use of org.hl7.fhir.r4.model.codesystems.ResourceTypes.ENCOUNTER in project hl7v2-fhir-converter by LinuxForHealth.
the class HL7EventTypeFHIRConversionTest method validate_evn_segment.
@Test
void validate_evn_segment() {
String hl7message = "MSH|^~\\&|||||||ADT^A01^ADT_A01|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6||||||\r" + // + "EVN||||851||20210319134735|\r" // TODO, not working with this value
"EVN||||O||20210319134735|\r" + "PV1|1|I||R|||||||||R|1||||||||||||||||||||||||||||||||||||||";
String json = ftv.convert(hl7message, OPTIONS);
assertThat(json).isNotBlank();
FHIRContext context = new FHIRContext(true, false);
IBaseResource bundleResource = context.getParser().parseResource(json);
assertThat(bundleResource).isNotNull();
Bundle b = (Bundle) bundleResource;
List<BundleEntryComponent> e = b.getEntry();
// Find the encounter from the FHIR bundle.
List<Resource> encounterResource = e.stream().filter(v -> ResourceType.Encounter == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
assertThat(encounterResource).hasSize(1);
Encounter encounter = (Encounter) encounterResource.get(0);
// ENV.4 is used for reasonCode
List<CodeableConcept> reasonCodes = encounter.getReasonCode();
assertEquals(1, reasonCodes.size());
CodeableConcept encounterReason = encounter.getReasonCodeFirstRep();
Coding encounterReasonCoding = encounterReason.getCodingFirstRep();
// assertThat(encounterReasonCoding.getCode()).isEqualTo("851"); // TODO, should be able to use user-defined values
assertThat(encounterReasonCoding.getCode()).isEqualTo("O");
// EVN.6 is used for start period (with no end) if there is no PV1.44
Base period = encounter.getNamedProperty("period").getValues().get(0);
String startPeriod = period.getNamedProperty("start").getValues().get(0).toString();
int endPeriodSize = period.getNamedProperty("end").getValues().size();
assertThat(startPeriod).isEqualTo("DateTimeType[2021-03-19T13:47:35+08:00]");
assertThat(endPeriodSize).isZero();
}
use of org.hl7.fhir.r4.model.codesystems.ResourceTypes.ENCOUNTER in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7MessageTest method test_encounter_with_observation.
@Test
void test_encounter_with_observation() throws IOException {
ResourceModel rsm = ResourceReader.getInstance().generateResourceModel("resource/Patient");
HL7FHIRResourceTemplateAttributes attributes = new HL7FHIRResourceTemplateAttributes.Builder().withResourceName("Patient").withResourceModel(rsm).withSegment("PID").withIsReferenced(true).withRepeats(false).build();
HL7FHIRResourceTemplate patient = new HL7FHIRResourceTemplate(attributes);
ResourceModel encounter = ResourceReader.getInstance().generateResourceModel("resource/Encounter");
HL7FHIRResourceTemplateAttributes attributesEncounter = new HL7FHIRResourceTemplateAttributes.Builder().withResourceName("Encounter").withResourceModel(encounter).withSegment("PV1").withIsReferenced(true).withRepeats(false).withAdditionalSegments(Lists.newArrayList("PV2", "OBX")).build();
HL7FHIRResourceTemplate encounterFH = new HL7FHIRResourceTemplate(attributesEncounter);
ResourceModel obsModel = ResourceReader.getInstance().generateResourceModel("resource/Observation");
HL7FHIRResourceTemplateAttributes attributesObs = new HL7FHIRResourceTemplateAttributes.Builder().withResourceName("Observation").withResourceModel(obsModel).withSegment("OBX").withIsReferenced(true).withRepeats(true).build();
HL7FHIRResourceTemplate obsTemplate = new HL7FHIRResourceTemplate(attributesObs);
HL7MessageModel message = new HL7MessageModel("ADT", Lists.newArrayList(patient, encounterFH, obsTemplate));
String hl7message = "MSH|^~\\&|SE050|050|PACS|050|20120912011230||ADT^A01|102|T|2.6|||AL|NE|764|ASCII||||||^4086::132:2A57:3C28^IPv6\r" + "EVN||201209122222\r" + "PID|0010||PID1234^5^M11^A^MR^HOSP~1234568965^^^USA^SS||DOE^JOHN^A^||19800202|F||W|111 TEST_STREET_NAME^^TEST_CITY^NY^111-1111^USA||(905)111-1111|||S|ZZ|12^^^124|34-13-312||||TEST_BIRTH_PLACE\r" + "PV1|1|ff|yyy|EL|ABC||200^ATTEND_DOC_FAMILY_TEST^ATTEND_DOC_GIVEN_TEST|201^REFER_DOC_FAMILY_TEST^REFER_DOC_GIVEN_TEST|202^CONSULTING_DOC_FAMILY_TEST^CONSULTING_DOC_GIVEN_TEST|MED|||||B6|E|272^ADMITTING_DOC_FAMILY_TEST^ADMITTING_DOC_GIVEN_TEST||48390|||||||||||||||||||||||||201409122200|20150206031726\r" + "OBX|1|NM|0135-4^TotalProtein||7.3|gm/dl|5.9-8.4||||F|||||2740^TRDSE^Janetary~2913^MRTTE^Darren^F~3065^MGHOBT^Paul^J~4723^LOTHDEW^Robert^L|\r" + "AL1|1|DRUG|00000741^OXYCODONE||HYPOTENSION\r" + "AL1|2|DRUG|00001433^TRAMADOL||SEIZURES~VOMITING\r";
String json = message.convert(hl7message, engine);
LOGGER.debug(json);
IBaseResource bundleResource = context.getParser().parseResource(json);
assertThat(bundleResource).isNotNull();
Bundle b = (Bundle) bundleResource;
List<BundleEntryComponent> e = b.getEntry();
List<Resource> obsResource = e.stream().filter(v -> ResourceType.Observation == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
assertThat(obsResource).hasSize(1);
List<Resource> pracResource = e.stream().filter(v -> ResourceType.Practitioner == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
assertThat(pracResource).hasSize(8);
List<Resource> encounterResource = e.stream().filter(v -> ResourceType.Encounter == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
assertThat(encounterResource).hasSize(1);
Encounter encounterRes = ResourceUtils.getResourceEncounter(encounterResource.get(0), context);
Reference patRef = encounterRes.getSubject();
assertThat(patRef.isEmpty()).isFalse();
List<Reference> obsRef = encounterRes.getReasonReference();
assertThat(obsRef).hasSize(1);
}
use of org.hl7.fhir.r4.model.codesystems.ResourceTypes.ENCOUNTER in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7MessageTest method test_patient_encounter.
@Test
void test_patient_encounter() throws IOException {
ResourceModel rsm = ResourceReader.getInstance().generateResourceModel("resource/Patient");
HL7FHIRResourceTemplateAttributes attributes = new HL7FHIRResourceTemplateAttributes.Builder().withResourceName("Patient").withResourceModel(rsm).withSegment("PID").withIsReferenced(true).withRepeats(false).build();
HL7FHIRResourceTemplate patient = new HL7FHIRResourceTemplate(attributes);
ResourceModel encounter = ResourceReader.getInstance().generateResourceModel("resource/Encounter");
HL7FHIRResourceTemplateAttributes attributesEncounter = new HL7FHIRResourceTemplateAttributes.Builder().withResourceName("Encounter").withResourceModel(encounter).withSegment("PV1").withIsReferenced(true).withRepeats(false).withAdditionalSegments(Lists.newArrayList("PV2")).build();
HL7FHIRResourceTemplate encounterFH = new HL7FHIRResourceTemplate(attributesEncounter);
HL7MessageModel message = new HL7MessageModel("ADT", Lists.newArrayList(patient, encounterFH));
String hl7message = "MSH|^~\\&|SE050|050|PACS|050|201209121212||ADT^A01|102|T|2.7|||AL|NE\r" + "EVN||201209122222\r" + "PID|||1234^^^^SR^20021212^20200120~1234-12^^^^LR^~3872^^^^MR~221345671^^^^SS^~430078856^^^^MA^||KENNEDY^JOHN^FITZGERALD^JR^^^L| BOUVIER^^^^^^M|19900607|M|KENNEDY^BABYBOY^^^^^^B|2106-3^linuxforhealthTE^HL70005|123 MAIN ST^APT 3B^LEXINGTON^MA^00210^^M^MSA CODE^MA034~345 ELM\r" + "PV1|1|ff|yyy|EL|||200^ATTEND_DOC_FAMILY_TEST^ATTEND_DOC_GIVEN_TEST|201^REFER_DOC_FAMILY_TEST^REFER_DOC_GIVEN_TEST|202^CONSULTING_DOC_FAMILY_TEST^CONSULTING_DOC_GIVEN_TEST|MED|||||B6|E|272^ADMITTING_DOC_FAMILY_TEST^ADMITTING_DOC_GIVEN_TEST||48390|||||||||||||||||||||||||201409122200|20000206031726\r" + "AL1|0001|DA|98798^problem|SV|sneeze|20120808\r";
String json = message.convert(hl7message, engine);
assertThat(json).isNotBlank();
IBaseResource bundleResource = context.getParser().parseResource(json);
assertThat(bundleResource).isNotNull();
Bundle b = (Bundle) bundleResource;
List<BundleEntryComponent> e = b.getEntry();
List<Resource> patientResource = e.stream().filter(v -> ResourceType.Patient == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
assertThat(patientResource).hasSize(1);
List<Resource> encounterResource = e.stream().filter(v -> ResourceType.Encounter == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
assertThat(encounterResource).hasSize(1);
Encounter enc = ResourceUtils.getResourceEncounter(encounterResource.get(0), context);
Reference ref = enc.getSubject();
assertThat(ref.isEmpty()).isFalse();
}
use of org.hl7.fhir.r4.model.codesystems.ResourceTypes.ENCOUNTER in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ORUMessageTest method test_oru_with_specimen.
// 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")
@Test
void test_oru_with_specimen() throws IOException {
String hl7message = "MSH|^~\\\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|200603081747|security|ORU^R01|MSGID000005|T|2.6\r" + "PID||45483|45483||SMITH^SUZIE^||20160813|M|||123 MAIN STREET^^SCHENECTADY^NY^12345||(123)456-7890|||||^^^T||||||||||||\r" + "OBR|1||986^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|1051-2^New Born Screening^LN|||20151009173644|||||||||||||002|||||F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^||||3065^Mahoney^Paul^J|\r" + "OBX|1|ST|TS-F-01-002^Endocrine Disorders^L||obs report||||||F\r" + "SPM|1|SpecimenID||BLD|||||||P||||||201410060535|201410060821||Y||||||1\r";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
// Verify that the right resources are created
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
assertThat(patientResource).hasSize(1);
List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
assertThat(diagnosticReport).hasSize(1);
List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
assertThat(servReqResource).hasSize(1);
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
assertThat(obsResource).hasSize(1);
List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
assertThat(practitionerResource).hasSize(1);
List<Resource> specimenResource = ResourceUtils.getResourceList(e, ResourceType.Specimen);
assertThat(specimenResource).hasSize(1);
// Expecting only the above resources, no extras!
assertThat(e).hasSize(6);
// /////////////////////////////////////////
// Now confirm content of the diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
// Verify status from OBR.25
assertThat(diag.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag.getCategory()).isEmpty();
// Verify code from OBR.4
assertThat(diag.hasCode()).isTrue();
List<Coding> codings = diag.getCode().getCoding();
assertThat(codings).hasSize(1);
Coding coding = codings.get(0);
assertThat(coding.hasDisplay()).isTrue();
assertThat(coding.getDisplay()).hasToString("New Born Screening");
assertThat(coding.hasCode()).isTrue();
assertThat(coding.getCode()).hasToString("1051-2");
assertThat(coding.hasSystem()).isTrue();
assertThat(coding.getSystem()).hasToString("http://loinc.org");
// Verify encounter reference
assertThat(diag.getEncounter().isEmpty()).isTrue();
// Verify subject reference
assertThat(diag.getSubject().isEmpty()).isFalse();
// Verify effectiveDateTime from OBR.7 and OBR.8
// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2015-10-09T17:36:44+08:00");
// Verify issued from OBR.22
assertThat(diag.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag.getResultsInterpreter()).hasSize(1);
// Verify basedOn is ref to the ServiceRequest created for ORC or OBR
assertThat(diag.getBasedOn()).hasSize(1);
assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
// Verify specimen reference
List<Reference> spmRef = diag.getSpecimen();
assertThat(spmRef).hasSize(1);
assertThat(spmRef.get(0).isEmpty()).isFalse();
// Verify result reference
List<Reference> obsRef = diag.getResult();
assertThat(obsRef).hasSize(1);
assertThat(obsRef.get(0).isEmpty()).isFalse();
// Verify presentedForm from OBX of type ST - No attachments expected because OBX of type not TX creates an Observation.
List<Attachment> attachments = diag.getPresentedForm();
Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
// //////////////////////////////////
for (Resource res : obsResource) {
// Verify encounter reference
Observation obs = (Observation) res;
assertThat(obs.getEncounter().isEmpty()).isTrue();
// Verify subject reference to Patient exists
assertThat(obs.getSubject().isEmpty()).isFalse();
assertThat(obs.getSubject().getReference().substring(0, 8)).isEqualTo("Patient/");
}
}
use of org.hl7.fhir.r4.model.codesystems.ResourceTypes.ENCOUNTER in project hl7v2-fhir-converter by LinuxForHealth.
the class Hl7ORUMessageTest method test_oru_with_multiple_reports.
// 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")
@Test
void test_oru_with_multiple_reports() throws IOException {
String hl7message = "MSH|^~\\\\&|SendTest1|Sendfac1|Receiveapp1|Receivefac1|200603081747|security|ORU^R01|MSGID000005|T|2.6\r" + "PID||45483|45483||SMITH^SUZIE^||20160813|M|||123 MAIN STREET^^SCHENECTADY^NY^12345||(123)456-7890|||||^^^T||||||||||||\r" + "OBR|1||986^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|112^Final Echocardiogram Report|||20151009173644|||||||||||||002|||||F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^||||3068^JOHN^Paul^J|\r" + "OBX|1|ST|TS-F-01-007^Endocrine Disorders 7^L||obs report||||||F\r" + "OBX|2|ST|TS-F-01-008^Endocrine Disorders 8^L||ECHOCARDIOGRAPHIC REPORT||||||F\r" + "OBR|1||98^IA PHIMS Stage^2.16.840.1.114222.4.3.3.5.1.2^ISO|113^Echocardiogram Report|||20151009173644|||||||||||||002|||||F|||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^||||3065^Mahoney^Paul^J|\r" + "OBX|1|CWE|625-4^Bacteria identified in Stool by Culture^LN^^^^2.33^^result1|1|27268008^Salmonella^SCT^^^^20090731^^Salmonella species|||A^A^HL70078^^^^2.5|||P|||20120301|||^^^^^^^^Bacterial Culture||201203140957||||||\r" + "OBX|2|ST|TS-F-01-002^Endocrine Disorders^L||ECHOCARDIOGRAPHIC REPORT Group 2||||||F\r";
List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
// Verify that the right resources are being created
List<Resource> patientResource = ResourceUtils.getResourceList(e, ResourceType.Patient);
assertThat(patientResource).hasSize(1);
List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
assertThat(obsResource).hasSize(4);
List<Resource> practitionerResource = ResourceUtils.getResourceList(e, ResourceType.Practitioner);
assertThat(practitionerResource).hasSize(2);
List<Resource> diagnosticReport = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
assertThat(diagnosticReport).hasSize(2);
List<Resource> servReqResource = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
assertThat(servReqResource).hasSize(2);
// Expecting only the above resources, no extras!
assertThat(e).hasSize(11);
// /////////////////////////////////////////
// Now confirm content of the FIRST diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
// Verify status from OBR.25
assertThat(diag.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag.getCategory()).isEmpty();
// Verify code from OBR.4
assertThat(diag.hasCode()).isTrue();
List<Coding> codings = diag.getCode().getCoding();
assertThat(codings).hasSize(1);
Coding coding = codings.get(0);
assertThat(coding.hasDisplay()).isTrue();
assertThat(coding.getDisplay()).hasToString("Final Echocardiogram Report");
assertThat(coding.hasCode()).isTrue();
assertThat(coding.getCode()).hasToString("112");
assertThat(coding.hasSystem()).isFalse();
// Verify encounter reference
assertThat(diag.getEncounter().isEmpty()).isTrue();
// Verify subject reference
assertThat(diag.getSubject().isEmpty()).isFalse();
// Verify effectiveDateTime from OBR.7 and OBR.8
// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
assertThat(diag.getEffectiveDateTimeType().asStringValue()).isEqualTo("2015-10-09T17:36:44+08:00");
// Verify issued from OBR.22
assertThat(diag.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag.getResultsInterpreter()).hasSize(1);
// Verify basedOn is ref to the ServiceRequest created for ORC or OBR
assertThat(diag.getBasedOn()).hasSize(1);
assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
// Verify specimen reference
assertThat(diag.getSpecimen()).isEmpty();
// Verify result reference
List<Reference> obsRef = diag.getResult();
assertThat(obsRef).hasSize(2);
assertThat(obsRef.get(0).isEmpty()).isFalse();
// Verify presentedForm from OBX of type TX - In this case no attachments created because the OBX is not of type TX.
List<Attachment> attachments = diag.getPresentedForm();
Assertions.assertEquals(0, attachments.size(), "Unexpected number of attachments");
// /////////////////////////////////////////
// Now confirm content of the SECOND diagnosticReport because we don't have separate tests for DiagnosticReport
// /////////////////////////////////////////
DiagnosticReport diag2 = ResourceUtils.getResourceDiagnosticReport(diagnosticReport.get(0), context);
// Verify status from OBR.25
assertThat(diag2.getStatus().toCode()).isEqualTo("final");
// Verify category from OBR.24
assertThat(diag2.getCategory()).isEmpty();
// Verify code from OBR.4
assertThat(diag2.hasCode()).isTrue();
List<Coding> codings2 = diag2.getCode().getCoding();
assertThat(codings2).hasSize(1);
Coding coding2 = codings.get(0);
assertThat(coding2.hasDisplay()).isTrue();
assertThat(coding2.getDisplay()).hasToString("Final Echocardiogram Report");
assertThat(coding2.hasCode()).isTrue();
assertThat(coding2.getCode()).hasToString("112");
assertThat(coding2.hasSystem()).isFalse();
// Verify encounter reference
assertThat(diag2.getEncounter().isEmpty()).isTrue();
// Verify subject reference
assertThat(diag2.getSubject().isEmpty()).isFalse();
// Verify effectiveDateTime from OBR.7 and OBR.8
// This also verifies the type, confirming effectiveDateTime was set rather than effectivePeriod
assertThat(diag2.getEffectiveDateTimeType().asStringValue()).isEqualTo("2015-10-09T17:36:44+08:00");
// Verify issued from OBR.22
assertThat(diag2.getIssued()).isNull();
// Verify resultsInterpreter from OBR.32
assertThat(diag2.getResultsInterpreter()).hasSize(1);
// Verify basedOn is ref to the ServiceRequest created for ORC or OBR
assertThat(diag.getBasedOn()).hasSize(1);
assertThat(diag.getBasedOn().get(0).getReference().substring(0, 15)).isEqualTo("ServiceRequest/");
// Verify specimen reference
assertThat(diag2.getSpecimen()).isEmpty();
// Verify result reference
List<Reference> obsRef2 = diag2.getResult();
assertThat(obsRef2).hasSize(2);
assertThat(obsRef2.get(0).isEmpty()).isFalse();
// Verify presentedForm from OBX of type TX - In this case no attachments created because the OBX is not type TX.
List<Attachment> attachments2 = diag2.getPresentedForm();
Assertions.assertEquals(0, attachments2.size(), "Unexpected number of attachments");
// //////////////////////////////////
for (Resource res : obsResource) {
// Verify encounter reference is not set
Observation obs = (Observation) res;
assertThat(obs.getEncounter().isEmpty()).isTrue();
// Verify subject reference to Patient exists
Base subject = ResourceUtils.getValue(obs, "subject");
assertThat(ResourceUtils.getValueAsString(subject, "reference").substring(0, 8)).isEqualTo("Patient/");
}
}
Aggregations