use of org.hl7.fhir.r5.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);
}
use of org.hl7.fhir.r5.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);
}
use of org.hl7.fhir.r5.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.");
}
use of org.hl7.fhir.r5.model.Observation 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());
}
use of org.hl7.fhir.r5.model.Observation in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ObservationFHIRConversionTest method testObservationCeResultUnknownSystem.
// NOTE that even though we are testing for it CE is not part of HL7 V2.6
@Test
void testObservationCeResultUnknownSystem() throws IOException {
String hl7message = baseMessage + "OBX|1|CE|93000&CMP^LIN^CPT4|11|1305^No significant change was found^MEIECG";
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.getValueCodeableConcept()).isNotNull();
assertThat(obs.getStatus()).isNotNull();
CodeableConcept cc = obs.getValueCodeableConcept();
assertThat(cc.getCoding()).isNotNull();
assertThat(cc.getCoding().get(0)).isNotNull();
assertThat(cc.getCoding().get(0).getSystem()).isNull();
assertThat(cc.getCoding().get(0).getCode()).isEqualTo("1305");
assertThat(cc.getText()).isEqualTo("No significant change was found");
}
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