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

Example 26 with Observation

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

the class Hl7ServiceRequestFHIRConversionTest method test_ppr_pc1_service_request.

@Test
void test_ppr_pc1_service_request() throws IOException {
    // Currently only tests limited items, TODO add tests for other field
    String hl7message = "MSH|^~\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|202101010000|security|PPR^PC1^PPR_PC1|1|P^I|2.6||||||ASCII||\n" + "PID|||1234^^^^MR||DOE^JANE^|||F|||||||||||||||||||||\n" + "PV1||I|6N^1234^A^GENHOS|||||||SUR||||||||S||||||||||||||||||||||||||\n" + "PRB|AD||202101010000|aortic stenosis|53692||2|||202101010000\n" + "OBX|1|NM|111^TotalProtein||7.5|gm/dl|5.9-8.4||||W\n" + "ORC|NW|1000^OE|9999999^RX||SC|E|^Q6H^D10^^^R\n" + "OBR|1|TESTID|TESTID|||202101010000|202101010000||||||||||||||||||F||||||WEAKNESS||||||||||||\n" + "OBX|1|TX|||ECHOCARDIOGRAPHIC REPORT||||||F|||202101010000|||\n" + "OBX|2|TX|||NORMAL LV CHAMBER SIZE WITH MILD CONCENTRIC LVH||||||F|||202101010000|||\n";
    String json = ftv.convert(hl7message, OPTIONS);
    assertThat(json).isNotBlank();
    IBaseResource bundleResource = context.getParser().parseResource(json);
    Bundle b = (Bundle) bundleResource;
    List<BundleEntryComponent> e = b.getEntry();
    // OBX under PRB (the PROBLEM.PROBLEM_OBSERVATION.OBSERVATION) creates an Observation resource
    // Verifying this OBX to assure ServiceRequest is using correct OBX information
    List<Resource> obsResource = e.stream().filter(v -> ResourceType.Observation == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    Observation o = (Observation) obsResource.get(0);
    assertEquals("111", o.getCode().getCodingFirstRep().getCode());
    assertEquals("TotalProtein", o.getCode().getText());
    // From OBX.11 'W'
    assertEquals("Entered in Error", o.getStatus().getDisplay());
    List<Resource> serviceRequestResource = e.stream().filter(v -> ResourceType.ServiceRequest == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    ServiceRequest sr = (ServiceRequest) serviceRequestResource.get(0);
    assertEquals(1, serviceRequestResource.size());
    // From ORC.5 'SC'
    assertEquals("Active", sr.getStatus().getDisplay());
    // Ensure the intent is set to "order" for all messages
    assertEquals("order", sr.getIntentElement().getValueAsString());
    // status defaults to "unknown"
    hl7message = "MSH|^~\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|202101010000|security|PPR^PC1^PPR_PC1|1|P^I|2.6||||||ASCII||\n" + "PID|||1234^^^^MR||DOE^JANE^|||F|||||||||||||||||||||\n" + "PV1||I|6N^1234^A^GENHOS|||||||SUR||||||||S||||||||||||||||||||||||||\n" + "PRB|AD||202101010000|aortic stenosis|53692||2|||202101010000\n" + "ORC|NW|1000^OE|9999999^RX|||E|^Q6H^D10^^^R\n";
    json = ftv.convert(hl7message, OPTIONS);
    assertThat(json).isNotBlank();
    bundleResource = context.getParser().parseResource(json);
    b = (Bundle) bundleResource;
    e = b.getEntry();
    serviceRequestResource = e.stream().filter(v -> ResourceType.ServiceRequest == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    sr = (ServiceRequest) serviceRequestResource.get(0);
    // Default since no OBX in message
    assertEquals("Unknown", sr.getStatus().getDisplay());
}

Example 27 with Observation

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

the class Hl7NoteFHIRConverterTest method testNoteCreationMutiplePPR.

// Test that multiple problems (PRB) each with multiple notes (NTE) are associated with the correct NTE / PRB
// and that there is no "bleed"
@Test
void testNoteCreationMutiplePPR() throws IOException {
    // TODO: Add PC2 and PC3 tests in future
    String message = "PPR^PC1";
    String hl7message = "MSH|^~\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|200603081747|security|" + message + "|1|P^I|2.6||||||ASCII||\n" + "PID|||555444222111^^^MPI&GenHosp&L^MR||james^anderson|||M||||||||||||||\n" + "PV1||I|||||||||||||||||1400|||||||||||||||||||||||||199501102300\n" + "PRB|AD|200603150625|aortic stenosis|53692||2||200603150625\n" + "NTE|1|O|TEST PRBa NOTE AA line 1|\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" + "NTE|1|L|TEST OBXb NOTE BB line 1|\n" + "NTE|2|L|TEST NOTE BB line 2|\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" + "NTE|1|L|TEST OBXc NOTE CC line 1|\n" + "NTE|2|L|TEST NOTE CC line 2|\n" + "NTE|3|L|TEST NOTE CC line 3|\n" + "PRB|AD|200603150625|I47.2^Ventricular tachycardia^ICD-10-CM|53692||2||200603150625\n" + "NTE|1|O|TEST PRBd NOTE DD line 1|\n" + "NTE|2|O|TEST NOTE DD line 2|\n" + "NTE|3|O|TEST NOTE DD line 3|\n" + "OBX|1|NM|8595^BP Mean|1|88|MM HG|||||F|||20180520230000|||\n" + "NTE|1|L|TEST OBXe NOTE EE line 1|\n" + "NTE|2|L|TEST NOTE EE line 2|\n" + "NTE|3|L|TEST NOTE EE line 3|\n" + "OBX|2|NM|7302^Resp Rate|1|19||||||F|||20180520230000|||\n" + // Single NTE to ensure it is created correctly
    "NTE|1|L|TEST OBXf NOTE FF line 1|\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> patients = ResourceUtils.getResourceList(e, ResourceType.Patient);
    assertThat(patients).hasSize(1);
    // Two Conditions from two PRBs. One has "... stenosis" and notes AA, One has "... Tachycardia" and notes DD
    List<Resource> conditions = ResourceUtils.getResourceList(e, ResourceType.Condition);
    assertThat(conditions).hasSize(2);
    Condition condStenosis = ResourceUtils.getResourceCondition(conditions.get(0), ResourceUtils.context);
    Condition condTachy = ResourceUtils.getResourceCondition(conditions.get(1), ResourceUtils.context);
    // Figure out which is first and reassign if needed for testing
    if (!condStenosis.getCode().getCodingFirstRep().getCode().contains("aortic stenosis")) {
        Condition temp = condStenosis;
        condStenosis = condTachy;
        condTachy = temp;
    }
    // Test the conditions have the correct NTE's associated and have correct content.
    // NOTE: the note contains an Annotation, which contains a MarkdownType that has the string.
    // Must use getTextElement().getValueAsString() to see untrimmed contents.
    assertThat(condStenosis.hasNote()).isTrue();
    assertThat(condStenosis.getNote()).hasSize(1);
    assertThat(condStenosis.getNote().get(0).getTextElement().getValueAsString()).isEqualTo("TEST PRBa NOTE AA line 1  \nTEST NOTE AA line 2  \nTEST NOTE AA line 3");
    assertThat(condTachy.hasNote()).isTrue();
    assertThat(condTachy.getNote()).hasSize(1);
    assertThat(condTachy.getNote().get(0).getTextElement().getValueAsString()).isEqualTo("TEST PRBd NOTE DD line 1  \nTEST NOTE DD line 2  \nTEST NOTE DD line 3");
    // Four observations.  Two associated with the first problem and two with the second
    // This map tells us what Annotation text is associated with an Observation code
    Map<String, String> matchObsCodeToNotes = new HashMap<>();
    matchObsCodeToNotes.put("17985", "TEST OBXb NOTE BB line 1  \nTEST NOTE BB line 2  \nTEST NOTE BB line 3");
    matchObsCodeToNotes.put("17853", "TEST OBXc NOTE CC line 1  \nTEST NOTE CC line 2  \nTEST NOTE CC line 3");
    matchObsCodeToNotes.put("8595", "TEST OBXe NOTE EE line 1  \nTEST NOTE EE line 2  \nTEST NOTE EE line 3");
    matchObsCodeToNotes.put("7302", "TEST OBXf NOTE FF line 1");
    // This map tells us what Parent should be associated with an Observation code
    Map<String, String> matchObsCodeToParent = new HashMap<>();
    matchObsCodeToParent.put("17985", "aortic stenosis");
    matchObsCodeToParent.put("17853", "aortic stenosis");
    matchObsCodeToParent.put("8595", "I47.2");
    matchObsCodeToParent.put("7302", "I47.2");
    List<Resource> observations = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(observations).hasSize(4);
    int observationsVerified = 0;
    // For the list of Conditions
    for (int condIndex = 0; condIndex < conditions.size(); condIndex++) {
        // condIndex is index for condition
        // Get the list of Observation references
        Condition cond = ResourceUtils.getResourceCondition(conditions.get(condIndex), ResourceUtils.context);
        List<ConditionEvidenceComponent> evidences = cond.getEvidence();
        for (int evidenceIndex = 0; evidenceIndex < evidences.size(); evidenceIndex++) {
            // Get the evidence Observation reference
            String obsReferenceId = evidences.get(evidenceIndex).getDetailFirstRep().getReference();
            // Find the referenced observation
            for (int obsIndex = 0; obsIndex < observations.size(); obsIndex++) {
                // If the Id's match
                if (obsReferenceId.contains(observations.get(obsIndex).getId())) {
                    // Check the contents and the parent
                    Observation obs = ResourceUtils.getResourceObservation(observations.get(obsIndex), ResourceUtils.context);
                    String code = obs.getCode().getCodingFirstRep().getCode().toString();
                    // The Annotation text should match the mapped text for this key
                    assertThat(obs.getNoteFirstRep().getText()).hasToString(matchObsCodeToNotes.get(code));
                    // The parent Condition code.coding.code should match the expected mapped code for this key
                    assertThat(cond.getCode().getCodingFirstRep().getCode()).hasToString(matchObsCodeToParent.get(code));
                    observationsVerified++;
                    break;
                }
            }
        }
    }
    // This confirms ALL of the observations were checked.
    assertThat(observationsVerified).isEqualTo(4);
}

Example 28 with Observation

use of org.hl7.fhir.r4.model.Observation 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 29 with Observation

use of org.hl7.fhir.r4.model.Observation 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 30 with Observation

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

the class Hl7ObservationFHIRConversionTest method testObservationSTMultiplePartsResult.

@Test
void testObservationSTMultiplePartsResult() throws IOException {
    String hl7message = baseMessage + "OBX|1|ST|^Type of protein feed^L||HYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%~Fifth line, as part of a repeated field||||||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.getValueStringType()).isNotNull();
    StringType q = obs.getValueStringType();
    assertThat(q.asStringValue()).isEqualTo("HYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%. Fifth line, as part of a repeated field.");
}