use of org.hl7.fhir.r4.model.Annotation in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7MDMMessageTest method test_mdm_ORDER_with_OBXnotTX.
@ParameterizedTest
@ValueSource(strings = { "MDM^T02", "MDM^T06" })
void test_mdm_ORDER_with_OBXnotTX(String message) throws IOException {
// Also check NTE working for MDM messages.
String hl7message = "MSH|^~\\&|HNAM|W|RAD_IMAGING_REPORT|W|20180118111520||" + message + "|<MESSAGEID>|P|2.6\r" + "EVN||20150502090000|\r" + "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\r" + "PV1||O||||||||||||||||||||||||||||||||||||||||||199501102300\r" + "ORC|NW|622470H432|||||^^^^^R||||||||||||||\r" + "OBR|1|622470H432|102397CE432|||20170725143849|20180102|||||||||||||||||RAD|O||^^^^^R||||REASON_ID_1^REASON_TEXT_1||||\r" + // 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" + "TXA|1|HP^History and physical examination|TX||||201801171442||||||||||||AV|||||\r" + "OBX|1|NM|Most Current Weight^Most current measured weight (actual)||90|kg\r" + // Observation NTE has a practitioner reference in second NTE.5. Annotation uses the first valid NTE.5
"NTE|1|L|TEST OBX NOTE BB line 1|\n" + "NTE|2|L|TEST NOTE BB line 2||Pract2ID^Pract2Last^Pract2First|\n";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
// Check for the expected resources
List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
// from EVN, PV1
assertThat(encounterResource).hasSize(1);
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
// from PID
assertThat(patientResource).hasSize(1);
List<Resource> serviceRequestResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
// from ORC, OBR
assertThat(serviceRequestResource).hasSize(1);
// Light check that ServiceRequest contains NTE for ORC/OBR; Deep check of NTE in Hl7NoteFHIRConverterTest.
ServiceRequest serviceRequest = ResourceUtils.getResourceServiceRequest(serviceRequestResource.get(0), ResourceUtils.context);
assertThat(serviceRequest.hasNote()).isTrue();
assertThat(serviceRequest.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(serviceRequest.getNote().get(0).getTextElement().getValueAsString()).isEqualTo("TEST ORC/OBR NOTE AA line 1 \nTEST NOTE AA line 2");
assertThat(serviceRequest.getNote().get(0).hasAuthorReference()).isTrue();
List<Resource> documentReferenceResource = ResourceUtils.getResourceList(e, ResourceType.DocumentReference);
// from TXA
assertThat(documentReferenceResource).hasSize(1);
List<Resource> observationResources = ResourceUtils.getResourceList(e, ResourceType.Observation);
// from OBX(not type TX)
assertThat(observationResources).hasSize(1);
// Light check that Observation contains NTE for OBX; Deep check of NTE in Hl7NoteFHIRConverterTest.
Observation observation = ResourceUtils.getResourceObservation(observationResources.get(0), ResourceUtils.context);
// Validate the note contents and reference existance.
assertThat(observation.hasNote()).isTrue();
assertThat(observation.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(observation.getNote().get(0).getTextElement().getValueAsString()).isEqualTo("TEST OBX NOTE BB line 1 \nTEST NOTE BB line 2");
assertThat(observation.getNote().get(0).hasAuthorReference()).isTrue();
// Two Practitioners, one for the serviceRequest, one for the Observation
List<Resource> practitioners = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
// from NTE.4 references
assertThat(practitioners).hasSize(2);
// Confirm that no extra resources are created
assertThat(e.size()).isEqualTo(7);
}
use of org.hl7.fhir.r4.model.Annotation 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);
}
use of org.hl7.fhir.r4.model.Annotation 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.r4.model.Annotation 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.r4.model.Annotation in project quality-measure-and-cohort-service by Alvearie.
the class R4ParameterDefinitionWithDefaultToCohortParameterConverterTest method testAnnotation__shouldThrowException.
@Test(expected = UnsupportedFhirTypeException.class)
public void testAnnotation__shouldThrowException() {
ParameterDefinition parameterDefinition = getBaseParameterDefinition("Annotation");
Annotation fhirValue = new Annotation();
parameterDefinition.addExtension(CDMConstants.PARAMETER_DEFAULT_URL, fhirValue);
R4ParameterDefinitionWithDefaultToCohortParameterConverter.toCohortParameter(parameterDefinition);
}
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