^|||F||||||||||||||||||||||\n" + "PV1||||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|OP||||||||||||||||||||||\n" + // RXO.5 through RXO.35 not used.
    "RXO|00054418425^Dexamethasone 4 MG Oral Tablet^NDC^^^^^^dexamethasone (DECADRON) 4 MG TABS|100|150|CC||||||||||||||||||||||||||\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> medicationRequestList = ResourceUtils.getResourceList(e, ResourceType.MedicationRequest);
    // Confirm that one medicationRequest was created.
    assertThat(medicationRequestList).hasSize(1);
    MedicationRequest medicationRequest = ResourceUtils.getResourceMedicationRequest(medicationRequestList.get(0), ResourceUtils.context);
    Range doseRange = medicationRequest.getDosageInstructionFirstRep().getDoseAndRateFirstRep().getDoseRange();
    // doseRange.low(RXO.2)
    assertThat(doseRange.getLow().getValue()).hasToString("100.0");
    // RXO.4
    assertThat(doseRange.getLow().getUnit()).isEqualTo("CC");
    // Defaulted
    assertThat(doseRange.getLow().getSystem()).isEqualTo("http://unitsofmeasure.org");
    // doseRange.high(RXO.3)
    assertThat(doseRange.getHigh().getValue()).hasToString("150.0");
    // RXO.4
    assertThat(doseRange.getHigh().getUnit()).isEqualTo("CC");
    // Defaulted
    assertThat(doseRange.getHigh().getSystem()).isEqualTo("http://unitsofmeasure.org");
    // Verify no extraneous resources
    // Expect MedicationRequest and Patient
    assertThat(e).hasSize(2);
}

Example 2 with Range

use of org.molgenis.api.metadata.v3.model.Range in project quality-measure-and-cohort-service by Alvearie.

the class CQLToFHIRMeasureReportHelperTest method testIntervalQuantity_shouldReturnRange.

@Test
public void testIntervalQuantity_shouldReturnRange() {
    String unit = "ml";
    BigDecimal startAmount = new BigDecimal("4.0");
    BigDecimal endAmount = new BigDecimal("5.0");
    Quantity startQuantity = new Quantity().withUnit(unit).withValue(startAmount);
    Quantity endQuantity = new Quantity().withUnit(unit).withValue(endAmount);
    IBaseDatatype fhirTypeValue = CQLToFHIRMeasureReportHelper.getFhirTypeValue(new Interval(startQuantity, true, endQuantity, true));
    assertTrue(fhirTypeValue instanceof Range);
    Range castResult = (Range) fhirTypeValue;
    verifyBaseTypeAsQuantity(castResult.getLow(), startAmount, unit);
    verifyBaseTypeAsQuantity(castResult.getHigh(), endAmount, unit);
}

Example 3 with Range

use of org.molgenis.api.metadata.v3.model.Range 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));
}

Example 4 with Range

use of org.molgenis.api.metadata.v3.model.Range in project quality-measure-and-cohort-service by Alvearie.

the class R4ParameterDefinitionWithDefaultToCohortParameterConverterTest method testRange__shouldReturnIntervalParameterOfQuantityParameter.

@Test
public void testRange__shouldReturnIntervalParameterOfQuantityParameter() {
    ParameterDefinition parameterDefinition = getBaseParameterDefinition("Range");
    String lowString = "1.5";
    String highString = "2.5";
    BigDecimal lowValue = new BigDecimal(lowString);
    BigDecimal highValue = new BigDecimal(highString);
    String unit = "ml";
    Range fhirValue = new Range().setLow(new org.hl7.fhir.r4.model.Quantity().setValue(lowValue).setUnit(unit)).setHigh(new org.hl7.fhir.r4.model.Quantity().setValue(highValue).setUnit(unit));
    parameterDefinition.addExtension(CDMConstants.PARAMETER_DEFAULT_URL, fhirValue);
    IntervalParameter expectedParameter = new IntervalParameter(new QuantityParameter().setUnit(unit).setAmount(lowString), true, new QuantityParameter().setUnit(unit).setAmount(highString), true);
    assertEquals(expectedParameter, R4ParameterDefinitionWithDefaultToCohortParameterConverter.toCohortParameter(parameterDefinition));
}

Example 5 with Range

use of org.molgenis.api.metadata.v3.model.Range in project quality-measure-and-cohort-service by Alvearie.

the class FHIRRestUtilsTest method testConstructAppropriateJsonRange.

@Test
public void testConstructAppropriateJsonRange() {
    ParameterDefinition definition = new ParameterDefinition();
    definition.setType("Range");
    Extension extension = new Extension();
    extension.setUrl("http://ibm.com/fhir/cdm/StructureDefinition/default-value");
    Range range = new Range();
    Quantity lowQuantity = new Quantity();
    lowQuantity.setUnit("year");
    lowQuantity.setValue(10);
    Quantity highQuantity = new Quantity();
    highQuantity.setUnit("year");
    highQuantity.setValue(100);
    range.setLow(lowQuantity);
    range.setHigh(highQuantity);
    extension.setValue(range);
    List<Extension> extensions = new ArrayList<>();
    extensions.add(extension);
    definition.setExtension(extensions);
    String defaultResult = FHIRRestUtils.complicatedTypeValueConstructor(definition);
    assertEquals("{\"low\":{\"value\":10,\"unit\":\"year\"},\"high\":{\"value\":100,\"unit\":\"year\"}}", defaultResult);
}