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

Example 51 with DocumentReference

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

the class Iti65RequestConverter method processDocumentReference.

/**
 * ITI-65: process DocumentReference resource from Bundle
 * @param reference
 * @param entry
 */
public void processDocumentReference(DocumentReference reference, DocumentEntry entry) {
    if (reference.getIdElement() != null) {
        entry.setEntryUuid(reference.getIdElement().getIdPart());
    } else {
        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 status=superseded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        case SUPERSEDED: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")));
        }
    }
    Extension deletionStatus = reference.getExtensionByUrl("http://fhir.ch/ig/ch-epr-mhealth/StructureDefinition/ch-ext-deletionstatus");
    if (deletionStatus != null) {
        if (deletionStatus.getValue() instanceof Coding) {
            Coding value = (Coding) deletionStatus.getValue();
            String code = value.getCode();
            entry.setExtraMetadata(Collections.singletonMap("urn:e-health-suisse:2019:deletionStatus", Collections.singletonList("urn:e-health-suisse:2019:deletionStatus:" + code)));
        }
    }
    // Patient.identifier.use element set to ‘usual’.
    if (context.hasSourcePatientInfo()) {
        entry.setSourcePatientId(transformReferenceToIdentifiable(context.getSourcePatientInfo(), reference));
        entry.setSourcePatientInfo(transformReferenceToPatientInfo(context.getSourcePatientInfo(), reference));
    }
}

Example 52 with DocumentReference

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

the class Iti65RequestConverter method convert.

/**
 * convert ITI-65 to ITI-41 request
 * @param requestBundle
 * @return
 */
public ProvideAndRegisterDocumentSet convert(@Body Bundle requestBundle) {
    SubmissionSet submissionSet = new SubmissionSet();
    ProvideAndRegisterDocumentSetBuilder builder = new ProvideAndRegisterDocumentSetBuilder(true, submissionSet);
    // create mapping fullUrl -> resource for each resource in bundle
    Map<String, Resource> resources = new HashMap<String, Resource>();
    ListResource manifestNeu = null;
    for (Bundle.BundleEntryComponent requestEntry : requestBundle.getEntry()) {
        Resource resource = requestEntry.getResource();
        /*if (resource instanceof DocumentManifest) {
            	manifest = (DocumentManifest) resource;            	
            } else*/
        if (resource instanceof DocumentReference) {
            resources.put(requestEntry.getFullUrl(), resource);
        } else if (resource instanceof ListResource) {
            manifestNeu = (ListResource) resource;
        // resources.put(requestEntry.getFullUrl(), resource);
        } else if (resource instanceof Binary) {
            resources.put(requestEntry.getFullUrl(), resource);
        } else {
            throw new IllegalArgumentException(resource + " is not allowed here");
        }
    }
    /*if (manifest != null) {
		  processDocumentManifest(manifest, submissionSet);
	    } else {*/
    processDocumentManifest(manifestNeu, submissionSet);
    // set limited metadata
    for (CanonicalType profile : requestBundle.getMeta().getProfile()) {
        if ("http://ihe.net/fhir/StructureDefinition/IHE_MHD_Provide_Comprehensive_DocumentBundle".equals(profile.getValue())) {
            submissionSet.setLimitedMetadata(false);
        } else if ("http://ihe.net/fhir/StructureDefinition/IHE_MHD_Provide_Minimal_DocumentBundle".equals(profile.getValue())) {
            submissionSet.setLimitedMetadata(true);
        } else if ("http://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Comprehensive.ProvideBundle".equals(profile.getValue())) {
            submissionSet.setLimitedMetadata(false);
        } else if ("http://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.Minimal.ProvideBundle".equals(profile.getValue())) {
            submissionSet.setLimitedMetadata(true);
        }
    }
    // process all resources referenced in DocumentManifest.content
    for (ListEntryComponent listEntry : manifestNeu.getEntry()) {
        Reference content = listEntry.getItem();
        String refTarget = content.getReference();
        Resource resource = resources.get(refTarget);
        if (resource instanceof DocumentReference) {
            DocumentReference documentReference = (DocumentReference) resource;
            Document doc = new Document();
            DocumentEntry entry = new DocumentEntry();
            processDocumentReference(documentReference, entry);
            doc.setDocumentEntry(entry);
            entry.setRepositoryUniqueId(config.getRepositoryUniqueId());
            // create associations
            for (DocumentReferenceRelatesToComponent relatesTo : documentReference.getRelatesTo()) {
                Reference target = relatesTo.getTarget();
                DocumentRelationshipType code = relatesTo.getCode();
                Association association = new Association();
                switch(code) {
                    case REPLACES:
                        association.setAssociationType(AssociationType.REPLACE);
                        break;
                    case TRANSFORMS:
                        association.setAssociationType(AssociationType.TRANSFORM);
                        break;
                    case SIGNS:
                        association.setAssociationType(AssociationType.SIGNS);
                        break;
                    case APPENDS:
                        association.setAssociationType(AssociationType.APPEND);
                        break;
                    default:
                }
                association.setSourceUuid(entry.getEntryUuid());
                association.setTargetUuid(transformUriFromReference(target));
                builder.withAssociation(association);
            }
            // get binary content from attachment.data or from referenced Binary resource
            Attachment attachment = documentReference.getContentFirstRep().getAttachment();
            if (attachment.hasData()) {
                doc.setDataHandler(new DataHandler(new ByteArrayDataSource(attachment.getData(), attachment.getContentType())));
                byte[] decoded = attachment.getData();
                entry.setSize((long) decoded.length);
                entry.setHash(SHAsum(decoded));
            } else if (attachment.hasUrl()) {
                String contentURL = attachment.getUrl();
                Resource binaryContent = resources.get(contentURL);
                if (binaryContent instanceof Binary) {
                    String contentType = attachment.getContentType();
                    Binary binary = (Binary) binaryContent;
                    if (binary.hasContentType() && !binary.getContentType().equals(contentType))
                        throw new InvalidRequestException("ContentType in Binary and in DocumentReference must match");
                    doc.setDataHandler(new DataHandler(new ByteArrayDataSource(binary.getData(), contentType)));
                    byte[] decoded = binary.getData();
                    entry.setSize((long) decoded.length);
                    entry.setHash(SHAsum(decoded));
                    Identifier masterIdentifier = documentReference.getMasterIdentifier();
                    binary.setUserData("masterIdentifier", noPrefix(masterIdentifier.getValue()));
                }
            }
            builder.withDocument(doc);
        }
    }
    return builder.build();
}

Example 53 with DocumentReference

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

the class Iti65ResponseConverter method translateToFhir.

/**
 * convert ITI-41 response to ITI-65 response
 */
@Override
public Object translateToFhir(Response input, Map<String, Object> parameters) {
    if (input.getStatus().equals(Status.SUCCESS)) {
        Bundle responseBundle = new Bundle();
        Bundle requestBundle = (Bundle) parameters.get(Utils.KEPT_BODY);
        responseBundle.getMeta().addProfile("http://profiles.ihe.net/ITI/MHD/StructureDefinition/IHE.MHD.ProvideDocumentBundleResponse");
        for (Bundle.BundleEntryComponent requestEntry : requestBundle.getEntry()) {
            Bundle.BundleEntryResponseComponent response = new Bundle.BundleEntryResponseComponent().setStatus("201 Created").setLastModified(new Date());
            if (requestEntry.getResource() instanceof Binary) {
                String uniqueId = (String) requestEntry.getResource().getUserData("masterIdentifier");
                response.setLocation(config.getUriMagXdsRetrieve() + "?uniqueId=" + uniqueId + "&repositoryUniqueId=" + config.getRepositoryUniqueId());
            } else if (requestEntry.getResource() instanceof ListResource) {
                String id = config.getSchemeMapper().getScheme(((ListResource) requestEntry.getResource()).getId());
                response.setLocation("List/" + id);
            } else if (requestEntry.getResource() instanceof DocumentReference) {
                String id = config.getSchemeMapper().getScheme(((DocumentReference) requestEntry.getResource()).getId());
                response.setLocation("DocumentReference/" + id);
            }
            responseBundle.addEntry().setResponse(response);
        }
        return responseBundle;
    } else {
        processError(input);
        return null;
    }
}