Examples with MR org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR used on opensource projects

Example 91 with MR

use of org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7OrderRequestFHIRConversionTest method testBroadORCPlusOBRFields.

// This test is a companion to testBroadORCFields.   ORC and OBR records often have repeated data; one taking priority over the other.
// Read comments carefully.  This sometimes tests the secondary value and may be the opposite to the tests in testBroadORCFields.
@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 testBroadORCPlusOBRFields() {
    String hl7message = "MSH|^~\\&|||||20180924152907|34001|ORU^R01^ORU_R01|213|T|2.6|||||||||||\n" + // PID.18 is used as backup identifier visit number because PV1.19 is empty
    "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||665544||||||||||||\n" + // PV1.19 is empty and not used as visit number identifier
    "PV1|1|E|||||||||||||||||||||||||||||||||||||||||||\n" + // 7. ORC.16 is set to a reason code (but it is ignored because it is secondary to OBR.31, which is present in this case and therefore overrides ORC.16)
    "ORC|RE|248648498^|248648498^|||||||||||||042^Human immunodeficiency virus [HIV] disease [42]^I9CDX^^^^29|||||||||||||||\n" + // 14. OBR.6 creates ServiceRequest.authoredOn
    "OBR|1|248648498^|248648498^|83036E^HEMOGLOBIN A1C^PACSEAP^^^^^^HEMOGLOBIN A1C||20120606120606|20170707150707||||L|||||54321678^SCHMIDT^FRIEDA^^MD^^^^NPI^D^^^NPI||||||20180924152900|||F||||||HIV^HIV/Aids^L^^^^V1|323232&Mahoney&Paul&J||||||||||||||||||\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> serviceRequestList = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
    // Important that we have exactly one service request (no duplication).  OBR creates it as a reference.
    assertThat(serviceRequestList).hasSize(1);
    ServiceRequest serviceRequest = ResourceUtils.getResourceServiceRequest(serviceRequestList.get(0), context);
    assertThat(serviceRequest.hasStatus()).isTrue();
    assertThat(serviceRequest.hasIdentifier()).isTrue();
    assertThat(serviceRequest.getIdentifier()).hasSize(3);
    // Identifier 1: visit number should be set by in this test by secondary PID.18
    // ORU_RO1 records do not create the ServiceRequest directly.  They create a DiagnosticReport and it creates the ServiceRequest.
    // This makes sure the specification for ORU_RO1.DiagnosticReport is specifying PID correctly in AdditionalSegments.
    // Extensive testing of identifiers is done in Hl7IdentifierFHIRConversionTest.java
    Identifier identifier = serviceRequest.getIdentifier().get(0);
    String value = identifier.getValue();
    String system = identifier.getSystem();
    // PID.18
    assertThat(value).isEqualTo("665544");
    assertThat(system).isNull();
    CodeableConcept type = identifier.getType();
    DatatypeUtils.checkCommonCodeableConceptAssertions(type, "VN", "Visit number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
    // No requisition in the serviceRequest.
    assertThat(serviceRequest.hasRequisition()).isFalse();
    // OBR.6 should create authoredOn because ORC.9 is not filled in
    assertThat(serviceRequest.hasAuthoredOn()).isTrue();
    assertThat(serviceRequest.getAuthoredOnElement().toString()).containsPattern("2012-06-06T12:06:06");
    // OBR.7 is used to create an ServiceRequest.occurrenceDateTime date because ORC.15 is empty
    assertThat(serviceRequest.hasOccurrenceDateTimeType()).isTrue();
    assertThat(serviceRequest.getOccurrenceDateTimeType().toString()).containsPattern("2017-07-07T15:07:07");
    // OBR.31 should create the ServiceRequest.reasonCode CWE
    assertThat(serviceRequest.hasReasonCode()).isTrue();
    assertThat(serviceRequest.getReasonCode()).hasSize(1);
    DatatypeUtils.checkCommonCodeableConceptVersionedAssertions(serviceRequest.getReasonCodeFirstRep(), "HIV", "HIV/Aids", "urn:id:L", "HIV/Aids", "V1");
    // OBR.16 should create an ServiceRequest.requester reference & display
    assertThat(serviceRequest.hasRequester()).isTrue();
    assertThat(serviceRequest.getRequester().hasDisplay()).isTrue();
    assertThat(serviceRequest.getRequester().getDisplay()).isEqualTo("FRIEDA SCHMIDT MD");
    assertThat(serviceRequest.getRequester().hasReference()).isTrue();
    String requesterRef = serviceRequest.getRequester().getReference();
    Practitioner pract = ResourceUtils.getSpecificPractitionerFromBundleEntriesList(e, requesterRef);
    // Confirm that the matching practitioner by ID has the correct content (simple validation)
    // Should be OBR.16 because ORC.12 is empty.
    // Check the practitioner content in detail, validating subfields.
    assertThat(pract.getIdentifier()).hasSize(1);
    // OBR.16.1
    assertThat(pract.getIdentifierFirstRep().getValue()).isEqualTo("54321678");
    // OBR.16.9, tests known system logic
    assertThat(pract.getIdentifierFirstRep().getSystem()).isEqualTo("http://hl7.org/fhir/sid/us-npi");
    DatatypeUtils.checkCommonCodeableConceptAssertions(pract.getIdentifierFirstRep().getType(), "NPI", "National provider identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", // OBR.16.13
    null);
    assertThat(pract.getName()).hasSize(1);
    // Combined OBR.16.2 - OBR.16.7
    assertThat(pract.getNameFirstRep().getTextElement().toString()).hasToString("FRIEDA SCHMIDT MD");
    // OBR.16.10
    assertThat(pract.getNameFirstRep().getUseElement().getCode()).isEqualTo("usual");
    // OBR.4 maps to ServiceRequest.code.  Verify resulting CodeableConcept.
    assertThat(serviceRequest.hasCode()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(serviceRequest.getCode(), "83036E", "HEMOGLOBIN A1C", "urn:id:PACSEAP", "HEMOGLOBIN A1C");
    List<Resource> diagnosticReportList = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
    assertThat(diagnosticReportList).hasSize(1);
    DiagnosticReport diagnosticReport = ResourceUtils.getResourceDiagnosticReport(diagnosticReportList.get(0), context);
    // OBR.4 ALSO maps to DiagnosticReport.code.  Verify resulting CodeableConcept.
    assertThat(diagnosticReport.hasCode()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(diagnosticReport.getCode(), "83036E", "HEMOGLOBIN A1C", "urn:id:PACSEAP", "HEMOGLOBIN A1C");
    assertThat(diagnosticReport.hasBasedOn()).isTrue();
    assertThat(diagnosticReport.getBasedOn()).hasSize(1);
    // OBR.7 maps to create an DiagnosticReport.effectiveDateTime
    assertThat(diagnosticReport.hasEffectiveDateTimeType()).isTrue();
    assertThat(diagnosticReport.getEffectiveDateTimeType().toString()).containsPattern("2017-07-07T15:07:07");
    // Check for DiagnosticReport.issued instant of OBR.22
    assertThat(diagnosticReport.hasIssued()).isTrue();
    // NOTE: The data is kept as an InstantType, and is extracted with .toInstant
    // thus results in a different format than other time stamps that are based on DateTimeType
    assertThat(diagnosticReport.getIssued().toInstant().toString()).contains("2018-09-24T07:29:00Z");
    // Get the diagnosticReport.resultsInterpreter, which should match the Practitioner data from OBR.32
    assertThat(diagnosticReport.hasResultsInterpreter()).isTrue();
    assertThat(diagnosticReport.getResultsInterpreter()).hasSize(1);
    String resultsInterpreterRef = diagnosticReport.getResultsInterpreter().get(0).getReference();
    pract = ResourceUtils.getSpecificPractitionerFromBundleEntriesList(e, resultsInterpreterRef);
    // Confirm that the matching practitioner by ID has the correct content (simple validation)
    // Should be the value OBR.32
    assertThat(pract.getIdentifierFirstRep().getValue()).isEqualTo("323232");
    assertThat(pract.getName()).hasSize(1);
    assertThat(pract.getName().get(0).getTextElement()).hasToString("Paul J Mahoney");
    // Check for OBR.25 mapped to DiagnosticReport.status
    assertThat(diagnosticReport.hasStatus()).isTrue();
    assertThat(diagnosticReport.getStatusElement().getCode()).isEqualTo("final");
}

Example 92 with MR

use of org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7PatientFHIRConversionTest method test_patient_additional_demographics.

// Tests the PD1 segment with all supported message types.
@ParameterizedTest
@ValueSource(strings = { "MSH|^~\\&|hl7Integration|hl7Integration|||||ADT^A01|||2.6|\r", // "MSH|^~\\&|hl7Integration|hl7Integration|||||ADT^A04|||2.6|\r",
"MSH|^~\\&|hl7Integration|hl7Integration|||||ADT^A08|||2.6|\r", // "MSH|^~\\&|hl7Integration|hl7Integration|||||ADT^A31|||2.6|\r",
"MSH|^~\\&|hl7Integration|hl7Integration|||||ADT^A34|||2.6|\r", "MSH|^~\\&|hl7Integration|hl7Integration|||||ADT^A40|||2.6|\r", // MDM messages are not tested here because they do not contain PD1 segments
"MSH|^~\\&|hl7Integration|hl7Integration|||||OMP^O09|||2.6|\r", "MSH|^~\\&|hl7Integration|hl7Integration|||||ORM^O01|||2.6|\r", "MSH|^~\\&|hl7Integration|hl7Integration|||||ORU^R01|||2.6|\r", "MSH|^~\\&|hl7Integration|hl7Integration|||||RDE^O11|||2.6|\r", "MSH|^~\\&|hl7Integration|hl7Integration|||||RDE^O25|||2.6|\r", "MSH|^~\\&|hl7Integration|hl7Integration|||||VXU^V04|||2.6|\r" })
void test_patient_additional_demographics(String msh) {
    String hl7message = msh + "PID|1||1234^^^AssigningAuthority^MR||TEST^PATIENT|\r" + "PD1|||Sample Family Practice^^2222|1111^LastName^ClinicianFirstName^^^^Title||||||||||||A|\r";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
    assertThat(patientResource).hasSize(1);
    Patient patient = getResourcePatient(patientResource.get(0));
    List<Reference> refs = patient.getGeneralPractitioner();
    assertThat(refs.size()).isPositive();
    List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
    assertThat(practitionerResource).hasSize(1);
    Practitioner doc = getResourcePractitioner(practitionerResource.get(0));
    String lastName = doc.getName().get(0).getFamily();
    assertThat(lastName).isEqualTo("LastName");
}

Example 93 with MR

use of org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7PatientFHIRConversionTest method patient_use_name_conversion_test.

@Test
void patient_use_name_conversion_test() {
    String patientUseName = "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||TestPatient^John^M^^^^B|MILLER^MARTHA^G^^^^M|20140227|M||2106-3^WHITE^CDCREC|1234 W FIRST ST^^BEVERLY HILLS^CA^90210^^H||^PRN^PH^^^555^5555555||ENG^English^HL70296|||||||2186-5^ not Hispanic or Latino^CDCREC||Y|2\r";
    Patient patientObjUsualName = PatientUtils.createPatientFromHl7Segment(ftv, patientUseName);
    java.util.List<org.hl7.fhir.r4.model.HumanName> name = patientObjUsualName.getName();
    HumanName.NameUse useName = name.get(0).getUse();
    assertThat(useName).isEqualTo(HumanName.NameUse.OFFICIAL);
}

Example 94 with MR

use of org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7TelecomFHIRConversionTest method patient_no_telcom_test.

@Test
void patient_no_telcom_test() {
    String patientNoPhone = "MSH|^~\\&|MIICEHRApplication|MIIC|MIIC|MIIC|201705130822||VXU^V04^VXU_V04|test1100|P|2.5.1|||AL|AL|||||Z22^CDCPHINVS|^^^^^MIIC^SR^^^MIIC|MIIC\n" + "PID|1||12345678^^^^MR|ALTID|Moose^Mickey^J^III^^^||20060504|M||||||||||||||||||||||\n";
    Patient patient = PatientUtils.createPatientFromHl7Segment(ftv, patientNoPhone);
    assertThat(patient.hasTelecom()).isFalse();
}

Example 95 with MR

use of org.hl7.fhir.r4.model.codesystems.V3Hl7PublishingDomain.MR in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7MedicationRequestFHIRConversionTest method dosageInstructionTestPatientInstructionRXE.

@Test
void dosageInstructionTestPatientInstructionRXE() {
    // Test dosageInstruction.patietInstruction (RXE.7)
    String hl7message = "MSH|^~\\&||||||S1|RDE^O11||T|2.6|||||||||\n" + "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\n" + "ORC|NW||||||||||||||||||||||||||||\n" + "RXE||DUONEB3INH^3 ML PLAS CONT : IPRATROPIUM-ALBUTEROL 0.5-2.5 (3) MG/3ML IN SOLN^ADS||||" + // RXE.7 to dosageInstruction.patientInstruction
    "|333^Take 1 tablet by mouth every 6 (six) hours.|||||||||||||||||||||||||||||||||\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);
    String patInstruct = medicationRequest.getDosageInstructionFirstRep().getPatientInstruction();
    // dosageInstruction.patientInstruction (RXE.7.1 and 7.2 separated by a ':')
    assertThat(patInstruct).isEqualTo("333:Take 1 tablet by mouth every 6 (six) hours.");
    // Verify no extraneous resources
    // Expect MedicationRequest, Patient
    assertThat(e).hasSize(2);
}