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

Example 1 with DocumentReferenceContentComponent

use of org.hl7.fhir.r4.model.DocumentReference.DocumentReferenceContentComponent 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 2 with DocumentReferenceContentComponent

use of org.hl7.fhir.r4.model.DocumentReference.DocumentReferenceContentComponent in project summary-care-record-api by NHSDigital.

the class GetScrService method buildDocumentReferenceContent.

private DocumentReferenceContentComponent buildDocumentReferenceContent(String nhsNumber, String scrId) {
    DocumentReferenceContentComponent content = new DocumentReferenceContentComponent();
    String attachmentUrl = String.format(ATTACHMENT_URL, getScrUrl(), scrId, nhsNumber);
    content.setAttachment(new Attachment().setUrl(attachmentUrl));
    return content;
}

Example 3 with DocumentReferenceContentComponent

use of org.hl7.fhir.r4.model.DocumentReference.DocumentReferenceContentComponent in project summary-care-record-api by NHSDigital.

the class GetScrService method buildDocumentReference.

private DocumentReference buildDocumentReference(String nhsNumber, EventListQueryResponse response, Patient patient) {
    DocumentReference documentReference = new DocumentReference();
    documentReference.setId(randomUUID());
    documentReference.addSecurityLabel(new CodeableConcept(new Coding().setCode(response.getViewPermission().getFhirValue()).setSystem(ACS_SYSTEM)));
    documentReference.setStatus(CURRENT);
    documentReference.setType(GP_SUMMARY_SNOMED);
    documentReference.setSubject(new Reference(patient));
    DocumentReferenceContentComponent content = buildDocumentReferenceContent(nhsNumber, response.getLatestScrId());
    documentReference.addContent(content);
    documentReference.setMasterIdentifier(new Identifier().setValue(response.getLatestScrId()).setSystem(SCR_ID_SYSTEM));
    DocumentReferenceContextComponent context = new DocumentReferenceContextComponent();
    context.addEvent(GP_SUMMARY_SNOMED);
    documentReference.setContext(context);
    return documentReference;
}

Example 4 with DocumentReferenceContentComponent

use of org.hl7.fhir.r4.model.DocumentReference.DocumentReferenceContentComponent in project org.hl7.fhir.core by hapifhir.

the class ArgonautConverter method makeDocumentReference.

private void makeDocumentReference(CDAUtilities cda, Convert convert, Element doc, Context context) throws Exception {
    scanSection("document", doc);
    DocumentReference ref = new DocumentReference();
    ref.setId(context.getBaseId() + "-document");
    ref.setMasterIdentifier(convert.makeIdentifierFromII(cda.getChild(doc, "id")));
    ref.setSubject(context.getSubjectRef());
    ref.setType(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(doc, "code")), null));
    ref.addAuthor(context.getAuthorRef());
    ref.setCreatedElement(convert.makeDateTimeFromTS(cda.getChild(doc, "effectiveTime")));
    ref.setIndexedElement(InstantType.now());
    ref.setStatus(DocumentReferenceStatus.CURRENT);
    ref.addSecurityLabel(inspectCode(convert.makeCodeableConceptFromCD(cda.getChild(doc, "confidentialityCode")), null));
    DocumentReferenceContentComponent cnt = ref.addContent();
    cnt.getAttachment().setContentType("application/hl7-v3+xml").setUrl("Binary/" + context.getBaseId()).setLanguage(convertLanguage(cda.getChild(doc, "language")));
    // for (Element ti : cda.getChildren(doc, "templateId"))
    // cnt.addFormat().setSystem("urn:oid:1.3.6.1.4.1.19376.1.2.3").setCode(value)("urn:oid:"+ti.getAttribute("root"));
    ref.setContext(new DocumentReferenceContextComponent());
    ref.getContext().setPeriod(convert.makePeriodFromIVL(cda.getChild(cda.getChild(doc, "serviceEvent"), "effectiveTime")));
    for (CodeableConcept cc : context.getEncounter().getType()) ref.getContext().addEvent(cc);
    ref.setDescription(cda.getChild(doc, "title").getTextContent());
    ref.setCustodian(new Reference().setReference("Organization/" + processOrganization(cda.getDescendent(doc, "custodian/assignedCustodian/representedCustodianOrganization"), cda, convert, context).getId()));
    Practitioner p = processPerformer(cda, convert, context, cda.getChild(doc, "legalAuthenticator"), "assignedEntity", "assignedPerson");
    ref.setAuthenticator(new Reference().setReference("Practitioner/" + p.getId()).setDisplay(p.getUserString("display")));
    saveResource(ref);
}

Example 5 with DocumentReferenceContentComponent

use of org.hl7.fhir.r4.model.DocumentReference.DocumentReferenceContentComponent in project MobileAccessGateway by i4mi.

the class Iti65RequestConverter method processDocumentReference.

/**
 * ITI-65: process DocumentReference resource from Bundle
 * @param reference
 * @param entry
 */
private void processDocumentReference(DocumentReference reference, DocumentEntry entry) {
    entry.assignEntryUuid();
    reference.setId(entry.getEntryUuid());
    Identifier masterIdentifier = reference.getMasterIdentifier();
    entry.setUniqueId(noPrefix(masterIdentifier.getValue()));
    // limitedMetadata -> meta.profile canonical [0..*]
    // No action
    // availabilityStatus -> status code {DocumentReferenceStatus} [1..1]
    // approved -> status=current
    // deprecated -> status=superseded
    // Other status values are allowed but are not defined in this mapping to XDS.
    DocumentReferenceStatus status = reference.getStatus();
    switch(status) {
        case CURRENT:
            entry.setAvailabilityStatus(AvailabilityStatus.APPROVED);
            break;
        case SUPERSEDED:
            entry.setAvailabilityStatus(AvailabilityStatus.DEPRECATED);
            break;
        default:
            throw new InvalidRequestException("Unknown document status");
    }
    // contentTypeCode -> type CodeableConcept [0..1]
    CodeableConcept type = reference.getType();
    entry.setTypeCode(transform(type));
    // classCode -> category CodeableConcept [0..*]
    List<CodeableConcept> category = reference.getCategory();
    entry.setClassCode(transform(category));
    // patientId -> subject Reference(Patient| Practitioner| Group| Device) [0..1],
    Reference subject = reference.getSubject();
    entry.setPatientId(transformReferenceToIdentifiable(subject, reference));
    // creationTime -> date instant [0..1]
    entry.setCreationTime(timestampFromDate(reference.getDateElement()));
    // PractitionerRole| Organization| Device| Patient| RelatedPerson) [0..*]
    for (Reference authorRef : reference.getAuthor()) {
        entry.getAuthors().add(transformAuthor(authorRef, reference.getContained(), null));
    }
    if (reference.hasAuthenticator()) {
        Reference authenticatorRef = reference.getAuthenticator();
        Resource authenticator = findResource(authenticatorRef, reference.getContained());
        if (authenticator instanceof Practitioner) {
            entry.setLegalAuthenticator(transform((Practitioner) authenticator));
        } else if (authenticator instanceof PractitionerRole) {
            Practitioner practitioner = (Practitioner) findResource(((PractitionerRole) authenticator).getPractitioner(), reference.getContained());
            if (practitioner != null)
                entry.setLegalAuthenticator(transform(practitioner));
        } else
            throw new InvalidRequestException("No authenticator of type Organization supported.");
    }
    // title -> description string [0..1]
    String title = reference.getDescription();
    if (title != null)
        entry.setTitle(localizedString(title));
    // confidentialityCode -> securityLabel CodeableConcept [0..*] Note: This
    // is NOT the DocumentReference.meta, as that holds the meta tags for the
    // DocumentReference itself.
    List<CodeableConcept> securityLabels = reference.getSecurityLabel();
    transformCodeableConcepts(securityLabels, entry.getConfidentialityCodes());
    // mimeType -> content.attachment.contentType [1..1] code [0..1]
    DocumentReferenceContentComponent content = reference.getContentFirstRep();
    if (content == null)
        throw new InvalidRequestException("Missing content field in DocumentReference");
    Attachment attachment = content.getAttachment();
    if (attachment == null)
        throw new InvalidRequestException("Missing attachment field in DocumentReference");
    entry.setMimeType(attachment.getContentType());
    // languageCode -> content.attachment.language code [0..1]
    entry.setLanguageCode(attachment.getLanguage());
    // size -> content.attachment.size integer [0..1] The size is calculated
    if (attachment.hasSize())
        entry.setSize((long) attachment.getSize());
    // on the data prior to base64 encoding, if the data is base64 encoded.
    // hash -> content.attachment.hash string [0..1]
    byte[] hash = attachment.getHash();
    if (hash != null)
        entry.setHash(Hex.encodeHexString(hash));
    // comments -> content.attachment.title string [0..1]
    String comments = attachment.getTitle();
    if (comments != null)
        entry.setComments(localizedString(comments));
    // creationTime -> content.attachment.creation dateTime [0..1]
    if (attachment.hasCreation()) {
        if (entry.getCreationTime() == null)
            entry.setCreationTime(timestampFromDate(attachment.getCreationElement()));
        else if (!timestampFromDate(attachment.getCreationElement()).equals(entry.getCreationTime()))
            throw new InvalidRequestException("DocumentReference.date does not match attachment.creation element");
    }
    // formatCode -> content.format Coding [0..1]
    Coding coding = content.getFormat();
    entry.setFormatCode(transform(coding));
    DocumentReferenceContextComponent context = reference.getContext();
    // Instead: referenceIdList -> related.identifier
    for (Reference ref : context.getRelated()) {
        Identifiable refId = transformReferenceToIdentifiable(ref, reference);
        if (refId != null) {
            ReferenceId referenceId = new ReferenceId();
            referenceId.setAssigningAuthority(new CXiAssigningAuthority(null, refId.getAssigningAuthority().getUniversalId(), refId.getAssigningAuthority().getUniversalIdType()));
            referenceId.setId(refId.getId());
            entry.getReferenceIdList().add(referenceId);
        }
    }
    // Currently not mapped
    /*for (Reference encounterRef : context.getEncounter()) {
        	ReferenceId referenceId = new ReferenceId();
        	Identifiable id = transformReferenceToIdentifiable(encounterRef, reference);
        	if (id != null) {
        	  referenceId.setIdTypeCode(ReferenceId.ID_TYPE_ENCOUNTER_ID);        	
        	  referenceId.setId(id.getId());
        	  //referenceId.setAssigningAuthority(new CXiAid.getAssigningAuthority().getUniversalId());
			  entry.getReferenceIdList().add(referenceId );
        }*/
    // eventCodeList -> context.event CodeableConcept [0..*]
    List<CodeableConcept> events = context.getEvent();
    transformCodeableConcepts(events, entry.getEventCodeList());
    // serviceStartTime serviceStopTime -> context.period Period [0..1]
    Period period = context.getPeriod();
    if (period != null) {
        entry.setServiceStartTime(timestampFromDate(period.getStartElement()));
        entry.setServiceStopTime(timestampFromDate(period.getEndElement()));
    }
    // healthcareFacilityTypeCode -> context.facilityType CodeableConcept
    // [0..1]
    entry.setHealthcareFacilityTypeCode(transformCodeableConcept(context.getFacilityType()));
    // practiceSettingCode -> context.practiceSetting CodeableConcept [0..1]
    entry.setPracticeSettingCode(transformCodeableConcept(context.getPracticeSetting()));
    Extension originalRole = reference.getExtensionByUrl("http://fhir.ch/ig/ch-epr-mhealth/StructureDefinition/ch-ext-author-authorrole");
    if (originalRole != null) {
        if (originalRole.getValue() instanceof Coding) {
            Coding value = (Coding) originalRole.getValue();
            String system = noPrefix(value.getSystem());
            String code = value.getCode();
            entry.setExtraMetadata(Collections.singletonMap("urn:e-health-suisse:2020:originalProviderRole", Collections.singletonList(code + "^^^&" + system + "&ISO")));
        }
    }
    // Patient.identifier.use element set to ‘usual’.
    if (context.hasSourcePatientInfo()) {
        entry.setSourcePatientId(transformReferenceToIdentifiable(context.getSourcePatientInfo(), reference));
        entry.setSourcePatientInfo(transformReferenceToPatientInfo(context.getSourcePatientInfo(), reference));
    }
}