use of org.hl7.fhir.r4b.model.Bundle.BundleEntryComponent in project hl7v2-fhir-converter by LinuxForHealth.
the class HL7OMLMessageTest method testOMLO21WithSpecimen.
@Test
public void testOMLO21WithSpecimen() throws IOException {
String hl7message = "MSH|^~\\&||Test System|||20210917110100||OML^O21^OML_O21|||2.6\r" + "PID|1||7659afb9-0dfc-d744-1f40-5b9314807108^^^^MR||Feeney^Sam^^^^^L|||M||||||||\r" + "ORC|NW|8125550e-04db-11ec-a9a8-086d41d421ca^^ID^UUID||||||||||\r" + "OBR|1|8125550e-04db-11ec-a9a8-086d41d421ca^^ID^UUID||58410-2^CBC panel - Blood by Automated count^LN||||||||||||\r" + "SPM|1|SpecimenID||BLD|||||||P||||||201410060535|201410060821||Y||||||1\r";
String json = ftv.convert(hl7message, OPTIONS_PRETTYPRINT);
assertThat(json).isNotBlank();
IBaseResource bundleResource = context.getParser().parseResource(json);
assertThat(bundleResource).isNotNull();
Bundle b = (Bundle) bundleResource;
List<BundleEntryComponent> e = b.getEntry();
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
// from PID
assertThat(patientResource).hasSize(1);
List<Resource> specimenResource = ResourceUtils.getResourceList(e, ResourceType.Specimen);
// from SPM
assertThat(specimenResource).hasSize(1);
List<Resource> serviceResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
// from ORC
assertThat(serviceResource).hasSize(1);
List<Resource> diagnosticresource = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
// from OBR
assertThat(diagnosticresource).hasSize(1);
// Verify the specimen reference
DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticresource.get(0), context);
List<Reference> spmRef = diag.getSpecimen();
assertThat(spmRef.isEmpty()).isFalse();
// from SPM
assertThat(spmRef).hasSize(1);
assertThat(spmRef.get(0).isEmpty()).isFalse();
// Confirm that there are no extra resources
assertThat(e.size()).isEqualTo(4);
}
use of org.hl7.fhir.r4b.model.Bundle.BundleEntryComponent in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7CustomMessageTest method getBundleEntryFromHL7Message.
// Need custom convert sequence with options that turn off FHIR validation.
private static List<BundleEntryComponent> getBundleEntryFromHL7Message(String hl7message) {
// Testing loading of config which happens once per instantiation
HL7ToFHIRConverter ftv = new HL7ToFHIRConverter();
// Need custom options that turn off FHIR validation.
String json = ftv.convert(hl7message, OPTIONS);
assertThat(json).isNotNull();
FHIRContext context = new FHIRContext();
IBaseResource bundleResource = context.getParser().parseResource(json);
assertThat(bundleResource).isNotNull();
Bundle b = (Bundle) bundleResource;
return b.getEntry();
}
use of org.hl7.fhir.r4b.model.Bundle.BundleEntryComponent in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7FinancialInsuranceTest method testInsuranceCoverageByRelatedFields.
// 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
// The breadth of this test is sufficent for multiple message type coverage, so other tests are not parameterized.
@ValueSource(strings = { "DFT^P03^DFT_P03", "VXU^V04^VXU_V04", "ADT^A01^ADT_A01", "ADT^A03^ADT_A03", // ADT^A04 uses structure ADT_A01
"ADT^A04^ADT_A01", // ADT^A08 uses structure ADT_A01
"ADT^A08^ADT_A01", // ADT^A28 uses structure ADT_A05
"ADT^A28^ADT_A05", // ADT^A31 uses structure ADT_A05
"ADT^A31^ADT_A05" })
// Also test IN2.2 Social Security number
void testInsuranceCoverageByRelatedFields(String messageType) throws IOException {
String hl7message = "MSH|^~\\&|||||20151008111200||" + messageType + "|MSGID000001|T|2.6|||||||||\n" + "EVN||20210407191342||||||\n" + "PID|||MR1^^^XYZ^MR||DOE^JANE^|||F||||||||||||||||||||||\n" + "PV1||I||||||||||||||||||||||||||||||||||||||||||\n" + // FT1.7 is required transaction code (currently not used)
"FT1||||20201231145045||CG|FAKE|||||||||||||||||||||||||||||||||||||\n" + // IN1.2.4, IN1.2.6 to second XV Coverage.identifier
"IN1|1|Value1^^System3^Value4^^System6" + // IN1.5 to 15 NOT REFERENCED (See test testBasicInsuranceCoverageFields)
"|IdValue1^^^IdSystem4^^^^|Large Blue Organization|||||||||||" + // IN1.23 through IN1.35 NOT REFERENCED
"|DoeFake^Judy^^^Rev.|PAR|19780429|19 Rose St^^Faketown^CA^ZIP5||||||||||||||||" + // IN1.50 through IN1.53 NOT REFERENCED
"|MEMBER36|||||||F|||Value46|||J494949^^^Large HMO^XX||||\n" + // IN2.9 through IN2.60 not used
"IN2||777-88-9999||||MEDICARE06||MEDICAID08|| |||||||||| ||||||||||| |||||||||| |||||||||| ||||||||||" + // IN2.63.18 to Organization Contact telecom .rank
"MEMBER61||^^^^^555^7677777^^^^^^20201231145045^20211231145045^^^^1|";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
List<Resource> encounters = ResourceUtils.getResourceList(e, ResourceType.Encounter);
// From PV1
assertThat(encounters).hasSize(1);
List<Resource> patients = ResourceUtils.getResourceList(e, ResourceType.Patient);
// From PID
assertThat(patients).hasSize(1);
Patient patient = (Patient) patients.get(0);
String patientId = patient.getId();
// From PID.3, IN1.49, IN2.6, IN2.8
assertThat(patient.getIdentifier()).hasSize(4);
Identifier patientIdentifier = patient.getIdentifier().get(0);
// PID.3.1
assertThat(patientIdentifier.getValue()).isEqualTo("MR1");
// PID.3.4
assertThat(patientIdentifier.getSystem()).isEqualTo("urn:id:XYZ");
DatatypeUtils.checkCommonCodeableConceptAssertions(patientIdentifier.getType(), "MR", "Medical record number", "http://terminology.hl7.org/CodeSystem/v2-0203", // PID.3.5
null);
patientIdentifier = patient.getIdentifier().get(1);
// IN1.49.1
assertThat(patientIdentifier.getValue()).isEqualTo("J494949");
// IN1.49.4
assertThat(patientIdentifier.getSystem()).isEqualTo("urn:id:Large_HMO");
DatatypeUtils.checkCommonCodeableConceptAssertions(patientIdentifier.getType(), "XX", null, "http://terminology.hl7.org/CodeSystem/v2-0203", // IN1.49.5
null);
patientIdentifier = patient.getIdentifier().get(2);
// IN2.8
assertThat(patientIdentifier.getValue()).isEqualTo("MEDICAID08");
// No system for IN2.8
assertThat(patientIdentifier.hasSystem()).isFalse();
DatatypeUtils.checkCommonCodeableConceptAssertions(patientIdentifier.getType(), "MA", "Patient Medicaid number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
patientIdentifier = patient.getIdentifier().get(3);
// IN2.6
assertThat(patientIdentifier.getValue()).isEqualTo("MEDICARE06");
// No system for IN2.6
assertThat(patientIdentifier.hasSystem()).isFalse();
DatatypeUtils.checkCommonCodeableConceptAssertions(patientIdentifier.getType(), "MC", "Patient's Medicare number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
List<Resource> organizations = ResourceUtils.getResourceList(e, ResourceType.Organization);
// From Payor created by IN1
assertThat(organizations).hasSize(1);
List<Resource> coverages = ResourceUtils.getResourceList(e, ResourceType.Coverage);
// From IN1 segment
assertThat(coverages).hasSize(1);
Coverage coverage = (Coverage) coverages.get(0);
// Confirm Coverage Identifiers - Order matches order of identifier_X in Coverage.yml
// XV, XV, XV, MB, MA, MC, SN
assertThat(coverage.getIdentifier()).hasSize(7);
// IN1.2.1
assertThat(coverage.getIdentifier().get(0).getValue()).isEqualTo("Value1");
// IN1.2.3
assertThat(coverage.getIdentifier().get(0).getSystem()).isEqualTo("urn:id:System3");
// No use, here
assertThat(coverage.getIdentifier().get(0).getUse()).isNull();
DatatypeUtils.checkCommonCodeableConceptAssertions(coverage.getIdentifier().get(0).getType(), "XV", "Health Plan Identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
// IN1.2.4
assertThat(coverage.getIdentifier().get(1).getValue()).isEqualTo("Value4");
// IN1.2.6
assertThat(coverage.getIdentifier().get(1).getSystem()).isEqualTo("urn:id:System6");
// No use, here
assertThat(coverage.getIdentifier().get(1).getUse()).isNull();
DatatypeUtils.checkCommonCodeableConceptAssertions(coverage.getIdentifier().get(1).getType(), "XV", "Health Plan Identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
// IN1.46
assertThat(coverage.getIdentifier().get(2).getValue()).isEqualTo("Value46");
// No system, here
assertThat(coverage.getIdentifier().get(2).getSystem()).isNull();
// Use is enumeration "old"
assertThat(coverage.getIdentifier().get(2).getUseElement().getCode()).hasToString("old");
DatatypeUtils.checkCommonCodeableConceptAssertions(coverage.getIdentifier().get(2).getType(), "XV", "Health Plan Identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
// IN2.61 takes priority over IN1.36
assertThat(coverage.getIdentifier().get(3).getValue()).isEqualTo("MEMBER61");
// No system, here
assertThat(coverage.getIdentifier().get(3).getSystem()).isNull();
// No use, here
assertThat(coverage.getIdentifier().get(3).getUse()).isNull();
DatatypeUtils.checkCommonCodeableConceptAssertions(coverage.getIdentifier().get(3).getType(), "MB", "Member Number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
// IN2.8
assertThat(coverage.getIdentifier().get(4).getValue()).isEqualTo("MEDICAID08");
// No system, here
assertThat(coverage.getIdentifier().get(4).getSystem()).isNull();
// No use, here
assertThat(coverage.getIdentifier().get(4).getUse()).isNull();
DatatypeUtils.checkCommonCodeableConceptAssertions(coverage.getIdentifier().get(4).getType(), "MA", "Patient Medicaid number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
// IN2.6
assertThat(coverage.getIdentifier().get(5).getValue()).isEqualTo("MEDICARE06");
// No system, here
assertThat(coverage.getIdentifier().get(5).getSystem()).isNull();
// No use, here
assertThat(coverage.getIdentifier().get(5).getUse()).isNull();
DatatypeUtils.checkCommonCodeableConceptAssertions(coverage.getIdentifier().get(5).getType(), "MC", "Patient's Medicare number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
// IN1.36
assertThat(coverage.getIdentifier().get(6).getValue()).isEqualTo("MEMBER36");
// No system, here
assertThat(coverage.getIdentifier().get(6).getSystem()).isNull();
// No use, here
assertThat(coverage.getIdentifier().get(6).getUse()).isNull();
DatatypeUtils.checkCommonCodeableConceptAssertions(coverage.getIdentifier().get(6).getType(), "SN", "Subscriber Number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
// Confirm Coverage Beneficiary references to Patient, and Payor references to Organization
assertThat(coverage.getBeneficiary().getReference()).isEqualTo(patientId);
assertThat(coverage.getPayorFirstRep().getReference()).isEqualTo(organizations.get(0).getId());
// Expect one RelatedPerson
List<Resource> relatedPersons = ResourceUtils.getResourceList(e, ResourceType.RelatedPerson);
// From IN1.16 through IN1.19; IN1.43; INI.49
assertThat(relatedPersons).hasSize(1);
RelatedPerson related = (RelatedPerson) relatedPersons.get(0);
// Check RelatedPerson identifiers
assertThat(related.getIdentifier()).hasSize(2);
// IN1.49.1
assertThat(related.getIdentifier().get(0).getValue()).isEqualTo("J494949");
// IN1.49.4
assertThat(related.getIdentifier().get(0).getSystem()).isEqualTo("urn:id:Large_HMO");
// IN1.49.5
DatatypeUtils.checkCommonCodeableConceptAssertions(// IN1.49.5
related.getIdentifier().get(0).getType(), // IN1.49.5
"XX", // Display value looked up from code 'XX'
"Organization identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
// IN2.2
assertThat(related.getIdentifier().get(1).getValue()).isEqualTo("777-88-9999");
// No system to assign
assertThat(related.getIdentifier().get(1).hasSystem()).isFalse();
DatatypeUtils.checkCommonCodeableConceptAssertions(related.getIdentifier().get(1).getType(), "SS", "Social Security number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
// Check RelatedPerson name. IN1.16 name is standard XPN, tested exhaustively in other tests.
assertThat(related.getName()).hasSize(1);
HumanName relatedName = related.getName().get(0);
// IN1.16.1
assertThat(relatedName.getFamily()).isEqualTo("DoeFake");
// IN1.16.2
assertThat(relatedName.getGiven().get(0).getValueAsString()).isEqualTo("Judy");
// IN1.16.6
assertThat(relatedName.getPrefixAsSingleString()).hasToString("Rev.");
// from IN1.16 aggregate
assertThat(relatedName.getText()).isEqualTo("Rev. Judy DoeFake");
// Check RelatedPerson birth and gender
// IN1.18
assertThat(related.getBirthDateElement().toString()).containsPattern("1978-04-29");
Enumerations.AdministrativeGender gen = related.getGender();
// IN1.43
assertThat(gen).isNotNull().isEqualTo(Enumerations.AdministrativeGender.FEMALE);
// Check the RelatedPerson address. IN1.19 is a standard XAD address, which is tested exhaustively in other tests.
assertThat(related.getAddress()).hasSize(1);
assertThat(related.getAddress().get(0).getLine().get(0).getValueAsString()).isEqualTo(// IN1.19.1
"19 Rose St");
// IN1.19.3
assertThat(related.getAddress().get(0).getCity()).isEqualTo("Faketown");
// IN1.19.4
assertThat(related.getAddress().get(0).getState()).isEqualTo("CA");
// IN1.19.5
assertThat(related.getAddress().get(0).getPostalCode()).isEqualTo("ZIP5");
// Check RelatedPerson telecom. IN2.63 is standard XTN, tested exhaustively in other tests.
// telecom is type ContactPoint
ContactPoint contactPoint = related.getTelecomFirstRep();
// default type hardcoded.
assertThat(contactPoint.getSystemElement().getCode()).hasToString("phone");
// Hard-coded to home. IN2.63.2 is not mapped (ignored).
assertThat(contactPoint.getUseElement().getCode()).isEqualTo("home");
// Hard-coded to home. IN2.63.2 is not mapped (ignored).
;
// IN2.63.6, IN2.63.7 via getFormattedTelecomNumberValue
assertThat(contactPoint.getValue()).hasToString("(555) 767 7777");
// IN2.63.13
assertThat(contactPoint.getPeriod().getStartElement().toString()).containsPattern("2020-12-31T14:50:45");
// IN2.63.14
assertThat(contactPoint.getPeriod().getEndElement().toString()).containsPattern("2021-12-31T14:50:45");
// IN2.63.18
assertThat(contactPoint.getRank()).isEqualTo(1);
// Check coverage relationship
DatatypeUtils.checkCommonCodeableConceptAssertions(coverage.getRelationship(), "child", "Child", "http://terminology.hl7.org/CodeSystem/subscriber-relationship", // IN1.17
null);
// Check relatedPerson relationship
assertThat(related.getRelationship()).hasSize(1);
DatatypeUtils.checkCommonCodeableConceptAssertions(related.getRelationship().get(0), "PRN", "parent", "http://terminology.hl7.org/CodeSystem/v3-RoleCode", // IN1.17
null);
// Confirm the Coverage (subscriber) references the RelatedPerson
assertThat(coverage.getSubscriber().getReference()).isEqualTo(related.getId());
// Confirm the RelatedPerson references the Patient
assertThat(related.getPatient().getReference()).isEqualTo(patientId);
// Confirm coverage.Order
// IN1.1 backup for missing IN1.22
assertThat(coverage.getOrder()).isEqualTo(1);
// Confirm there are no unaccounted for resources
// Expected: Coverage, Organization, Patient, Encounter, RelatedPerson
assertThat(e).hasSize(5);
}
use of org.hl7.fhir.r4b.model.Bundle.BundleEntryComponent in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7FinancialInsuranceTest method testInsuranceCoverageUnknownRelationship.
@Test
// As part of the test, there is a valid code in IN2.72 that would create a related person, but it should be ignored.
void testInsuranceCoverageUnknownRelationship() throws IOException {
String hl7message = "MSH|^~\\&|TEST|TEST|||20220101120000||DFT^P03|1234|P|2.6\n" + // + "EVN||20210407191342||||||\n"
"PID|||workers_comp^^^XYZ^MR||DOE^JANE^|||F||||||||||||||||||||||\n" + "PV1||I||||||||||||||||||||||||||||||||||||||||||\n" + // FT1.7 is required transaction code (currently not used)
"FT1||||20201231145045||CG|FAKE|||||||||||||||||||||||||||||||||||||\n" + // IN1.2.4, IN1.2.6 to second XV Coverage.identifier
"IN1|1|Value1^^System3^Value4^^System6" + // IN1.5 through 15 NOT REFERENCED (Tested in testBasicInsuranceCoverageFields)
"|IdValue1^^^IdSystem4^^^^|Large Blue Organization|||||||||||" + // IN1.18 through IN1.53 NOT REFERENCED
"||05||||||||||||||||||||||||||||||||||||\n" + // IN2.1 through IN2.71 NOT REFERENCED
"IN2||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||" + // A valid code in IN2.72 does not take priority over an invalid code in IN1.17.
"04|\n";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
List<Resource> encounters = ResourceUtils.getResourceList(e, ResourceType.Encounter);
// From PV1
assertThat(encounters).hasSize(1);
List<Resource> patients = ResourceUtils.getResourceList(e, ResourceType.Patient);
// From PID
assertThat(patients).hasSize(1);
Patient patient = (Patient) patients.get(0);
String patientId = patient.getId();
List<Resource> organizations = ResourceUtils.getResourceList(e, ResourceType.Organization);
// From Payor created by IN1
assertThat(organizations).hasSize(1);
Organization org = (Organization) organizations.get(0);
// Check organization Id's
assertThat(org.getIdentifier()).hasSize(1);
// Org identifiers checked deeply in other tests
List<Resource> coverages = ResourceUtils.getResourceList(e, ResourceType.Coverage);
// From IN1 segment
assertThat(coverages).hasSize(1);
Coverage coverage = (Coverage) coverages.get(0);
// Confirm Coverage Identifiers
// XV, XV
assertThat(coverage.getIdentifier()).hasSize(2);
// Coverage Identifiers deep check in testBasicInsuranceCoverageFields
// Because the relationship is 05, an unknown code, no subscriber is created
assertThat(coverage.hasSubscriber()).isFalse();
// Confirm Coverage Beneficiary references to Patient, and Payor references to Organization
assertThat(coverage.getBeneficiary().getReference()).isEqualTo(patientId);
assertThat(coverage.getPayorFirstRep().getReference()).isEqualTo(organizations.get(0).getId());
// Expect no RelatedPerson because IN1.17 was an unknown code
List<Resource> relatedPersons = ResourceUtils.getResourceList(e, ResourceType.RelatedPerson);
// No related person should be created because IN1.17 was an unknown code
assertThat(relatedPersons).isEmpty();
// Check coverage.relationship (from SubscriberRelationship mapping)
DatatypeUtils.checkCommonCodeableConceptAssertions(coverage.getRelationship(), "05", null, null, // IN1.17, because it is unkown there is no system or display.
null);
// Confirm there are no unaccounted for resources
// Expected: Coverage, Organization, Patient, Encounter
assertThat(e).hasSize(4);
}
use of org.hl7.fhir.r4b.model.Bundle.BundleEntryComponent 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");
}
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