use of org.hl7.fhir.dstu2.model.Reference 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.dstu2.model.Reference 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.dstu2.model.Reference 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.dstu2.model.Reference in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7OrderRequestFHIRConversionTest method testMDMT02ServiceRequest.
// This test assures the MDM_T02 is properly enabled.
// It focuses on _differences_ in MDM not tested above, then does general confirmation of other fields
@Test
void testMDMT02ServiceRequest() {
String hl7message = "MSH|^~\\&|Epic|PQA|WHIA|IBM|20170920141233||MDM^T02^MDM_T02|M1005|D|2.6\r" + "EVN|T02|20170920141233|||\r" + "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\r" + "PV1|1|I|||||||||||||||||||||||||||||||||||||\r" + // ORC.15 is occurenceDateTime
"ORC|NW|P1005|F1005|P1005|SC|D|1||20170920141233|||1212^docProvider^docOrdering|||20170920141233|\r" + // OBR.31 used for reason code
"OBR|1|P1005|F1005|71260^CT Chest without contrast^ICD10|||||||||||||||||||||||||||exam reason ID^PREAURICULAR EDEMA text||||\r";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
List<Resource> serviceRequestList = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
assertThat(serviceRequestList).hasSize(1);
ServiceRequest serviceRequest = ResourceUtils.getResourceServiceRequest(serviceRequestList.get(0), context);
// Expect 3 identifiers (VN, PLAC, FILL)
assertThat(serviceRequest.hasIdentifier()).isTrue();
assertThat(serviceRequest.getIdentifier()).hasSize(3);
// ORC.12 should create an ServiceRequest.requester reference
assertThat(serviceRequest.hasRequester()).isTrue();
assertThat(serviceRequest.getRequester().hasDisplay()).isTrue();
assertThat(serviceRequest.getRequester().getDisplay()).isEqualTo("docOrdering docProvider");
assertThat(serviceRequest.getRequester().hasReference()).isTrue();
String requesterRef = serviceRequest.getRequester().getReference();
Practitioner pract = ResourceUtils.getSpecificPractitionerFromBundleEntriesList(e, requesterRef);
// Confirm that the matching practitioner by ID has the correct content (simple validation)
// Should be ORC.12.1
assertThat(pract.getIdentifierFirstRep().getValue()).isEqualTo("1212");
// OBR.31 is the reason code
assertThat(serviceRequest.hasReasonCode()).isTrue();
assertThat(serviceRequest.getReasonCode()).hasSize(1);
DatatypeUtils.checkCommonCodeableConceptAssertions(serviceRequest.getReasonCodeFirstRep(), "exam reason ID", "PREAURICULAR EDEMA text", null, "PREAURICULAR EDEMA text");
// OBR.4 is the code
assertThat(serviceRequest.hasCode()).isTrue();
DatatypeUtils.checkCommonCodeableConceptAssertions(serviceRequest.getCode(), "71260", "CT Chest without contrast", "http://hl7.org/fhir/sid/icd-10-cm", "CT Chest without contrast");
// General over valdation of presence of fields:
// ORC.5
assertThat(serviceRequest.hasStatus()).isTrue();
assertThat(serviceRequest.hasIntent()).isTrue();
assertThat(serviceRequest.hasSubject()).isTrue();
// ORC.9
assertThat(serviceRequest.hasAuthoredOn()).isTrue();
}
use of org.hl7.fhir.dstu2.model.Reference in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7OrderRequestFHIRConversionTest method testBroadORCPlusOBRFields2.
@Test
void testBroadORCPlusOBRFields2() {
String hl7message = "MSH|^~\\&|||||20180924152907|34001|ORU^R01^ORU_R01|213|T|2.6|||||||||||\n" + // PID.18 is empty, MSH.7 will be used as identifier visit number
"PID|||1234^^^^MR||DOE^JANE^|||F||||||||||||||||||||||\n" + // PV1.19 is empty, MSH.7 will be used as identifier visit number
"PV1|1|E|||||||||||||||||||||||||||||||||||||||||||\n" + // ORC.5 with purposely bad code to see that 'unknown' is result
"ORC|RE|248648498^|248648498^||ZZ||||20120628071200||||||||||||||||||||||\n" + "OBR|1|248648498^|248648498^|83036E^HEMOGLOBIN A1C^PACSEAP^^^^^^HEMOGLOBIN A1C|||||||L||||||||||||||F||^^^20120606120606|||||||||||||||||||||||\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> 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();
assertThat(serviceRequest.hasIdentifier()).isTrue();
assertThat(serviceRequest.getIdentifier()).hasSize(3);
// Identifier 1: visit number should be set by in this test by tertiary MSH.7
// See notes about identifier testing in previous tests
Identifier identifier = serviceRequest.getIdentifier().get(0);
String value = identifier.getValue();
String system = identifier.getSystem();
// MSH.7 as a string, not as a date
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);
// OBR.27[0].4 should create an ServiceRequest.occurrenceDateTime date
assertThat(serviceRequest.hasOccurrenceDateTimeType()).isTrue();
assertThat(serviceRequest.getOccurrenceDateTimeType().toString()).containsPattern("2012-06-06T12:06:06");
// // ORC.5 creates the serviceRequest.status() purposely an unknown code
assertThat(serviceRequest.hasStatus()).isTrue();
assertThat(serviceRequest.getStatusElement().getCode()).isEqualTo("unknown");
}
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