Examples with System org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System used on opensource projects

Example 51 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7IdentifierFHIRConversionTest method procedureIdentifierTest.

@Test
void procedureIdentifierTest() {
    // with PR1 and PID segments used to create identifiers
    String procedureMsg = "MSH|^~\\&|HL7Soup|Instance1|MCM||200911021022|Security|ADT^A01^ADT_A01|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM|CDP|^4086::132:2A57:3C28^IPV6|^4086::132:2A57:3C25^IPV6|\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|78654^^^ACME||||N\n" + "ROL|5897|UP|AD||20210322133821|20210322133822|10||Hospital|ST||||USA\n" + "PR1|1|ICD10|B45678|Fix break|20210322155008|A|75||V46|80|||32|1|D22|G45|1|G|P98|X|0|0\n";
    Procedure procedure = ResourceUtils.getProcedure(ftv, procedureMsg);
    // Expect 2 identifiers
    assertThat(procedure.hasIdentifier()).isTrue();
    assertThat(procedure.getIdentifier()).hasSize(2);
    List<Identifier> identifiers = procedure.getIdentifier();
    // Match the three id's to position; we can't depend on an order.
    int posExtId = getIdentifierPositionByValue("P98", identifiers);
    assertThat(posExtId).isNotSameAs(-1);
    int posACME = getIdentifierPositionByValue("78654", identifiers);
    assertThat(posACME).isNotSameAs(-1);
    // Identifier 1: PR1.19
    Identifier identifier = procedure.getIdentifier().get(posExtId);
    String value = identifier.getValue();
    String system = identifier.getSystem();
    // PR1.19.1
    assertThat(value).isEqualTo("P98");
    assertThat(system).isEqualTo("urn:id:extID");
    // Identifier 2: Visit number from PID-18
    identifier = procedure.getIdentifier().get(posACME);
    value = identifier.getValue();
    system = identifier.getSystem();
    // PID.18.1
    assertThat(value).isEqualTo("78654");
    // PID.18.4
    assertThat(system).isEqualTo("urn:id:ACME");
    CodeableConcept type = identifier.getType();
    DatatypeUtils.checkCommonCodeableConceptAssertions(type, "VN", "Visit number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
    // Test: MSH.7 and PV1.19
    String procedureMSH = "MSH|^~\\&||Instance1|MCM||200911021022|Security|ADT^A01^ADT_A01|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM|CDP|^4086::132:2A57:3C28^IPV6|^4086::132:2A57:3C25^IPV6|\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1||I|6N^1234^A^GENERAL HOSPITAL2|||||||SUR||||||||S|8846511|A|||||||||||||||||||SF|K||||20170215080000\n" + "ROL|5897|UP|AD||20210322133821|20210322133822|10||Hospital|ST||||USA\n" + "PR1|1|ICD10|B45678|Fix break|20210322155008|A|75||V46|80|||32|1|D22|G45|1|G||X|0|0\n";
    procedure = ResourceUtils.getProcedure(ftv, procedureMSH);
    // Expect 2 identifiers
    assertThat(procedure.hasIdentifier()).isTrue();
    assertThat(procedure.getIdentifier()).hasSize(2);
    identifiers = procedure.getIdentifier();
    // Match the three id's to position; we can't depend on an order.
    posExtId = getIdentifierPositionByValue("200911021022", identifiers);
    assertThat(posExtId).isNotSameAs(-1);
    int posVN = getIdentifierPositionByValue("8846511", identifiers);
    assertThat(posVN).isNotSameAs(-1);
    // Identifier 1: PR1
    identifier = procedure.getIdentifier().get(posExtId);
    value = identifier.getValue();
    system = identifier.getSystem();
    // MSH.7
    assertThat(value).isEqualTo("200911021022");
    assertThat(system).isEqualTo("urn:id:extID");
    // Identifier 2: Visit number from PV1-19
    identifier = procedure.getIdentifier().get(posVN);
    String valueOBR = identifier.getValue();
    system = identifier.getSystem();
    // PV1.19.1
    assertThat(valueOBR).isEqualTo("8846511");
    // No System PV1.19.2 DNE
    assertThat(system).isNull();
    type = identifier.getType();
    DatatypeUtils.checkCommonCodeableConceptAssertions(type, "VN", "Visit number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
}

Example 52 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7IdentifierFHIRConversionTest method serviceRequestIdentifierTest5.

// NOTE: ORU_RO1 records do not create the ServiceRequest directly.  They create a DiagnosticReport and it creates the ServiceRequest.
// This test makes sure the specification for ORU_RO1.DiagnosticReport is specifying PID and PV1 correctly in AdditionalSegments.
@Test
void serviceRequestIdentifierTest5() {
    // Test 3:
    // - MSH.7 as the visit number
    // - filler from ORC
    // - placer from ORC
    String serviceRequest = "MSH|^~\\&|||||20180924152907|34001|ORU^R01^ORU_R01|213|T|2.6|||||||||||\n" + // PID.18 is empty so MSH.7 with be used as backup identifier visit number
    "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\n" + // PV1.19 is empty so MSH.7 with be used as backup identifier visit number
    "PV1|1|E|||||||||||||||||||||||||||||||||||||||||||\n" + // 1. ORC.3 is used as Filler because it has priority over OBR.3
    "ORC|RE|222298|222299|ML18267-C00001^Beaker||||||||||||||||||||||||||||\n" + // 11. OBR.3 ignored as Filler
    "OBR|1|||83036E^HEMOGLOBIN A1C^PACSEAP^^^^^^HEMOGLOBIN A1C|||||||||||||||||||||||||||||||||||||||||||\n";
    ServiceRequest serviceReq = ResourceUtils.getServiceRequest(ftv, serviceRequest);
    // Expect 3 identifiers
    assertThat(serviceReq.hasIdentifier()).isTrue();
    assertThat(serviceReq.getIdentifier()).hasSize(3);
    // Expect 3 identifiers
    assertThat(serviceReq.hasIdentifier()).isTrue();
    assertThat(serviceReq.getIdentifier()).hasSize(3);
    List<Identifier> identifiers = serviceReq.getIdentifier();
    // Match the three id's to position; we can't depend on an order.
    int posVN = getIdentifierPositionByValue("20180924152907", identifiers);
    assertThat(posVN).isNotSameAs(-1);
    int posFILLER = getIdentifierPositionByValue("222299", identifiers);
    assertThat(posFILLER).isNotSameAs(-1);
    int posPLACER = getIdentifierPositionByValue("222298", identifiers);
    assertThat(posPLACER).isNotSameAs(-1);
    // Identifier 1: visit number should be set by MSH.7
    Identifier identifier = serviceReq.getIdentifier().get(posVN);
    String value = identifier.getValue();
    String system = identifier.getSystem();
    // MSH.7
    assertThat(value).isEqualTo("20180924152907");
    assertThat(system).isNull();
    CodeableConcept type = identifier.getType();
    DatatypeUtils.checkCommonCodeableConceptAssertions(type, "VN", "Visit number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
    // Identifier 2: filler
    identifier = serviceReq.getIdentifier().get(posFILLER);
    value = identifier.getValue();
    system = identifier.getSystem();
    // ORC.3
    assertThat(value).isEqualTo("222299");
    assertThat(system).isNull();
    type = identifier.getType();
    DatatypeUtils.checkCommonCodeableConceptAssertions(type, "FILL", "Filler Identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
    // Identifier 3: placer
    identifier = serviceReq.getIdentifier().get(posPLACER);
    value = identifier.getValue();
    system = identifier.getSystem();
    // ORC.2
    assertThat(value).isEqualTo("222298");
    assertThat(system).isNull();
    type = identifier.getType();
    DatatypeUtils.checkCommonCodeableConceptAssertions(type, "PLAC", "Placer Identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
}

Example 53 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7PatientFHIRConversionTest method patientCommunicationLanguage.

@Test
void patientCommunicationLanguage() {
    String patientSpeaksEnglishWithSystem = "MSH|^~\\&|MyEMR|DE-000001| |CAIRLO|20160701123030-0700||VXU^V04^VXU_V04|CA0001|P|2.6|||ER|AL|||||Z22^CDCPHINVS|DE-000001\r" + "PID|1||PA123456^^^MYEMR^MR||DOE^JOHN|||M|||||||ENG^English^HL70296|||||||||Y|2\r";
    // NO coding system given in the CWE
    String patientEnglishNoSystem = "MSH|^~\\&|MyEMR|DE-000001| |CAIRLO|20160701123030-0700||VXU^V04^VXU_V04|CA0001|P|2.6|||ER|AL|||||Z22^CDCPHINVS|DE-000001\r" + "PID|1||PA123456^^^MYEMR^MR||DOE^JANE|||M|||||||ENG^English|||||||||Y|2\r";
    // NO coding system given in the CWE
    String patientEnglishCodeOnly = "MSH|^~\\&|MyEMR|DE-000001| |CAIRLO|20160701123030-0700||VXU^V04^VXU_V04|CA0001|P|2.6|||ER|AL|||||Z22^CDCPHINVS|DE-000001\r" + "PID|1||PA123456^^^MYEMR^MR||DOE^JANE|||M|||||||ENG|||||||||Y|2\r";
    Patient patientObjEnglish = PatientUtils.createPatientFromHl7Segment(ftv, patientSpeaksEnglishWithSystem);
    assertThat(patientObjEnglish.hasCommunication()).isTrue();
    assertThat(patientObjEnglish.getCommunication().get(0).getPreferred()).isTrue();
    assertThat(patientObjEnglish.getCommunication()).hasSize(1);
    Patient.PatientCommunicationComponent cc = patientObjEnglish.getCommunication().get(0);
    assertThat(cc.getPreferred()).isTrue();
    assertThat(cc.getLanguage().getText()).isEqualTo("English");
    Coding code = cc.getLanguage().getCodingFirstRep();
    assertThat(code.getCode()).isEqualTo("ENG");
    assertThat(code.getSystem()).isEqualTo("urn:id:v2-0296");
    assertThat(code.getDisplay()).isEqualTo("English");
    Patient patientObjNoSystem = PatientUtils.createPatientFromHl7Segment(ftv, patientEnglishNoSystem);
    assertThat(patientObjNoSystem.hasCommunication()).isTrue();
    assertThat(patientObjNoSystem.getCommunication().get(0).getPreferred()).isTrue();
    assertThat(patientObjNoSystem.getCommunication()).hasSize(1);
    Patient.PatientCommunicationComponent ccNoCode = patientObjNoSystem.getCommunication().get(0);
    assertThat(ccNoCode.getPreferred()).isTrue();
    assertThat(ccNoCode.getLanguage().getText()).isEqualTo("English");
    Coding codeNo = ccNoCode.getLanguage().getCodingFirstRep();
    assertThat(codeNo.getCode()).isEqualTo("ENG");
    assertThat(code.getDisplay()).isEqualTo("English");
    assertThat(codeNo.hasDisplay()).isTrue();
    Patient patientObjCodeOnly = PatientUtils.createPatientFromHl7Segment(ftv, patientEnglishCodeOnly);
    assertThat(patientObjCodeOnly.hasCommunication()).isTrue();
    assertThat(patientObjCodeOnly.getCommunication().get(0).getPreferred()).isTrue();
    assertThat(patientObjCodeOnly.getCommunication()).hasSize(1);
    Patient.PatientCommunicationComponent ccCodeOnly = patientObjCodeOnly.getCommunication().get(0);
    assertThat(ccCodeOnly.getPreferred()).isTrue();
    assertThat(ccCodeOnly.getLanguage().hasText()).isFalse();
    Coding coding = ccCodeOnly.getLanguage().getCodingFirstRep();
    assertThat(coding.getCode()).isEqualTo("ENG");
    assertThat(coding.getSystem()).isNull();
    assertThat(coding.getDisplay()).isNull();
}

Example 54 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System in project hl7v2-fhir-converter by LinuxForHealth.

the class DatatypeUtils method checkCommonCodeableConceptVersionedAssertions.

// Common check for values of a codeable concept, including version.  Null in any input indicates it should check False
// Assumes 1 coding and only checks the first one.
public static void checkCommonCodeableConceptVersionedAssertions(CodeableConcept cc, String code, String display, String system, String text, String version) {
    if (text == null) {
        assertThat(cc.hasText()).isFalse();
    } else {
        assertThat(cc.hasText()).isTrue();
        assertThat(cc.getText()).isEqualTo(text);
    }
    if (code == null && display == null && system == null && version == null) {
        assertThat(cc.hasCoding()).isFalse();
    } else {
        assertThat(cc.hasCoding()).isTrue();
        assertThat(cc.getCoding().size()).isEqualTo(1);
        Coding coding = cc.getCoding().get(0);
        checkCommonCodingAssertions(coding, code, display, system, version);
    }
}

Example 55 with System

use of org.hl7.gravity.refimpl.sdohexchange.sdohmappings.System 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());
}