Examples with Observation org.hl7.fhir.r4.model.Observation used on opensource projects

Example 16 with Observation

use of org.hl7.fhir.r4.model.Observation in project hl7v2-fhir-converter by LinuxForHealth.

the class HL7EventTypeFHIRConversionTest method validateEVNsegmentWithOBXreference.

@Test
void validateEVNsegmentWithOBXreference() {
    // When there is an OBX record, it should create a reason reference in the encounter segment
    String hl7message = "MSH|^~\\&|||||||ADT^A01^ADT_A01|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6||||||\r" + "EVN||||7525|||\r" + "PV1|1|I||R|||||||||R|1||||||||||||||||||||||||||||||200603150624|200603150625|||||||\r" + "OBX|1|CWE|DQW^Some text 1^SNM3|||||||||||||||||||||\r";
    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 Observation in the bundle
    List<Resource> obsResource = e.stream().filter(v -> ResourceType.Observation == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(obsResource).hasSize(1);
    Observation obs = (Observation) obsResource.get(0);
    // 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);
    assertThat(encounter.hasReasonReference()).isTrue();
    assertThat(encounter.getReasonReference()).hasSize(1);
    // Check that the cross reference is equal to the Observation id
    assertThat(encounter.getReasonReferenceFirstRep().getReference()).hasToString(obs.getId());
}

Example 17 with Observation

use of org.hl7.fhir.r4.model.Observation 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);
}

Example 18 with Observation

use of org.hl7.fhir.r4.model.Observation in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7MessageTest method test_observation.

@Test
void test_observation() throws IOException {
    ResourceModel rsm = ResourceReader.getInstance().generateResourceModel("resource/Observation");
    HL7FHIRResourceTemplateAttributes attributes = new HL7FHIRResourceTemplateAttributes.Builder().withResourceName("Observation").withResourceModel(rsm).withSegment("OBX").withIsReferenced(true).withRepeats(false).build();
    HL7FHIRResourceTemplate observation = new HL7FHIRResourceTemplate(attributes);
    HL7MessageModel message = new HL7MessageModel("ADT", Lists.newArrayList(observation));
    String hl7message = "MSH|^~\\&|hl7Integration|hl7Integration|||||ADT^A01|||2.3|\r" + "EVN|A01|20130617154644\r" + "PID|1|465 306 5961|000010016^^^MR~000010017^^^MR~000010018^^^MR|407623|Wood^Patrick^^Sr^MR||19700101|female|||High Street^^Oxford^^Ox1 4DP~George St^^Oxford^^Ox1 5AP|||||||\r" + "NK1|1|Wood^John^^^MR|Father||999-9999\r" + "NK1|2|Jones^Georgie^^^MSS|MOTHER||999-9999\r" + "PV1|1||Location||||||||||||||||261938_6_201306171546|||||||||||||||||||||||||20130617134644|||||||||\r" + "OBX|1|NM|0135-4^TotalProtein||7.3|gm/dl|5.9-8.4||||F|||||2740^Tsadok^Janetary~2913^Merrit^Darren^F~3065^Mahoney^Paul^J~4723^Loh^Robert^L~9052^Winter^Oscar^|\r";
    String json = message.convert(hl7message, engine);
    IBaseResource bundleResource = context.getParser().parseResource(json);
    assertThat(bundleResource).isNotNull();
    Bundle b = (Bundle) bundleResource;
    List<BundleEntryComponent> e = b.getEntry();
    // We expect observation because not TX in OBX
    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(5);
}

Example 19 with Observation

use of org.hl7.fhir.r4.model.Observation 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);
}

Example 20 with Observation

use of org.hl7.fhir.r4.model.Observation in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7MessageTest method test_messageHeader_with_ORU.

@Test
void test_messageHeader_with_ORU() throws IOException {
    ResourceModel rsm = ResourceReader.getInstance().generateResourceModel("resource/MessageHeader");
    HL7FHIRResourceTemplateAttributes attributes = new HL7FHIRResourceTemplateAttributes.Builder().withResourceName("MessageHeader").withResourceModel(rsm).withSegment("MSH").withAdditionalSegments(Lists.newArrayList("EVN")).withIsReferenced(false).withRepeats(false).build();
    HL7FHIRResourceTemplate messageHeaderTemplate = new HL7FHIRResourceTemplate(attributes);
    HL7MessageModel message = new HL7MessageModel("ORU", Lists.newArrayList(messageHeaderTemplate));
    String hl7message = "MSH|^~\\&|Amalga HIS|BUM|New Tester|MS|20111121103141||ORU^R01|2847970-201111211031|P|2.6|||AL|NE|764|ASCII||||||^4086::132:2A57:3C28^IPv6\r" + "EVN|A01|20130617154644||01\r" + "PID|1|465 306 5961|000010016^^^MR~000010017^^^MR~000010018^^^MR|407623|Wood^Patrick^^Sr^MR||19700101|female|||High Street^^Oxford^^Ox1 4DP~George St^^Oxford^^Ox1 5AP|||||||\r" + "NK1|1|Wood^John^^^MR|Father||999-9999\r" + "NK1|2|Jones^Georgie^^^MSS|MOTHER||999-9999\r" + "PV1|1||Location||||||||||||||||261938_6_201306171546|||||||||||||||||||||||||20130617134644|||||||||";
    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> messageHeader = e.stream().filter(v -> ResourceType.MessageHeader == v.getResource().getResourceType()).map(BundleEntryComponent::getResource).collect(Collectors.toList());
    assertThat(messageHeader).hasSize(1);
    MessageHeader msgH = ResourceUtils.getResourceMessageHeader(messageHeader.get(0), context);
    assertThat(msgH.getId()).isNotNull();
    assertThat(msgH.getEventCoding()).isNotNull();
    assertThat(msgH.getEventCoding().getSystem()).isEqualTo("http://terminology.hl7.org/CodeSystem/v2-0003");
    assertThat(msgH.getEventCoding().getCode()).isEqualTo("R01");
    assertThat(msgH.getEventCoding().getDisplay()).isEqualTo("ORU/ACK - Unsolicited transmission of an observation message");
    assertThat(msgH.getDestination()).hasSize(1);
    assertThat(msgH.getDestinationFirstRep().getName()).isEqualTo("New Tester");
    assertThat(msgH.getDestinationFirstRep().getEndpoint()).isEqualTo("MS");
    assertThat(msgH.getSource()).isNotNull();
    assertThat(msgH.getSource().getName()).isEqualTo("Amalga HIS");
    assertThat(msgH.getReason()).isNotNull();
    assertThat(msgH.getReason().getCoding().get(0).getSystem()).isEqualTo("http://terminology.hl7.org/CodeSystem/v2-0062");
    assertThat(msgH.getReason().getCoding().get(0).getCode()).isEqualTo("01");
    assertThat(msgH.getReason().getCoding().get(0).getDisplay()).isEqualTo("Patient request");
}