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

Example 6 with Meta

use of org.hl7.fhir.r5.model.Meta in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7PatientFHIRConversionTest method validate_data_lineage.

private void validate_data_lineage(String hl7message, String messageType, boolean millis) {
    String json = ftv.convert(hl7message, PatientUtils.OPTIONS);
    assertThat(json).isNotBlank();
    LOGGER.debug(json);
    IBaseResource bundleResource = context.getParser().parseResource(json);
    assertThat(bundleResource).isNotNull();
    Bundle b = (Bundle) bundleResource;
    List<BundleEntryComponent> e = b.getEntry();
    // Get bundle meta extensions *not using these currently*
    // Meta bundleMeta = b.getMeta();
    // List<Extension> bundleMetaExtensions = bundleMeta.getExtension();
    LOGGER.debug("Found {} resources.", e.stream().count());
    e.stream().forEach(bec -> {
        LOGGER.debug("Validating " + bec.getResource().getResourceType());
        Meta meta = bec.getResource().getMeta();
        List<Extension> extensions = meta.getExtension();
        LOGGER.debug("Found " + extensions.size() + " meta extensions");
        validate_lineage_json(extensions, messageType, millis);
    });
}

Example 7 with Meta

use of org.hl7.fhir.r5.model.Meta in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7NoteFHIRConverterTest method testMedicationRequestNoteCreation.

// 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")
@ParameterizedTest
@MethodSource("parmsTestMedicationRequestNoteCreation")
void testMedicationRequestNoteCreation(String message, String medicalRequestSegments) {
    // Minimal valid ORC message.  Requires RXO and RXR segments.
    String hl7message = "MSH|^~\\&||||IBM|20210101000000||" + message + "|MSGID|T|2.6\n" + "PID|||1234||DOE^JANE^|||F||||||||||||||||||||||\n" + "PV1||I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|OP|1234|1234|0827||||||||||||||||||||\n" + // May be RXO or RXO+RXE values from parmsTestMedicationRequestNoteCreation
    medicalRequestSegments + "NTE|1|O|TEST MedReq NOTE AA line 1||Pract1ID^Pract1Last^Pract1First|\n" + "NTE|2|O|TEST NOTE AA line 2|\n" + "NTE|3|O|TEST NOTE AA line 3|\n" + "OBX|1|NM|17985^GLYCOHEMOGLOBIN HGB A1C^LRR^^^^^^GLYCOHEMOGLOBIN HGB A1C||5.6|%|<6.0||||F||||||||||||||\n" + // GLYCOHEMOGLOBIN Observation NTE has a practitioner reference in NTE.5.  Note in second NTE. The first valid NTE.5 is used.
    "NTE|1|L|TEST OBXa NOTE BB line 1|\n" + "NTE|2|L|TEST NOTE BB line 2||Pract2ID^Pract2Last^Pract2First|\n" + "NTE|3|L|TEST NOTE BB line 3|\n" + "OBX|2|NM|17853^MEAN BLOOD GLUCOSE^LRR^^^^^^MEAN BLOOD GLUCOSE||114.02|mg/dL|||||F||||||||||||||\n" + // Glucose Observation NTE has no practitioner reference in NTE.5
    "NTE|1|L|TEST OBXb NOTE CC line 1|\n" + "NTE|2|L|TEST NOTE CC line 2|\n" + // Test that blank lines are preserved.
    "NTE|3|L| |\n" + "NTE|4|L|TEST NOTE CC line 4|\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    // Expect MedicationRequest containing NTE for RXO or RXE
    List<Resource> medicationRequests = ResourceUtils.getResourceList(e, ResourceType.MedicationRequest);
    assertThat(medicationRequests).hasSize(1);
    MedicationRequest medicationRequest = ResourceUtils.getResourceMedicationRequest(medicationRequests.get(0), ResourceUtils.context);
    assertThat(medicationRequest.hasNote()).isTrue();
    assertThat(medicationRequest.getNote()).hasSize(1);
    // NOTE: the note contains an Annotation, which contains a MarkdownType that has the string.
    // Must use getTextElement().getValueAsString() to see untrimmed contents.
    assertThat(medicationRequest.getNote().get(0).getTextElement().getValueAsString()).isEqualTo("TEST MedReq NOTE AA line 1  \nTEST NOTE AA line 2  \nTEST NOTE AA line 3");
    assertThat(medicationRequest.getNote().get(0).hasAuthorReference()).isTrue();
    String practitionerServReqRefId = medicationRequest.getNote().get(0).getAuthorReference().getReference();
    // Two observations.  One has GLYCOHEMOGLOBIN and notes BB, One has GLUCOSE and notes CC
    List<Resource> observations = ResourceUtils.getResourceList(e, ResourceType.Observation);
    // Should be 2 for ORU and ORM
    assertThat(observations).hasSize(2);
    Observation obsGlucose = ResourceUtils.getResourceObservation(observations.get(0), ResourceUtils.context);
    Observation obsHemoglobin = ResourceUtils.getResourceObservation(observations.get(1), ResourceUtils.context);
    // Figure out which is first and reassign if needed for testing
    if (obsGlucose.getCode().getText() != "MEAN BLOOD GLUCOSE") {
        Observation temp = obsGlucose;
        obsGlucose = obsHemoglobin;
        obsHemoglobin = temp;
    }
    // Validate the note contents and references
    assertThat(obsHemoglobin.hasNote()).isTrue();
    assertThat(obsHemoglobin.getNote()).hasSize(1);
    assertThat(obsHemoglobin.getNote().get(0).getTextElement().getValueAsString()).isEqualTo("TEST OBXa NOTE BB line 1  \nTEST NOTE BB line 2  \nTEST NOTE BB line 3");
    assertThat(obsHemoglobin.getNote().get(0).hasAuthorReference()).isTrue();
    String practitionerObsHemoglobinRefId = obsHemoglobin.getNote().get(0).getAuthorReference().getReference();
    assertThat(obsGlucose.hasNote()).isTrue();
    assertThat(obsGlucose.getNote()).hasSize(1);
    assertThat(obsGlucose.getNote().get(0).getTextElement().getValueAsString()).isEqualTo(// Test that blank lines are preserved.
    "TEST OBXb NOTE CC line 1  \nTEST NOTE CC line 2  \n   \nTEST NOTE CC line 4");
    assertThat(obsGlucose.getNote().get(0).hasAuthorReference()).isFalse();
    // Two Practitioners, one for the serviceRequest, one for the GLYCOHEMOGLOBIN Observation
    List<Resource> practitioners = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
    assertThat(practitioners).hasSize(2);
    Practitioner practitionerServReq = ResourceUtils.getResourcePractitioner(practitioners.get(0), ResourceUtils.context);
    Practitioner practitionerObsHemoglobin = ResourceUtils.getResourcePractitioner(practitioners.get(1), ResourceUtils.context);
    // Adjust to correct practitioner if needed
    if (!practitionerServReq.getIdentifierFirstRep().getValue().contentEquals("Pract1ID")) {
        Practitioner temp = practitionerObsHemoglobin;
        practitionerObsHemoglobin = practitionerServReq;
        practitionerServReq = temp;
    }
    // Check the values for the Practitioners and validate match to references.
    assertThat(practitionerServReq.getIdentifier()).hasSize(1);
    assertThat(practitionerServReq.getIdentifierFirstRep().getValue()).isEqualTo("Pract1ID");
    assertThat(practitionerServReq.getName()).hasSize(1);
    assertThat(practitionerServReq.getNameFirstRep().getText()).isEqualTo("Pract1First Pract1Last");
    // Check the cross-reference
    assertThat(practitionerServReq.getId()).isEqualTo(practitionerServReqRefId);
    // Sanity check to confirm data corruption in meta content has not returned.
    CodeableConcept ccSourceEventTrigger = (CodeableConcept) practitionerServReq.getMeta().getExtensionByUrl("http://ibm.com/fhir/cdm/StructureDefinition/source-event-trigger").getValue();
    assertThat(ccSourceEventTrigger.hasText()).isFalse();
    assertThat(practitionerObsHemoglobin.getIdentifier()).hasSize(1);
    assertThat(practitionerObsHemoglobin.getIdentifierFirstRep().getValue()).isEqualTo("Pract2ID");
    assertThat(practitionerObsHemoglobin.getName()).hasSize(1);
    assertThat(practitionerObsHemoglobin.getNameFirstRep().getText()).isEqualTo("Pract2First Pract2Last");
    // Check the cross-reference
    assertThat(practitionerObsHemoglobin.getId()).isEqualTo(practitionerObsHemoglobinRefId);
}

Example 8 with Meta

use of org.hl7.fhir.r5.model.Meta in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7NoteFHIRConverterTest method testNoteCreationServiceRequestMutipleOBX.

// 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")
@ParameterizedTest
@MethodSource("provideParmsForNoteCreationServiceRequestMutipleOBX")
void testNoteCreationServiceRequestMutipleOBX(String message, int numExpectedDiagnosticReports) {
    String hl7ORU = "MSH|^~\\&|||||20180924152907||" + message + "|213|T|2.3.1|||||||||||\n" + "PID|||Pract1ID^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\n" + // "NTE|1|O|TEST NOTE DD line 1|\n" + "NTE|2|O|TEST NOTE DD line 2 |\n" + "NTE|3|O|TEST NOTE D line 3|\n"
    "PV1|1|I||||||||||||||||||||||||||||||||||||||||||20180924152707|\n" + "ORC|RE|248648498^|248648498^|ML18267-C00001^Beaker|||||||||||||||||||||||||||\n" + "OBR|1|248648498^|248648498^|83036E^HEMOGLOBIN A1C^PACSEAP^^^^^^HEMOGLOBIN A1C||||||||||||||||||||||||||||||||||||\n" + // ServiceRequest NTE has a practitioner reference in NTE.5
    "NTE|1|O|TEST ORC/OBR NOTE AA line 1||Pract1ID^Pract1Last^Pract1First|\n" + "NTE|2|O|TEST NOTE AA line 2|\n" + "NTE|3|O|TEST NOTE AA line 3|\n" + "OBX|1|NM|17985^GLYCOHEMOGLOBIN HGB A1C^LRR^^^^^^GLYCOHEMOGLOBIN HGB A1C||5.6|%|<6.0||||F||||||||||||||\n" + // GLYCOHEMOGLOBIN Observation NTE has a practitioner reference in NTE.5.  Note in second NTE. The first valied NTE.5 is used.
    "NTE|1|L|TEST OBXa NOTE BB line 1|\n" + "NTE|2|L|TEST NOTE BB line 2||Pract2ID^Pract2Last^Pract2First|\n" + "NTE|3|L|TEST NOTE BB line 3|\n" + "OBX|2|NM|17853^MEAN BLOOD GLUCOSE^LRR^^^^^^MEAN BLOOD GLUCOSE||114.02|mg/dL|||||F||||||||||||||\n" + // Glucose Observation NTE has no practitioner reference in NTE.5
    "NTE|1|L|TEST OBXb NOTE CC line 1|\n" + "NTE|2|L|TEST NOTE CC line 2|\n" + // Test that blank lines are preserved.
    "NTE|3|L| |\n" + "NTE|4|L|TEST NOTE CC line 4|\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7ORU);
    List<Resource> diagnosticReports = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
    // DiagnosticReport expected for ORU, but not for ORM
    // From the OBR in the ORU test case
    assertThat(diagnosticReports).hasSize(numExpectedDiagnosticReports);
    // One ServiceRequest contains NTE for ORC/OBR
    List<Resource> serviceRequests = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
    assertThat(serviceRequests).hasSize(1);
    ServiceRequest serviceRequest = ResourceUtils.getResourceServiceRequest(serviceRequests.get(0), ResourceUtils.context);
    assertThat(serviceRequest.hasNote()).isTrue();
    assertThat(serviceRequest.getNote()).hasSize(1);
    // Processing adds "  \n" two spaces and a line feed between each line.
    // NOTE: the note contains an Annotation, which contains a MarkdownType that has the string.
    // Must use getTextElement().getValueAsString() to see untrimmed contents.
    assertThat(serviceRequest.getNote().get(0).getTextElement().getValueAsString()).isEqualTo("TEST ORC/OBR NOTE AA line 1  \nTEST NOTE AA line 2  \nTEST NOTE AA line 3");
    assertThat(serviceRequest.getNote().get(0).hasAuthorReference()).isTrue();
    String practitionerServReqRefId = serviceRequest.getNote().get(0).getAuthorReference().getReference();
    // Two observations.  One has GLYCOHEMOGLOBIN and notes BB, One has GLUCOSE and notes CC
    List<Resource> observations = ResourceUtils.getResourceList(e, ResourceType.Observation);
    // Should be 2 for ORU and ORM
    assertThat(observations).hasSize(2);
    Observation obsGlucose = ResourceUtils.getResourceObservation(observations.get(0), ResourceUtils.context);
    Observation obsHemoglobin = ResourceUtils.getResourceObservation(observations.get(1), ResourceUtils.context);
    // Figure out which is first and reassign if needed for testing
    if (obsGlucose.getCode().getText() != "MEAN BLOOD GLUCOSE") {
        Observation temp = obsGlucose;
        obsGlucose = obsHemoglobin;
        obsHemoglobin = temp;
    }
    // Validate the note contents and references
    assertThat(obsHemoglobin.hasNote()).isTrue();
    assertThat(obsHemoglobin.getNote()).hasSize(1);
    assertThat(obsHemoglobin.getNote().get(0).getTextElement().getValueAsString()).isEqualTo("TEST OBXa NOTE BB line 1  \nTEST NOTE BB line 2  \nTEST NOTE BB line 3");
    assertThat(obsHemoglobin.getNote().get(0).hasAuthorReference()).isTrue();
    String practitionerObsHemoglobinRefId = obsHemoglobin.getNote().get(0).getAuthorReference().getReference();
    assertThat(obsGlucose.hasNote()).isTrue();
    assertThat(obsGlucose.getNote()).hasSize(1);
    assertThat(obsGlucose.getNote().get(0).getTextElement().getValueAsString()).isEqualTo(// Test that blank lines are preserved.
    "TEST OBXb NOTE CC line 1  \nTEST NOTE CC line 2  \n   \nTEST NOTE CC line 4");
    assertThat(obsGlucose.getNote().get(0).hasAuthorReference()).isFalse();
    // Two Practitioners, one for the serviceRequest, one for the GLYCOHEMOGLOBIN Observation
    List<Resource> practitioners = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
    assertThat(practitioners).hasSize(2);
    Practitioner practitionerServReq = ResourceUtils.getResourcePractitioner(practitioners.get(0), ResourceUtils.context);
    Practitioner practitionerObsHemoglobin = ResourceUtils.getResourcePractitioner(practitioners.get(1), ResourceUtils.context);
    // Adjust to correct practitioner if needed
    if (!practitionerServReq.getIdentifierFirstRep().getValue().contentEquals("Pract1ID")) {
        Practitioner temp = practitionerObsHemoglobin;
        practitionerObsHemoglobin = practitionerServReq;
        practitionerServReq = temp;
    }
    // Check the values for the Practitioners and validate match to references.
    assertThat(practitionerServReq.getIdentifier()).hasSize(1);
    assertThat(practitionerServReq.getIdentifierFirstRep().getValue()).isEqualTo("Pract1ID");
    assertThat(practitionerServReq.getName()).hasSize(1);
    assertThat(practitionerServReq.getNameFirstRep().getText()).isEqualTo("Pract1First Pract1Last");
    // Check the cross-reference
    assertThat(practitionerServReq.getId()).isEqualTo(practitionerServReqRefId);
    // Sanity check to confirm data corruption in meta content has not returned.
    CodeableConcept ccSourceEventTrigger = (CodeableConcept) practitionerServReq.getMeta().getExtensionByUrl("http://ibm.com/fhir/cdm/StructureDefinition/source-event-trigger").getValue();
    assertThat(ccSourceEventTrigger.hasText()).isFalse();
    assertThat(practitionerObsHemoglobin.getIdentifier()).hasSize(1);
    assertThat(practitionerObsHemoglobin.getIdentifierFirstRep().getValue()).isEqualTo("Pract2ID");
    assertThat(practitionerObsHemoglobin.getName()).hasSize(1);
    assertThat(practitionerObsHemoglobin.getNameFirstRep().getText()).isEqualTo("Pract2First Pract2Last");
    // Check the cross-reference
    assertThat(practitionerObsHemoglobin.getId()).isEqualTo(practitionerObsHemoglobinRefId);
}

Example 9 with Meta

use of org.hl7.fhir.r5.model.Meta in project hl7v2-fhir-converter by LinuxForHealth.

the class HL7MessageEngine method initBundle.

private Bundle initBundle() {
    Bundle bundle = new Bundle();
    bundle.setType(this.bundleType);
    bundle.setId(UUID.randomUUID().toString());
    Meta m = new Meta();
    m.setLastUpdated(LocalDateTime.now().toDate());
    bundle.setMeta(m);
    return bundle;
}

Example 10 with Meta

use of org.hl7.fhir.r5.model.Meta in project BridgeServer2 by Sage-Bionetworks.

the class CRCController method createPatient.

Patient createPatient(Account account) {
    Patient patient = new Patient();
    patient.setActive(true);
    patient.setId(account.getId());
    Identifier identifier = new Identifier();
    identifier.setValue(account.getId());
    identifier.setSystem(USER_ID_VALUE_NS);
    patient.addIdentifier(identifier);
    Coding coding = new Coding();
    coding.setSystem("source");
    coding.setCode("sage");
    Meta meta = new Meta();
    meta.setTag(ImmutableList.of(coding));
    patient.setMeta(meta);
    HumanName name = new HumanName();
    if (isNotBlank(account.getFirstName())) {
        name.addGiven(account.getFirstName());
    }
    if (isNotBlank(account.getLastName())) {
        name.setFamily(account.getLastName());
    }
    patient.addName(name);
    Map<String, String> atts = account.getAttributes();
    if (isNotBlank(atts.get("gender"))) {
        if ("female".equalsIgnoreCase(atts.get("gender"))) {
            patient.setGender(AdministrativeGender.FEMALE);
        } else if ("male".equalsIgnoreCase(atts.get("gender"))) {
            patient.setGender(AdministrativeGender.MALE);
        } else {
            patient.setGender(AdministrativeGender.OTHER);
        }
    } else {
        patient.setGender(AdministrativeGender.UNKNOWN);
    }
    if (isNotBlank(atts.get("dob"))) {
        LocalDate localDate = LocalDate.parse(atts.get("dob"));
        patient.setBirthDate(localDate.toDate());
    }
    Address address = new Address();
    if (isNotBlank(atts.get("address1"))) {
        address.addLine(atts.get("address1"));
    }
    if (isNotBlank(atts.get("address2"))) {
        address.addLine(atts.get("address2"));
    }
    if (isNotBlank(atts.get("city"))) {
        address.setCity(atts.get("city"));
    }
    if (isNotBlank(atts.get("state"))) {
        address.setState(atts.get("state"));
    } else {
        address.setState("NY");
    }
    if (isNotBlank(atts.get("zip_code"))) {
        address.setPostalCode(atts.get("zip_code"));
    }
    patient.addAddress(address);
    if (isNotBlank(atts.get("home_phone"))) {
        ContactPoint contact = new ContactPoint();
        contact.setSystem(ContactPointSystem.PHONE);
        contact.setValue(atts.get("home_phone"));
        patient.addTelecom(contact);
    }
    if (account.getPhone() != null && TRUE.equals(account.getPhoneVerified())) {
        ContactPoint contact = new ContactPoint();
        contact.setSystem(ContactPointSystem.SMS);
        contact.setValue(account.getPhone().getNumber());
        patient.addTelecom(contact);
    }
    if (account.getEmail() != null && TRUE.equals(account.getEmailVerified())) {
        ContactPoint contact = new ContactPoint();
        contact.setSystem(ContactPointSystem.EMAIL);
        contact.setValue(account.getEmail());
        patient.addTelecom(contact);
    }
    Reference ref = new Reference("CUZUCK");
    ref.setDisplay("COVID Recovery Corps");
    ContactComponent contact = new ContactComponent();
    contact.setOrganization(ref);
    patient.addContact(contact);
    return patient;
}