Examples with DiagnosticReport org.hl7.fhir.dstu3.model.DiagnosticReport used on opensource projects

Example 6 with DiagnosticReport

use of org.hl7.fhir.dstu3.model.DiagnosticReport in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7IdentifierFHIRConversionTest method diagnosticReportIdentifierTestFillerPlacerFromOBR.

@Test
void diagnosticReportIdentifierTestFillerPlacerFromOBR() {
    // Filler and placer from OBR
    String diagnosticReport = "MSH|^~\\&|PROSLOV|MYHOSPITAL|WHIA|IBM|20170825010500||ORU^R01|MSGID22102712|T|2.6\n" + "PID|||1234||DOE^JANE^|||F||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1||20170825010500|MS|MS||||20170825010500|\n" + "OBR|1|CC_000000^OE PHIMS Stage|CD_000000|2244^General Order|||20170825010500||||||Relevant Clinical Information|||||||002|||||F\n" + "OBX|1|TX|||Impression: 1. Markedly intense metabolic activity corresponding with the area of nodular enhancement in the left oral cavity.||||||F|||20170825010500\n";
    DiagnosticReport report = ResourceUtils.getDiagnosticReport(ftv, diagnosticReport);
    // Expect 3 identifiers
    assertThat(report.hasIdentifier()).isTrue();
    assertThat(report.getIdentifier()).hasSize(3);
    List<Identifier> identifiers = report.getIdentifier();
    // Match the three id's to position; we can't depend on an order.
    int posExtId = getIdentifierPositionByValue("20170825010500", identifiers);
    assertThat(posExtId).isNotSameAs(-1);
    int posFILLER = getIdentifierPositionByValue("CD_000000", identifiers);
    assertThat(posFILLER).isNotSameAs(-1);
    int posPLACER = getIdentifierPositionByValue("CC_000000", identifiers);
    assertThat(posPLACER).isNotSameAs(-1);
    // Identifier 1: extID with MSH-7
    Identifier identifier = report.getIdentifier().get(posExtId);
    String value = identifier.getValue();
    String system = identifier.getSystem();
    // MSH-7
    assertThat(value).isEqualTo("20170825010500");
    assertThat(system).isEqualTo("urn:id:extID");
    // Identifier 2: Filler
    identifier = report.getIdentifier().get(posFILLER);
    value = identifier.getValue();
    system = identifier.getSystem();
    // OBR-3.1
    assertThat(value).isEqualTo("CD_000000");
    // OBR-3.2 is empty
    assertThat(system).isNull();
    CodeableConcept type = identifier.getType();
    DatatypeUtils.checkCommonCodeableConceptAssertions(type, "FILL", "Filler Identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
    // Identifier 3: Placer
    identifier = report.getIdentifier().get(posPLACER);
    value = identifier.getValue();
    system = identifier.getSystem();
    // OBR-2
    assertThat(value).isEqualTo("CC_000000");
    // OBR-2.2
    assertThat(system).isEqualTo("urn:id:OE_PHIMS_Stage");
    type = identifier.getType();
    DatatypeUtils.checkCommonCodeableConceptAssertions(type, "PLAC", "Placer Identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
}

Example 7 with DiagnosticReport

use of org.hl7.fhir.dstu3.model.DiagnosticReport 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 8 with DiagnosticReport

use of org.hl7.fhir.dstu3.model.DiagnosticReport in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7OrderRequestFHIRConversionTest method testAdditionalOBRFieldsNoORCSegment.

@Test
void testAdditionalOBRFieldsNoORCSegment() {
    String hl7message = "MSH|^~\\&|Epic|ATRIUS|||20180924152907|34001|ORU^R01^ORU_R01|213|T|2.6|||||||||PHLabReport-Ack^^2.16.840.1.114222.4.10.3^ISO||\n" + "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\n" + "PV1|1|E|||||||||||||||||||||||||||||||||||||||||||\n" + // ORC.15 is missing, so use OBR.7 as ServiceRequest.occurrenceDateTime
    "OBR|1|248648498^|248648498^|83036E^HEMOGLOBIN A1C^PACSEAP^^^^^^HEMOGLOBIN A1C|||20170707120707|20180808120808|||||||||||||||||F|||||||||||||||||||||||||\n";
    String json = ftv.convert(hl7message, PatientUtils.OPTIONS);
    assertThat(json).isNotBlank();
    IBaseResource bundleResource = context.getParser().parseResource(json);
    assertThat(bundleResource).isNotNull();
    Bundle bundle = (Bundle) bundleResource;
    List<BundleEntryComponent> e = bundle.getEntry();
    List<Resource> diagnosticReportList = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
    DiagnosticReport diagnosticReport = ResourceUtils.getResourceDiagnosticReport(diagnosticReportList.get(0), context);
    // OBR.7 and OBR.8 together map to DiagnosticReport.effectivePeriod
    assertThat(diagnosticReport.hasEffectivePeriod()).isTrue();
    assertThat(diagnosticReport.getEffectivePeriod().getStartElement().toString()).containsPattern("2017-07-07T12:07:07");
    assertThat(diagnosticReport.getEffectivePeriod().getEndElement().toString()).containsPattern("2018-08-08T12:08:08");
    List<Resource> serviceRequestList = e.stream().filter(v -> ResourceType.ServiceRequest == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    // 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();
    // OBR.7 should create an ServiceRequest.occurrenceDateTime date
    assertThat(serviceRequest.hasOccurrenceDateTimeType()).isTrue();
    assertThat(serviceRequest.getOccurrenceDateTimeType().toString()).containsPattern("2017-07-07T12:07:07");
    // ORC.5 is missing, so serviceRequest.status() should be unknown
    assertThat(serviceRequest.hasStatus()).isTrue();
    assertThat(serviceRequest.getStatusElement().getCode()).isEqualTo("unknown");
}

Example 9 with DiagnosticReport

use of org.hl7.fhir.dstu3.model.DiagnosticReport 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 10 with DiagnosticReport

use of org.hl7.fhir.dstu3.model.DiagnosticReport in project cqf-ruler by DBCG.

the class ActivityDefinitionApplyProvider method resolveDiagnosticReport.

private DiagnosticReport resolveDiagnosticReport(ActivityDefinition activityDefinition, String patientId) {
    DiagnosticReport diagnosticReport = new DiagnosticReport();
    diagnosticReport.setStatus(DiagnosticReport.DiagnosticReportStatus.UNKNOWN);
    diagnosticReport.setSubject(new Reference(patientId));
    if (activityDefinition.hasCode()) {
        diagnosticReport.setCode(activityDefinition.getCode());
    } else {
        throw new ActivityDefinitionApplyException("Missing required ActivityDefinition.code property for DiagnosticReport");
    }
    if (activityDefinition.hasRelatedArtifact()) {
        List<Attachment> presentedFormAttachments = new ArrayList<>();
        for (RelatedArtifact artifact : activityDefinition.getRelatedArtifact()) {
            Attachment attachment = new Attachment();
            if (artifact.hasUrl()) {
                attachment.setUrl(artifact.getUrl());
            }
            if (artifact.hasDisplay()) {
                attachment.setTitle(artifact.getDisplay());
            }
            presentedFormAttachments.add(attachment);
        }
        diagnosticReport.setPresentedForm(presentedFormAttachments);
    }
    return diagnosticReport;
}