Examples with USUAL org.hl7.fhir.dstu3.model.Identifier.IdentifierUse.USUAL used on opensource projects

Example 1 with USUAL

use of org.hl7.fhir.dstu3.model.Identifier.IdentifierUse.USUAL in project integration-adaptor-111 by nhsconnect.

the class CompositionMapper method mapComposition.

public Composition mapComposition(POCDMT000002UK01ClinicalDocument1 clinicalDocument, Encounter encounter, List<CarePlan> carePlans, List<QuestionnaireResponse> questionnaireResponseList, ReferralRequest referralRequest, List<PractitionerRole> practitionerRoles) {
    Composition composition = new Composition();
    composition.setIdElement(resourceUtil.newRandomUuid());
    Identifier docIdentifier = new Identifier();
    docIdentifier.setUse(USUAL);
    docIdentifier.setValue(clinicalDocument.getSetId().getRoot());
    composition.setTitle(COMPOSITION_TITLE).setType(createCodeableConcept()).setStatus(FINAL).setEncounter(resourceUtil.createReference(encounter)).setSubject(encounter.getSubject()).setDateElement(DateUtil.parse(clinicalDocument.getEffectiveTime().getValue())).setIdentifier(docIdentifier);
    if (clinicalDocument.getConfidentialityCode().isSetCode()) {
        composition.setConfidentiality(Composition.DocumentConfidentiality.valueOf(clinicalDocument.getConfidentialityCode().getCode()));
    }
    if (isNotEmpty(clinicalDocument.getRelatedDocumentArray()) && clinicalDocument.getRelatedDocumentArray(0).getParentDocument().getIdArray(0).isSetRoot()) {
        Identifier relatedDocIdentifier = new Identifier();
        relatedDocIdentifier.setUse(USUAL);
        relatedDocIdentifier.setValue(clinicalDocument.getRelatedDocumentArray(0).getParentDocument().getIdArray(0).getRoot());
        composition.addRelatesTo().setCode(Composition.DocumentRelationshipType.REPLACES).setTarget(relatedDocIdentifier);
    }
    practitionerRoles.stream().forEach(it -> composition.addAuthor(it.getPractitioner()));
    if (clinicalDocument.getComponent().isSetStructuredBody()) {
        for (POCDMT000002UK01Component3 component3 : clinicalDocument.getComponent().getStructuredBody().getComponentArray()) {
            SectionComponent sectionComponent = new SectionComponent();
            addSectionChildren(sectionComponent, component3.getSection());
            composition.addSection(sectionComponent);
        }
    }
    for (CarePlan carePlan : carePlans) {
        composition.addSection(buildSectionComponentFromResource(carePlan));
    }
    if (!referralRequest.isEmpty()) {
        composition.addSection(buildSectionComponentFromResource(referralRequest));
    }
    if (questionnaireResponseList != null) {
        addPathwaysToSection(composition, questionnaireResponseList);
    }
    return composition;
}

Example 2 with USUAL

use of org.hl7.fhir.dstu3.model.Identifier.IdentifierUse.USUAL in project org.hl7.fhir.core by hapifhir.

the class ProfileUtilitiesTests method testSlicingSimple.

/**
 * we're going to slice Patient.identifier
 */
private void testSlicingSimple() throws EOperationOutcome, Exception {
    StructureDefinition focus = new StructureDefinition();
    StructureDefinition base = context.fetchResource(StructureDefinition.class, "http://hl7.org/fhir/StructureDefinition/Patient").copy();
    focus.setUrl(Utilities.makeUuidUrn());
    focus.setBaseDefinition(base.getUrl());
    focus.setType(base.getType());
    focus.setDerivation(TypeDerivationRule.CONSTRAINT);
    // set the slice up
    ElementDefinition id = focus.getDifferential().addElement();
    id.setPath("Patient.identifier");
    id.getSlicing().setOrdered(false).setRules(SlicingRules.OPEN).addDiscriminator().setPath("use").setType(DiscriminatorType.VALUE);
    // first slice:
    id = focus.getDifferential().addElement();
    id.setPath("Patient.identifier");
    id.setSliceName("name1");
    id = focus.getDifferential().addElement();
    id.setPath("Patient.identifier.use");
    id.setFixed(new CodeType("usual"));
    // second slice:
    id = focus.getDifferential().addElement();
    id.setPath("Patient.identifier");
    id.setSliceName("name2");
    id = focus.getDifferential().addElement();
    id.setPath("Patient.identifier.use");
    id.setFixed(new CodeType("official"));
    List<ValidationMessage> messages = new ArrayList<ValidationMessage>();
    new ProfileUtilities(context, messages, null).generateSnapshot(base, focus, focus.getUrl(), "Simple Test");
    // 18 different: identifier + 8 inner children * 2
    boolean ok = base.getSnapshot().getElement().size() == focus.getSnapshot().getElement().size() - 18;
    for (int i = 0; i < base.getSnapshot().getElement().size(); i++) {
        if (ok) {
            ElementDefinition b = base.getSnapshot().getElement().get(i);
            ElementDefinition f = focus.getSnapshot().getElement().get(i <= 9 ? i : i + 18);
            if (!f.hasBase() || !b.getPath().equals(f.getBase().getPath()))
                ok = false;
            else {
                f.setBase(null);
                if (f.getPath().equals("Patient.identifier")) {
                    ok = f.hasSlicing();
                    if (ok)
                        f.setSlicing(null);
                }
                ok = Base.compareDeep(b, f, true);
            }
        }
    }
    // now, check that the slices we skipped are correct:
    for (int i = 10; i <= 18; i++) {
        if (ok) {
            ElementDefinition d1 = focus.getSnapshot().getElement().get(i);
            ElementDefinition d2 = focus.getSnapshot().getElement().get(i + 9);
            if (d1.getPath().equals("Patient.identifier.use")) {
                ok = d1.hasFixed() && d2.hasFixed() && !Base.compareDeep(d1.getFixed(), d2.getFixed(), true);
                if (ok) {
                    d1.setFixed(null);
                    d2.setFixed(null);
                }
            }
            if (d1.getPath().equals("Patient.identifier")) {
                ok = d1.hasSliceName() && d2.hasSliceName() && !Base.compareDeep(d1.getSliceNameElement(), d2.getSliceNameElement(), true);
                if (ok) {
                    d1.setSliceName(null);
                    d2.setSliceName(null);
                }
            }
            ok = Base.compareDeep(d1, d2, true);
        }
    }
    if (!ok) {
        compareXml(base, focus);
        throw new FHIRException("Snap shot generation slicing failed");
    } else
        System.out.println("Snap shot generation slicing passed");
}

Example 3 with USUAL

use of org.hl7.fhir.dstu3.model.Identifier.IdentifierUse.USUAL in project MobileAccessGateway by i4mi.

the class Iti67ResponseConverter method translateToFhir.

@Override
public List<DocumentReference> translateToFhir(QueryResponse input, Map<String, Object> parameters) {
    ArrayList<DocumentReference> list = new ArrayList<DocumentReference>();
    if (input != null && Status.SUCCESS.equals(input.getStatus())) {
        // process relationship association
        Map<String, List<DocumentReferenceRelatesToComponent>> relatesToMapping = new HashMap<String, List<DocumentReferenceRelatesToComponent>>();
        for (Association association : input.getAssociations()) {
            // Relationship type -> relatesTo.code code [1..1]
            // relationship reference -> relatesTo.target Reference(DocumentReference)
            String source = association.getSourceUuid();
            String target = association.getTargetUuid();
            AssociationType type = association.getAssociationType();
            DocumentReferenceRelatesToComponent relatesTo = new DocumentReferenceRelatesToComponent();
            if (type != null)
                switch(type) {
                    case APPEND:
                        relatesTo.setCode(DocumentRelationshipType.APPENDS);
                        break;
                    case REPLACE:
                        relatesTo.setCode(DocumentRelationshipType.REPLACES);
                        break;
                    case TRANSFORM:
                        relatesTo.setCode(DocumentRelationshipType.TRANSFORMS);
                        break;
                    case SIGNS:
                        relatesTo.setCode(DocumentRelationshipType.SIGNS);
                        break;
                }
            relatesTo.setTarget(new Reference().setReference("urn:oid:" + target));
            if (!relatesToMapping.containsKey(source))
                relatesToMapping.put(source, new ArrayList<DocumentReferenceRelatesToComponent>());
            relatesToMapping.get(source).add(relatesTo);
        }
        if (input.getDocumentEntries() != null) {
            for (DocumentEntry documentEntry : input.getDocumentEntries()) {
                DocumentReference documentReference = new DocumentReference();
                // FIXME do we need to cache this id in
                documentReference.setId(noUuidPrefix(documentEntry.getEntryUuid()));
                // relation to the DocumentManifest itself
                // for
                list.add(documentReference);
                // limitedMetadata -> meta.profile canonical [0..*]
                if (documentEntry.isLimitedMetadata()) {
                    documentReference.getMeta().addProfile("http://ihe.net/fhir/StructureDefinition/IHE_MHD_Query_Comprehensive_DocumentReference");
                } else {
                    documentReference.getMeta().addProfile("http://ihe.net/fhir/StructureDefinition/IHE_MHD_Comprehensive_DocumentManifest");
                }
                // uniqueId -> masterIdentifier Identifier [0..1] [1..1]
                if (documentEntry.getUniqueId() != null) {
                    documentReference.setMasterIdentifier((new Identifier().setValue("urn:oid:" + documentEntry.getUniqueId())));
                }
                // DocumentReference.identifier. use shall be ‘official’
                if (documentEntry.getEntryUuid() != null) {
                    documentReference.addIdentifier((new Identifier().setSystem("urn:ietf:rfc:3986").setValue(asUuid(documentEntry.getEntryUuid()))).setUse(IdentifierUse.OFFICIAL));
                }
                // Other status values are allowed but are not defined in this mapping to XDS.
                if (AvailabilityStatus.APPROVED.equals(documentEntry.getAvailabilityStatus())) {
                    documentReference.setStatus(DocumentReferenceStatus.CURRENT);
                }
                if (AvailabilityStatus.DEPRECATED.equals(documentEntry.getAvailabilityStatus())) {
                    documentReference.setStatus(DocumentReferenceStatus.SUPERSEDED);
                }
                // contentTypeCode -> type CodeableConcept [0..1]
                if (documentEntry.getTypeCode() != null) {
                    documentReference.setType(transform(documentEntry.getTypeCode()));
                }
                // classCode -> category CodeableConcept [0..*]
                if (documentEntry.getClassCode() != null) {
                    documentReference.addCategory((transform(documentEntry.getClassCode())));
                }
                // representing the XDS Affinity Domain Patient.
                if (documentEntry.getPatientId() != null) {
                    Identifiable patient = documentEntry.getPatientId();
                    documentReference.setSubject(transformPatient(patient));
                }
                // creationTime -> date instant [0..1]
                if (documentEntry.getCreationTime() != null) {
                    documentReference.setDate(Date.from(documentEntry.getCreationTime().getDateTime().toInstant()));
                }
                // PractitionerRole| Organization| Device| Patient| RelatedPerson) [0..*]
                if (documentEntry.getAuthors() != null) {
                    for (Author author : documentEntry.getAuthors()) {
                        documentReference.addAuthor(transformAuthor(author));
                    }
                }
                // legalAuthenticator -> authenticator Note 1
                // Reference(Practitioner|Practition erRole|Organization [0..1]
                Person person = documentEntry.getLegalAuthenticator();
                if (person != null) {
                    Practitioner practitioner = transformPractitioner(person);
                    documentReference.setAuthenticator((Reference) new Reference().setResource(practitioner));
                }
                // Relationship Association -> relatesTo [0..*]
                // [1..1]
                documentReference.setRelatesTo(relatesToMapping.get(documentEntry.getEntryUuid()));
                // title -> description string [0..1]
                if (documentEntry.getTitle() != null) {
                    documentReference.setDescription(documentEntry.getTitle().getValue());
                }
                // DocumentReference itself.
                if (documentEntry.getConfidentialityCodes() != null) {
                    documentReference.addSecurityLabel(transform(documentEntry.getConfidentialityCodes()));
                }
                DocumentReferenceContentComponent content = documentReference.addContent();
                Attachment attachment = new Attachment();
                content.setAttachment(attachment);
                // mimeType -> content.attachment.contentType [1..1] code [0..1]
                if (documentEntry.getMimeType() != null) {
                    attachment.setContentType(documentEntry.getMimeType());
                }
                // languageCode -> content.attachment.language code [0..1]
                if (documentEntry.getLanguageCode() != null) {
                    attachment.setLanguage(documentEntry.getLanguageCode());
                }
                // retrievable location of the document -> content.attachment.url uri
                // [0..1] [1..1
                // has to defined, for the PoC we define
                // $host:port/camel/$repositoryid/$uniqueid
                attachment.setUrl(config.getUriMagXdsRetrieve() + "?uniqueId=" + documentEntry.getUniqueId() + "&repositoryUniqueId=" + documentEntry.getRepositoryUniqueId());
                // size -> content.attachment.size integer [0..1] The size is calculated
                if (documentEntry.getSize() != null) {
                    attachment.setSize(documentEntry.getSize().intValue());
                }
                // on the data prior to base64 encoding, if the data is base64 encoded.
                if (documentEntry.getHash() != null) {
                    attachment.setHash(Hex.fromHex(documentEntry.getHash()));
                }
                // comments -> content.attachment.title string [0..1]
                if (documentEntry.getComments() != null) {
                    attachment.setTitle(documentEntry.getComments().getValue());
                }
                // TcreationTime -> content.attachment.creation dateTime [0..1]
                if (documentEntry.getCreationTime() != null) {
                    attachment.setCreation(Date.from(documentEntry.getCreationTime().getDateTime().toInstant()));
                }
                // formatCode -> content.format Coding [0..1]
                if (documentEntry.getFormatCode() != null) {
                    content.setFormat(transform(documentEntry.getFormatCode()).getCodingFirstRep());
                }
                DocumentReferenceContextComponent context = new DocumentReferenceContextComponent();
                documentReference.setContext(context);
                // referenceIdList -> context.encounter Reference(Encounter) [0..*] When
                // referenceIdList contains an encounter, and a FHIR Encounter is available, it
                // may be referenced.
                // Map to context.related
                List<ReferenceId> refIds = documentEntry.getReferenceIdList();
                if (refIds != null) {
                    for (ReferenceId refId : refIds) {
                        context.getRelated().add(transform(refId));
                    }
                }
                // eventCodeList -> context.event CodeableConcept [0..*]
                if (documentEntry.getEventCodeList() != null) {
                    documentReference.getContext().setEvent(transformMultiple(documentEntry.getEventCodeList()));
                }
                // serviceStartTime serviceStopTime -> context.period Period [0..1]
                if (documentEntry.getServiceStartTime() != null || documentEntry.getServiceStopTime() != null) {
                    Period period = new Period();
                    period.setStartElement(transform(documentEntry.getServiceStartTime()));
                    period.setEndElement(transform(documentEntry.getServiceStopTime()));
                    documentReference.getContext().setPeriod(period);
                }
                // [0..1]
                if (documentEntry.getHealthcareFacilityTypeCode() != null) {
                    context.setFacilityType(transform(documentEntry.getHealthcareFacilityTypeCode()));
                }
                // practiceSettingCode -> context.practiceSetting CodeableConcept [0..1]
                if (documentEntry.getPracticeSettingCode() != null) {
                    context.setPracticeSetting(transform(documentEntry.getPracticeSettingCode()));
                }
                // sourcePatientId and sourcePatientInfo -> context.sourcePatientInfo
                // Reference(Patient) [0..1] Contained Patient Resource with
                // Patient.identifier.use element set to ‘usual’.
                Identifiable sourcePatientId = documentEntry.getSourcePatientId();
                PatientInfo sourcePatientInfo = documentEntry.getSourcePatientInfo();
                Patient sourcePatient = new Patient();
                if (sourcePatientId != null) {
                    sourcePatient.addIdentifier((new Identifier().setSystem("urn:oid:" + sourcePatientId.getAssigningAuthority().getUniversalId()).setValue(sourcePatientId.getId())).setUse(IdentifierUse.OFFICIAL));
                }
                if (sourcePatientInfo != null) {
                    sourcePatient.setBirthDateElement(transformToDate(sourcePatientInfo.getDateOfBirth()));
                    String gender = sourcePatientInfo.getGender();
                    if (gender != null) {
                        switch(gender) {
                            case "F":
                                sourcePatient.setGender(Enumerations.AdministrativeGender.FEMALE);
                                break;
                            case "M":
                                sourcePatient.setGender(Enumerations.AdministrativeGender.MALE);
                                break;
                            case "U":
                                sourcePatient.setGender(Enumerations.AdministrativeGender.UNKNOWN);
                                break;
                            case "A":
                                sourcePatient.setGender(Enumerations.AdministrativeGender.OTHER);
                                break;
                        }
                    }
                    ListIterator<Name> names = sourcePatientInfo.getNames();
                    while (names.hasNext()) {
                        Name name = names.next();
                        sourcePatient.addName(transform(name));
                    }
                    ListIterator<Address> addresses = sourcePatientInfo.getAddresses();
                    while (addresses.hasNext()) {
                        Address address = addresses.next();
                        if (address != null)
                            sourcePatient.addAddress(transform(address));
                    }
                }
                if (sourcePatientId != null || sourcePatientInfo != null) {
                    context.getSourcePatientInfo().setResource(sourcePatient);
                }
            }
        }
    } else {
        processError(input);
    }
    return list;
}

Example 4 with USUAL

use of org.hl7.fhir.dstu3.model.Identifier.IdentifierUse.USUAL in project hl7v2-fhir-converter by LinuxForHealth.

the class Hl7OrderRequestFHIRConversionTest method testBroadORCPlusOBRFields.

// This test is a companion to testBroadORCFields.   ORC and OBR records often have repeated data; one taking priority over the other.
// Read comments carefully.  This sometimes tests the secondary value and may be the opposite to the tests in testBroadORCFields.
@Test
// 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")
void testBroadORCPlusOBRFields() {
    String hl7message = "MSH|^~\\&|||||20180924152907|34001|ORU^R01^ORU_R01|213|T|2.6|||||||||||\n" + // PID.18 is used as backup identifier visit number because PV1.19 is empty
    "PID|||1234^^^^MR||DOE^JANE^|||F||||||||||665544||||||||||||\n" + // PV1.19 is empty and not used as visit number identifier
    "PV1|1|E|||||||||||||||||||||||||||||||||||||||||||\n" + // 7. ORC.16 is set to a reason code (but it is ignored because it is secondary to OBR.31, which is present in this case and therefore overrides ORC.16)
    "ORC|RE|248648498^|248648498^|||||||||||||042^Human immunodeficiency virus [HIV] disease [42]^I9CDX^^^^29|||||||||||||||\n" + // 14. OBR.6 creates ServiceRequest.authoredOn
    "OBR|1|248648498^|248648498^|83036E^HEMOGLOBIN A1C^PACSEAP^^^^^^HEMOGLOBIN A1C||20120606120606|20170707150707||||L|||||54321678^SCHMIDT^FRIEDA^^MD^^^^NPI^D^^^NPI||||||20180924152900|||F||||||HIV^HIV/Aids^L^^^^V1|323232&Mahoney&Paul&J||||||||||||||||||\n";
    List<BundleEntryComponent> e = ResourceUtils.createFHIRBundleFromHL7MessageReturnEntryList(ftv, hl7message);
    List<Resource> serviceRequestList = ResourceUtils.getResourceList(e, ResourceType.ServiceRequest);
    // 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 secondary PID.18
    // ORU_RO1 records do not create the ServiceRequest directly.  They create a DiagnosticReport and it creates the ServiceRequest.
    // This makes sure the specification for ORU_RO1.DiagnosticReport is specifying PID correctly in AdditionalSegments.
    // Extensive testing of identifiers is done in Hl7IdentifierFHIRConversionTest.java
    Identifier identifier = serviceRequest.getIdentifier().get(0);
    String value = identifier.getValue();
    String system = identifier.getSystem();
    // PID.18
    assertThat(value).isEqualTo("665544");
    assertThat(system).isNull();
    CodeableConcept type = identifier.getType();
    DatatypeUtils.checkCommonCodeableConceptAssertions(type, "VN", "Visit number", "http://terminology.hl7.org/CodeSystem/v2-0203", null);
    // No requisition in the serviceRequest.
    assertThat(serviceRequest.hasRequisition()).isFalse();
    // OBR.6 should create authoredOn because ORC.9 is not filled in
    assertThat(serviceRequest.hasAuthoredOn()).isTrue();
    assertThat(serviceRequest.getAuthoredOnElement().toString()).containsPattern("2012-06-06T12:06:06");
    // OBR.7 is used to create an ServiceRequest.occurrenceDateTime date because ORC.15 is empty
    assertThat(serviceRequest.hasOccurrenceDateTimeType()).isTrue();
    assertThat(serviceRequest.getOccurrenceDateTimeType().toString()).containsPattern("2017-07-07T15:07:07");
    // OBR.31 should create the ServiceRequest.reasonCode CWE
    assertThat(serviceRequest.hasReasonCode()).isTrue();
    assertThat(serviceRequest.getReasonCode()).hasSize(1);
    DatatypeUtils.checkCommonCodeableConceptVersionedAssertions(serviceRequest.getReasonCodeFirstRep(), "HIV", "HIV/Aids", "urn:id:L", "HIV/Aids", "V1");
    // OBR.16 should create an ServiceRequest.requester reference & display
    assertThat(serviceRequest.hasRequester()).isTrue();
    assertThat(serviceRequest.getRequester().hasDisplay()).isTrue();
    assertThat(serviceRequest.getRequester().getDisplay()).isEqualTo("FRIEDA SCHMIDT MD");
    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 OBR.16 because ORC.12 is empty.
    // Check the practitioner content in detail, validating subfields.
    assertThat(pract.getIdentifier()).hasSize(1);
    // OBR.16.1
    assertThat(pract.getIdentifierFirstRep().getValue()).isEqualTo("54321678");
    // OBR.16.9, tests known system logic
    assertThat(pract.getIdentifierFirstRep().getSystem()).isEqualTo("http://hl7.org/fhir/sid/us-npi");
    DatatypeUtils.checkCommonCodeableConceptAssertions(pract.getIdentifierFirstRep().getType(), "NPI", "National provider identifier", "http://terminology.hl7.org/CodeSystem/v2-0203", // OBR.16.13
    null);
    assertThat(pract.getName()).hasSize(1);
    // Combined OBR.16.2 - OBR.16.7
    assertThat(pract.getNameFirstRep().getTextElement().toString()).hasToString("FRIEDA SCHMIDT MD");
    // OBR.16.10
    assertThat(pract.getNameFirstRep().getUseElement().getCode()).isEqualTo("usual");
    // OBR.4 maps to ServiceRequest.code.  Verify resulting CodeableConcept.
    assertThat(serviceRequest.hasCode()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(serviceRequest.getCode(), "83036E", "HEMOGLOBIN A1C", "urn:id:PACSEAP", "HEMOGLOBIN A1C");
    List<Resource> diagnosticReportList = ResourceUtils.getResourceList(e, ResourceType.DiagnosticReport);
    assertThat(diagnosticReportList).hasSize(1);
    DiagnosticReport diagnosticReport = ResourceUtils.getResourceDiagnosticReport(diagnosticReportList.get(0), context);
    // OBR.4 ALSO maps to DiagnosticReport.code.  Verify resulting CodeableConcept.
    assertThat(diagnosticReport.hasCode()).isTrue();
    DatatypeUtils.checkCommonCodeableConceptAssertions(diagnosticReport.getCode(), "83036E", "HEMOGLOBIN A1C", "urn:id:PACSEAP", "HEMOGLOBIN A1C");
    assertThat(diagnosticReport.hasBasedOn()).isTrue();
    assertThat(diagnosticReport.getBasedOn()).hasSize(1);
    // OBR.7 maps to create an DiagnosticReport.effectiveDateTime
    assertThat(diagnosticReport.hasEffectiveDateTimeType()).isTrue();
    assertThat(diagnosticReport.getEffectiveDateTimeType().toString()).containsPattern("2017-07-07T15:07:07");
    // Check for DiagnosticReport.issued instant of OBR.22
    assertThat(diagnosticReport.hasIssued()).isTrue();
    // NOTE: The data is kept as an InstantType, and is extracted with .toInstant
    // thus results in a different format than other time stamps that are based on DateTimeType
    assertThat(diagnosticReport.getIssued().toInstant().toString()).contains("2018-09-24T07:29:00Z");
    // Get the diagnosticReport.resultsInterpreter, which should match the Practitioner data from OBR.32
    assertThat(diagnosticReport.hasResultsInterpreter()).isTrue();
    assertThat(diagnosticReport.getResultsInterpreter()).hasSize(1);
    String resultsInterpreterRef = diagnosticReport.getResultsInterpreter().get(0).getReference();
    pract = ResourceUtils.getSpecificPractitionerFromBundleEntriesList(e, resultsInterpreterRef);
    // Confirm that the matching practitioner by ID has the correct content (simple validation)
    // Should be the value OBR.32
    assertThat(pract.getIdentifierFirstRep().getValue()).isEqualTo("323232");
    assertThat(pract.getName()).hasSize(1);
    assertThat(pract.getName().get(0).getTextElement()).hasToString("Paul J Mahoney");
    // Check for OBR.25 mapped to DiagnosticReport.status
    assertThat(diagnosticReport.hasStatus()).isTrue();
    assertThat(diagnosticReport.getStatusElement().getCode()).isEqualTo("final");
}

Example 5 with USUAL

use of org.hl7.fhir.dstu3.model.Identifier.IdentifierUse.USUAL in project integration-adaptor-111 by nhsconnect.

the class ListMapper method mapList.

public ListResource mapList(POCDMT000002UK01ClinicalDocument1 clinicalDocument, Encounter encounter, Collection<Resource> resourcesCreated, Reference deviceRef) {
    ListResource listResource = new ListResource();
    listResource.setIdElement(resourceUtil.newRandomUuid());
    Identifier docIdentifier = new Identifier();
    docIdentifier.setUse(USUAL);
    docIdentifier.setValue(clinicalDocument.getSetId().getRoot());
    listResource.setStatus(CURRENT).setTitle(LIST_TITLE).setMode(WORKING).setCode(createCodeConcept()).setSubject(encounter.getSubject()).setSourceTarget(encounter.getSubjectTarget()).setEncounter(resourceUtil.createReference(encounter)).setEncounterTarget(encounter).setDateElement(DateUtil.parse(clinicalDocument.getEffectiveTime().getValue())).setSource(deviceRef).setOrderedBy(createOrderByConcept());
    resourcesCreated.stream().sorted(resourceDateComparator).filter(it -> TRIAGE_RESOURCES.contains(it.getResourceType()) && it.hasId()).map(resourceUtil::createReference).map(ListResource.ListEntryComponent::new).forEach(listResource::addEntry);
    return listResource;
}