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

Example 1 with ObservationReferenceRangeComponent

use of org.hl7.fhir.r4.model.Observation.ObservationReferenceRangeComponent in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ObservationFHIRConversionTest method testObservationSN_valueQuantity_missing_comparator_result.

@Test
void testObservationSN_valueQuantity_missing_comparator_result() throws IOException {
    String hl7message = baseMessage + "OBX|1|SN|1554-5^GLUCOSE||^182|mg/dl|70_105||||F";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(1);
    Observation obs = (Observation) obsResource.get(0);
    // Check valueQuantity
    assertNotNull(obs.getValueQuantity());
    Quantity q = obs.getValueQuantity();
    // code only set if system exists
    assertNull(q.getCode());
    assertEquals("mg/dl", q.getUnit());
    assertNull(q.getSystem());
    assertEquals(182, q.getValue().floatValue());
    // no comparator passed in
    assertNull(q.getComparator());
    // Check referenceRange
    assertTrue(obs.hasReferenceRange());
    assertThat(obs.getReferenceRange()).hasSize(1);
    ObservationReferenceRangeComponent range = obs.getReferenceRangeFirstRep();
    assertNotNull(range);
    assertTrue(range.hasHigh());
    assertTrue(range.hasLow());
    Quantity high = range.getHigh();
    // uses OBX.6.1 for units not text in string
    assertEquals("mg/dl", high.getUnit());
    assertEquals(105f, high.getValue().floatValue());
    Quantity low = range.getLow();
    // uses OBX.6.1 for units not text in string
    assertEquals("mg/dl", low.getUnit());
    assertEquals(70f, low.getValue().floatValue());
    assertEquals("70_105", range.getText());
}

Example 2 with ObservationReferenceRangeComponent

use of org.hl7.fhir.r4.model.Observation.ObservationReferenceRangeComponent in project elexis-server by elexis.

the class ObservationTest method laboratoryObservations.

@Test
public void laboratoryObservations() throws FHIRException {
    // search by patient and category
    Bundle results = client.search().forResource(Observation.class).where(Observation.SUBJECT.hasId(AllTests.getTestDatabaseInitializer().getPatient().getId())).and(Condition.CATEGORY.exactly().code("laboratory")).returnBundle(Bundle.class).execute();
    assertNotNull(results);
    assertFalse(results.getEntry().isEmpty());
    @SuppressWarnings("unchecked") List<Observation> observations = (List<Observation>) ((List<?>) results.getEntry().parallelStream().map(be -> be.getResource()).collect(Collectors.toList()));
    for (Observation observation : observations) {
        assertTrue(observation.hasEffectiveDateTimeType());
        assertTrue(observation.hasValue());
        assertNotNull(observation.getCode());
        List<Coding> coding = observation.getCode().getCoding();
        assertFalse(coding.isEmpty());
        for (Coding code : coding) {
            if (code.getCode().contains("NUMERIC")) {
                if (observation.hasValueQuantity()) {
                    Quantity quantityValue = observation.getValueQuantity();
                    assertNotNull(quantityValue);
                } else if (observation.hasValueStringType()) {
                    StringType stringValue = observation.getValueStringType();
                    assertNotNull(stringValue);
                    assertTrue(Character.isDigit(stringValue.toString().charAt(0)));
                } else {
                    fail("Unexpected vaue type" + observation.getValue());
                }
                List<ObservationReferenceRangeComponent> refs = observation.getReferenceRange();
                assertFalse(refs.isEmpty());
            } else if (code.getCode().contains("TEXT")) {
                StringType stringValue = observation.getValueStringType();
                assertNotNull(stringValue);
            }
        }
    }
}

Example 3 with ObservationReferenceRangeComponent

use of org.hl7.fhir.r4.model.Observation.ObservationReferenceRangeComponent in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ObservationFHIRConversionTest method testObservationNmResult.

@Test
void testObservationNmResult() throws IOException {
    String hl7message = baseMessage + "OBX|1|NM|0135-4^TotalProtein||7.3|gm/dl|5.9-8.4|||R|F";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(1);
    Observation obs = (Observation) obsResource.get(0);
    assertThat(obs.getValueQuantity()).isNotNull();
    Quantity q = obs.getValueQuantity();
    assertThat(q.getUnit()).isEqualTo("gm/dl");
    assertThat(q.getValue().floatValue()).isEqualTo(7.3f);
    assertThat(obs.hasReferenceRange()).isTrue();
    assertThat(obs.getReferenceRange()).hasSize(1);
    ObservationReferenceRangeComponent range = obs.getReferenceRangeFirstRep();
    assertThat(range).isNotNull();
    assertThat(range.hasHigh()).isTrue();
    assertThat(range.hasLow()).isTrue();
    Quantity high = range.getHigh();
    assertThat(high.getUnit()).isEqualTo("gm/dl");
    assertThat(high.getValue().floatValue()).isEqualTo(8.4f);
    Quantity low = range.getLow();
    assertThat(low.getValue().floatValue()).isEqualTo(5.9f);
    assertThat(low.getUnit()).isEqualTo("gm/dl");
}

Example 4 with ObservationReferenceRangeComponent

use of org.hl7.fhir.r4.model.Observation.ObservationReferenceRangeComponent in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ObservationFHIRConversionTest method extendedObservationTestMostMessages.

// Tests most fields of OBX
@ParameterizedTest
@ValueSource(strings = { "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A01|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A03|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A04|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A08|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A28|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ADT^A31|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|OMP^O09|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ORM^O01|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|ORU^R01|||2.6||||||||2.6\r", "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|PPR^PC1|||2.6||||||||2.6\r", // "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|PPR^PC3|||2.6||||||||2.6\r",
"MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|VXU^V04|||2.6||||||||2.6\r" })
// Suppress warnings about too many assertions in a test.  Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
void extendedObservationTestMostMessages(String msh) throws IOException {
    String hl7message = msh + "OBX|1|CWE|DQW^Some text 1^SNM3|100|DQW^Other text 2^SNM3|mm^Text 3^SNM3|56-98|IND|25|ST|F|20210322153839|LKJ|20210320153850|N56|1111^ClinicianLastName^ClinicianFirstName^^^^Title|Manual^Text the 4th^SNM3|Device_1234567^mySystem|20210322153925|Observation Site^Text 5^SNM3|INST^Instance Identifier System||Radiology^Radiological Services|467 Albany Hospital^^Albany^NY|Cardiology^ContactLastName^Jane^Q^^Dr.^MD\r";
    // use special created engine
    String json = message.convert(hl7message, customEngine);
    IBaseResource bundleResource = context.getParser().parseResource(json);
    assertThat(bundleResource).isNotNull();
    Bundle b = (Bundle) bundleResource;
    List<BundleEntryComponent> e = b.getEntry();
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(1);
    Observation obs = (Observation) obsResource.get(0);
    assertThat(obs.hasValueCodeableConcept()).isTrue();
    // Check the coding  (OBX.3)
    assertThat(obs.hasCode()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getCode(), "DQW", "Some text 1", "http://terminology.hl7.org/CodeSystem/SNM3", "Some text 1");
    // Check the value  (OBX.5)
    assertThat(obs.hasValueCodeableConcept()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getValueCodeableConcept(), "DQW", "Other text 2", "http://terminology.hl7.org/CodeSystem/SNM3", "Other text 2");
    // OBX.6 is ignored because the record can only have one valueX and this one is valueCodeableConcept. See test test_observation_NM_result.
    assertThat(obs.hasReferenceRange()).isTrue();
    assertThat(obs.getReferenceRange()).hasSize(1);
    ObservationReferenceRangeComponent range = obs.getReferenceRangeFirstRep();
    assertThat(range).isNotNull();
    assertThat(range.hasHigh()).isTrue();
    assertThat(range.hasLow()).isTrue();
    Quantity high = range.getHigh();
    assertThat(high.getUnit()).isEqualTo("mm");
    assertThat(high.getValue().floatValue()).isEqualTo(98.0f);
    Quantity low = range.getLow();
    assertThat(low.getValue().floatValue()).isEqualTo(56.0f);
    assertThat(low.getUnit()).isEqualTo("mm");
    // Check interpretation (OBX.8)
    assertThat(obs.hasInterpretation()).isTrue();
    assertThat(obs.getInterpretation()).hasSize(1);
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getInterpretationFirstRep(), "IND", "Indeterminate", "http://terminology.hl7.org/CodeSystem/v2-0078", null);
    // Check the effective Date Time  (OBX.14)
    assertThat(obs.hasEffective()).isTrue();
    assertThat(obs.hasEffectiveDateTimeType()).isTrue();
    assertThat(obs.getEffectiveDateTimeType().asStringValue()).isEqualTo("2021-03-20T15:38:50+08:00");
    // Check performer  (OBX.16 Practictioner + OBX.23/OBX.24/OBX.25 Organization)
    assertThat(obs.hasPerformer()).isTrue();
    // Practioner and Organization
    assertThat(obs.getPerformer()).hasSize(2);
    // Get Practitioner and see that it is populated with OBX.16 information
    assertThat(obs.getPerformer().get(0).hasReference()).isTrue();
    List<Resource> practitionerResource = e.stream().filter(v -> ResourceType.Practitioner == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(practitionerResource).hasSize(1);
    Practitioner doctor = ResourceUtils.getResourcePractitioner(practitionerResource.get(0), ResourceUtils.context);
    assertThat(doctor.getName().get(0).getFamily()).isEqualTo("ClinicianLastName");
    // Get Organization and see that it is populated with OBX.23/OBX.24/OBX.25 information
    assertThat(obs.getPerformer().get(1).hasReference()).isTrue();
    List<Resource> organizationResource = e.stream().filter(v -> ResourceType.Organization == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(organizationResource).hasSize(1);
    Organization org = ResourceUtils.getResourceOrganization(organizationResource.get(0), ResourceUtils.context);
    // from OBX.23
    assertThat(org.getName()).isEqualTo("Radiology");
    assertThat(org.getAddress().get(0).getLine().get(0).getValueAsString()).isEqualTo(// from OBX.24
    "467 Albany Hospital");
    // from OBX.24
    assertThat(org.getAddress().get(0).getCity()).isEqualTo("Albany");
    // from OBX.24
    assertThat(org.getAddress().get(0).getState()).isEqualTo("NY");
    // from OBX.25
    assertThat(org.getContact().get(0).getName().getFamily()).isEqualTo("ContactLastName");
    // from OBX.25
    assertThat(org.getContact().get(0).getName().getGiven().get(0).getValueAsString()).isEqualTo("Jane");
    // from OBX.25
    assertThat(org.getContact().get(0).getName().getText()).isEqualTo("Dr. Jane Q ContactLastName");
    // purpose added because of OBX.25
    assertThat(org.getContact().get(0).hasPurpose()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(org.getContact().get(0).getPurpose(), "ADMIN", "Administrative", "http://terminology.hl7.org/CodeSystem/contactentity-type", "Organization Medical Director");
    // Check method  (OBX.17)
    assertThat(obs.hasMethod()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getMethod(), "Manual", "Text the 4th", "http://terminology.hl7.org/CodeSystem/SNM3", "Text the 4th");
    // Check device  (OBX.18)
    assertThat(obs.hasDevice()).isTrue();
    assertThat(obs.getDevice().hasReference()).isTrue();
    List<Resource> deviceResource = e.stream().filter(v -> ResourceType.Device == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(deviceResource).hasSize(1);
    Device device = ResourceUtils.getResourceDevice(deviceResource.get(0), ResourceUtils.context);
    assertThat(device.getIdentifier().get(0).getValue()).isEqualTo("Device_1234567");
    assertThat(device.getIdentifier().get(0).getSystem()).isEqualTo("urn:id:mySystem");
    // Check bodySite  (OBX.20)
    assertThat(obs.hasBodySite()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getBodySite(), "Observation Site", "Text 5", "http://terminology.hl7.org/CodeSystem/SNM3", "Text 5");
    // Check identifier  (OBX.21)
    assertThat(obs.hasIdentifier()).isTrue();
    assertThat(obs.getIdentifier()).hasSize(2);
    assertThat(obs.getIdentifier().get(1).getValue()).isEqualTo("INST");
    assertThat(obs.getIdentifier().get(1).getSystem()).isEqualTo("urn:id:Instance_Identifier_System");
    // OBX.23/OBX.24/OBX.25 went into Performer: Organization.  Checked above.
    // Check for ABSENCE of category (because no SPM)  Presence of category tested in extendedObservationUnusualRangesAndOtherTest
    assertThat(obs.hasCategory()).isFalse();
}

Example 5 with ObservationReferenceRangeComponent

use of org.hl7.fhir.r4.model.Observation.ObservationReferenceRangeComponent in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7ObservationFHIRConversionTest method extendedObservationUnusualRangesAndOtherTest.

// A companion test to extendedObservationCWEtest that looks for edge cases
@Test
// Suppress warnings about too many assertions in a test.  Justification: creating a FHIR message is very costly; we need to check many asserts per creation for efficiency.
@java.lang.SuppressWarnings("squid:S5961")
void extendedObservationUnusualRangesAndOtherTest() throws IOException {
    String ORU_r01 = "MSH|^~\\&|NIST Test Lab APP|NIST Lab Facility||NIST EHR Facility|20150926140551||ORU^R01|NIST-LOI_5.0_1.1-NG|T|2.5.1|||AL|AL|||||\r" + "PID|1||||DOE^JANE||||||||||||\r" + "ORC|NW|ORD448811^NIST EHR|R-511^NIST Lab Filler||||||20120628070100|||5742200012^Radon^Nicholas^^^^^^NPI^L^^^NPI\r" + "OBR|1|ORD448811^NIST EHR|R-511^NIST Lab Filler|1000^Hepatitis A B C Panel^99USL|||20120628070100|||||||||5742200012^Radon^Nicholas^^^^^^NPI^L^^^NPI\r" + "OBX|1|CWE|22314-9^Hepatitis A virus IgM Ab [Presence] in Serum^LN^HAVM^Hepatitis A IgM antibodies (IgM anti-HAV)^L^2.52||260385009^Negative (qualifier value)^SCT^NEG^NEGATIVE^L^201509USEd^^Negative (qualifier value)||Negative|N|||F|||20150925|||||201509261400\r" + "OBX|2|NM|22316-4^Hepatitis B virus core Ab [Units/volume] in Serum^LN^HBcAbQ^Hepatitis B core antibodies (anti-HBVc) Quant^L^2.52||0.70|[IU]/mL^international unit per milliliter^UCUM^IU/ml^^L^1.9|<0.50 IU/mL|H|||F|||20150925|||||201509261400\r" + "SPM|1|SpecimenID||BLOOD^Blood^^87612001^BLOOD^SCT^^||||Cord Art^Blood, Cord Arterial^^^^^^^|||P||||||201110060535|201110060821||Y||||||1\r";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, ORU_r01);
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(2);
    Observation obs = (Observation) obsResource.get(0);
    assertThat(obs.hasReferenceRange()).isTrue();
    assertThat(obs.getReferenceRange()).hasSize(1);
    ObservationReferenceRangeComponent range = obs.getReferenceRangeFirstRep();
    assertThat(range).isNotNull();
    assertThat(range.hasHigh()).isFalse();
    assertThat(range.hasLow()).isFalse();
    assertThat(range.hasText()).isTrue();
    assertThat(range.getText()).isEqualTo("Negative");
    obs = (Observation) obsResource.get(1);
    assertThat(obs.hasValueQuantity()).isTrue();
    Quantity q = obs.getValueQuantity();
    assertThat(q.hasUnit()).isTrue();
    assertThat(q.getUnit()).isEqualTo("[IU]/mL");
    assertThat(q.hasValue()).isTrue();
    assertThat(q.getValue().floatValue()).isEqualTo(0.7f);
    assertThat(q.hasSystem()).isTrue();
    assertThat(q.getSystem()).isEqualTo("http://unitsofmeasure.org");
    assertThat(obs.hasReferenceRange()).isTrue();
    assertThat(obs.getReferenceRange()).hasSize(1);
    range = obs.getReferenceRangeFirstRep();
    assertThat(range).isNotNull();
    assertThat(range.hasHigh()).isTrue();
    assertThat(range.hasLow()).isFalse();
    Quantity high = range.getHigh();
    assertThat(high.getUnit()).isEqualTo("[IU]/mL");
    assertThat(high.getValue().floatValue()).isEqualTo(0.5f);
    assertThat(range.hasText()).isTrue();
    assertThat(range.getText()).isEqualTo("<0.50 IU/mL");
    // Because there is an SPM record, there should be a category.  (Absence of SPM and category checkedin extendedObservationCWEtest)
    assertThat(obs.hasCategory()).isTrue();
    assertThat(obs.getCategory()).hasSize(1);
    DatatypeUtils.checkCommonCodeableConceptAssertions(obs.getCategoryFirstRep(), "laboratory", "Laboratory", "http://terminology.hl7.org/CodeSystem/observation-category", null);
}