Examples with Observation org.hl7.fhir.r5.model.Observation used on opensource projects

Example 6 with Observation

use of org.hl7.fhir.r5.model.Observation in project kindling by HL7.

the class ADLImporter method execute.

private void execute() throws Exception {
    // load config
    DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance();
    factory.setNamespaceAware(true);
    DocumentBuilder builder = factory.newDocumentBuilder();
    adlConfig = builder.parse(new FileInputStream(config)).getDocumentElement();
    // load ADL
    builder = factory.newDocumentBuilder();
    adl = builder.parse(new FileInputStream(source)).getDocumentElement();
    check("root", adl.getNamespaceURI(), "http://schemas.openehr.org/v1", "Wrong namespace for ADL XML");
    check("root", adl.getNodeName(), "archetype", "Wrong XML for ADL XML");
    check("root", XMLUtil.getNamedChild(adl, "adl_version").getTextContent(), "1.4", "unsupported ADL version");
    String id = XMLUtil.getFirstChild(XMLUtil.getNamedChild(adl, "archetype_id")).getTextContent().split("\\.")[1];
    String baseType = XMLUtil.getNamedChild(XMLUtil.getNamedChild(adl, "definition"), "rm_type_name").getTextContent();
    if (!baseType.equals("OBSERVATION"))
        return;
    // load texts from ontology
    List<Element> set = new ArrayList<Element>();
    Element ontology = XMLUtil.getNamedChild(adl, "ontology");
    Element term_definitions = XMLUtil.getNamedChild(ontology, "term_definitions");
    set.clear();
    XMLUtil.getNamedChildren(term_definitions, "items", set);
    for (Element item : set) {
        processTextItem(item);
    }
    // create structure definition
    StructureDefinition sd = new StructureDefinition();
    sd.setId("netha-" + id);
    sd.setUrl("http://hl7.org/fhir/StructureDefinition/" + sd.getId());
    sd.setKind(StructureDefinitionKind.LOGICAL);
    populateMetadata(set, sd);
    // load data and protocol
    Element definition = XMLUtil.getNamedChild(adl, "definition");
    NodeTreeEntry root = new NodeTreeEntry();
    root.typeName = XMLUtil.getNamedChild(definition, "rm_type_name").getTextContent();
    root.atCode = XMLUtil.getNamedChild(definition, "node_id").getTextContent();
    root.name = generateToken(root.atCode, true);
    sd.setName(root.name);
    root.cardinality = readCardinality("root", XMLUtil.getNamedChild(definition, "occurrences"));
    set.clear();
    XMLUtil.getNamedChildren(definition, "attributes", set);
    for (Element item : set) {
        // we're actually skipping this level - we don't care about data protocol etc.
        // XMLUtil.getNamedChild(XMLUtil.getNamedChild(item, "children"), "attributes");
        Element attributes = item;
        loadChildren(root.atCode, root, attributes);
    }
    dumpChildren("", root);
    genElements(sd, root.name, root);
    // save
    new XmlParser().setOutputStyle(OutputStyle.PRETTY).compose(new FileOutputStream(dest), sd);
    System.out.println("done. saved as " + dest);
}

Example 7 with Observation

use of org.hl7.fhir.r5.model.Observation in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7EncounterFHIRConversionTest method testEncounterReferencesObservationAndDiagnosis.

/**
 * Testing Encounter correctly references Observation AND Diagnosis when both are present.
 */
@Test
void testEncounterReferencesObservationAndDiagnosis() throws IOException {
    String hl7message = "MSH|^~\\&|hl7Integration|hl7Integration|||||ADT^A01|||2.6|\n" + "PID|||1234^^^^MR||DOE^JANE^|||F|||||||||||||||||||||\n" + "PV1|1|O|Location||||||||||||||||261938_6_201306171546|||||||||||||||||||||||||20130617134644|||||||||\n" + "OBX|1|SN|24467-3^CD3+CD4+ (T4 helper) cells [#/volume] in Blood^LN||=^440|{Cells}/uL^cells per microliter^UCUM|649-1346 cells/mcL|L|||F\r" + "DG1|1|ICD10|^Ovarian Cancer|||||||||||||||||||||\r";
    String json = ftv.convert(hl7message, OPTIONS);
    IBaseResource bundleResource = context.getParser().parseResource(json);
    assertThat(bundleResource).isNotNull();
    Bundle b = (Bundle) bundleResource;
    List<BundleEntryComponent> e = b.getEntry();
    List<Resource> obsResource = ResourceUtils.getResourceList(e, ResourceType.Observation);
    assertThat(obsResource).hasSize(1);
    List<Resource> encounterResource = ResourceUtils.getResourceList(e, ResourceType.Encounter);
    assertThat(encounterResource).hasSize(1);
    Encounter enc = (Encounter) encounterResource.get(0);
    List<Reference> reasonRefs = enc.getReasonReference();
    assertEquals(2, reasonRefs.size());
    // Guess at the order of the references
    Reference refObservation = reasonRefs.get(0);
    Reference refCondition = reasonRefs.get(1);
    // If guessed wrong, reverse them
    if (!refObservation.getReference().contains("Observation")) {
        refObservation = reasonRefs.get(1);
        refCondition = reasonRefs.get(0);
    }
    assertTrue(refObservation.getReference().contains("Observation"));
    assertTrue(refCondition.getReference().contains("Condition"));
}

Example 8 with Observation

use of org.hl7.fhir.r5.model.Observation in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7DocumentReferenceFHIRConversionTest method doc_ref_content_test.

@ParameterizedTest
@ValueSource(strings = { "MDM^T02", "MDM^T06" })
void doc_ref_content_test(String segment) {
    String documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1||TEXT||||201801180346||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + // Next three lines create an attachment
    "OBX|1|TX|||ECHOCARDIOGRAPHIC REPORT||||||F|||202101010000|||\n" + "OBX|2|TX|||NORMAL LV CHAMBER SIZE WITH MILD CONCENTRIC LVH||||||F|||202101010000|||\n" + "OBX|3|TX|||HYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%||||||F|||202101010000|||\n";
    DocumentReference report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
    DocumentReference.DocumentReferenceContentComponent content = report.getContentFirstRep();
    // Future TXA.3, currently always defaults to text/plain
    assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
    // TXA.7 date
    assertThat(content.getAttachment().getCreationElement().toString()).containsPattern("2018-01-18T03:46:00");
    assertThat(content.getAttachment().hasData()).isTrue();
    String decodedData = new String(Base64.getDecoder().decode(content.getAttachment().getDataElement().getValueAsString()));
    assertThat(decodedData).isEqualTo("ECHOCARDIOGRAPHIC REPORT\nNORMAL LV CHAMBER SIZE WITH MILD CONCENTRIC LVH\nHYPERDYNAMIC LV SYSTOLIC FUNCTION, VISUAL EF 80%");
    // TODO: Determine if we need to look at anything other than OBX.2 when it is TX
    // Leave this test in place as a reminder
    documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + "TXA|1||||||201801180346||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + // TODO: find better code for this test which is to see that OBX.2 is the fallback.
    "OBX|1|SN|||||||||F";
    report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
    content = report.getContentFirstRep();
    // Because the OBX is not TX, the content is put in an Observation
    // FHIR requires a Content element, so only a minimal one is created.
    // Future OBX.2 is the backup for content type, but currently always defaults to text/plain
    assertThat(content.getAttachment().hasContentType()).isTrue();
    // Currently always defaults to text/plain
    assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
    // TXA.7 date
    assertThat(content.getAttachment().getCreationElement().toString()).containsPattern("2018-01-18T03:46:00");
    assertThat(content.getAttachment().hasData()).isFalse();
    // Test that content is created even if TXA.7 is empty
    documentReferenceMessage = "MSH|^~\\&|HL7Soup|Instance1|MCM|Instance2|200911021022|Security|" + segment + "^MDM_T02|64322|P|2.6|123|456|ER|AL|USA|ASCII|en|2.6|56789^NID^UID|MCM||||\n" + "PID|1||000054321^^^MRN|||||||||||||M|CAT|||||N\n" + "PV1|1|I||||||||||||||||||||||||||||||||||||||||||\n" + "ORC|NW|||PGN001|SC|D|1|||MS|MS|||||\n" + "OBR|1||||||20170825010500|||||||||||||002|||||F||||||||\n" + // Ensure that empty TXA.7 still works
    "TXA|1||||||||<PHYSID1>||||||||||AV|||<PHYSID2>||\n" + "OBX|1|SN|||||||||F";
    report = ResourceUtils.getDocumentReference(ftv, documentReferenceMessage);
    content = report.getContentFirstRep();
    // Because the OBX is not TX, the content is put in an Observation
    // FHIR requires a Content element, so only a minimal one is created.
    // Currently always defaults to text/plain
    assertThat(content.getAttachment().hasContentType()).isTrue();
    // Currently always defaults to text/plain, even if not data for content
    assertThat(content.getAttachment().getContentType()).isEqualTo("text/plain");
    // No TXA.7 date
    assertThat(content.getAttachment().hasCreationElement()).isFalse();
    assertThat(content.getAttachment().hasData()).isFalse();
}

Example 9 with Observation

use of org.hl7.fhir.r5.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 10 with Observation

use of org.hl7.fhir.r5.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);
}