use of org.hl7.fhir.r4b.model.Attachment in project org.hl7.fhir.core by hapifhir.
the class LibraryRenderer method render.
public boolean render(XhtmlNode x, ResourceWrapper lib) throws FHIRFormatError, DefinitionException, IOException {
PropertyWrapper authors = lib.getChildByName("author");
PropertyWrapper editors = lib.getChildByName("editor");
PropertyWrapper reviewers = lib.getChildByName("reviewer");
PropertyWrapper endorsers = lib.getChildByName("endorser");
if ((authors != null && authors.hasValues()) || (editors != null && editors.hasValues()) || (reviewers != null && reviewers.hasValues()) || (endorsers != null && endorsers.hasValues())) {
boolean email = hasCT(authors, "email") || hasCT(editors, "email") || hasCT(reviewers, "email") || hasCT(endorsers, "email");
boolean phone = hasCT(authors, "phone") || hasCT(editors, "phone") || hasCT(reviewers, "phone") || hasCT(endorsers, "phone");
boolean url = hasCT(authors, "url") || hasCT(editors, "url") || hasCT(reviewers, "url") || hasCT(endorsers, "url");
x.h2().tx("Participants");
XhtmlNode t = x.table("grid");
if (authors != null) {
for (BaseWrapper cd : authors.getValues()) {
participantRow(t, "Author", cd, email, phone, url);
}
}
if (authors != null) {
for (BaseWrapper cd : editors.getValues()) {
participantRow(t, "Editor", cd, email, phone, url);
}
}
if (authors != null) {
for (BaseWrapper cd : reviewers.getValues()) {
participantRow(t, "Reviewer", cd, email, phone, url);
}
}
if (authors != null) {
for (BaseWrapper cd : endorsers.getValues()) {
participantRow(t, "Endorser", cd, email, phone, url);
}
}
}
PropertyWrapper artifacts = lib.getChildByName("relatedArtifact");
if (artifacts != null && artifacts.hasValues()) {
x.h2().tx("Related Artifacts");
XhtmlNode t = x.table("grid");
boolean label = false;
boolean display = false;
boolean citation = false;
for (BaseWrapper ra : artifacts.getValues()) {
label = label || ra.has("label");
display = display || ra.has("display");
citation = citation || ra.has("citation");
}
for (BaseWrapper ra : artifacts.getValues()) {
renderArtifact(t, ra, lib, label, display, citation);
}
}
PropertyWrapper parameters = lib.getChildByName("parameter");
if (parameters != null && parameters.hasValues()) {
x.h2().tx("Parameters");
XhtmlNode t = x.table("grid");
boolean doco = false;
for (BaseWrapper p : parameters.getValues()) {
doco = doco || p.has("documentation");
}
for (BaseWrapper p : parameters.getValues()) {
renderParameter(t, p, doco);
}
}
PropertyWrapper dataRequirements = lib.getChildByName("dataRequirement");
if (dataRequirements != null && dataRequirements.hasValues()) {
x.h2().tx("Data Requirements");
for (BaseWrapper p : dataRequirements.getValues()) {
renderDataRequirement(x, (DataRequirement) p.getBase());
}
}
PropertyWrapper contents = lib.getChildByName("content");
if (contents != null) {
x.h2().tx("Contents");
boolean isCql = false;
int counter = 0;
for (BaseWrapper p : contents.getValues()) {
Attachment att = (Attachment) p.getBase();
renderAttachment(x, att, isCql, counter, lib.getId());
isCql = isCql || (att.hasContentType() && att.getContentType().startsWith("text/cql"));
counter++;
}
}
return false;
}
use of org.hl7.fhir.r4b.model.Attachment in project nia-patient-switching-standard-adaptor by NHSDigital.
the class COPCMessageHandler method extractFragmentsAndLog.
private void extractFragmentsAndLog(PatientMigrationRequest migrationRequest, PatientAttachmentLog parentAttachmentLog, String conversationId, InboundMessage message) throws ParseException, SAXException, ValidationException, InlineAttachmentProcessingException {
List<EbxmlReference> attachmentReferenceDescription = new ArrayList<>();
attachmentReferenceDescription.addAll(xmlParseUtilService.getEbxmlAttachmentsData(message));
// first item is always the message payload reference so skip it
for (var index = 1; index < attachmentReferenceDescription.size(); index++) {
var payloadReference = attachmentReferenceDescription.get(index);
var descriptionString = "";
var messageId = "";
var fileUpload = false;
// in this instance there should only ever be one CID on a fragment index file
if (payloadReference.getHref().contains("cid:")) {
messageId = payloadReference.getHref().substring(payloadReference.getHref().indexOf("cid:") + "cid:".length());
descriptionString = message.getAttachments().get(0).getDescription();
// upload the file
attachmentHandlerService.storeAttachments(message.getAttachments(), conversationId);
fileUpload = true;
} else {
var localMessageId = payloadReference.getHref().substring(payloadReference.getHref().indexOf("mid:") + "mid:".length());
messageId = localMessageId;
var externalAttachmentResult = message.getExternalAttachments().stream().filter(attachment -> attachment.getMessageId().equals(localMessageId)).findFirst();
if (externalAttachmentResult == null || externalAttachmentResult.stream().count() != 1) {
throw new ValidationException("External Attachment in payload header does not match a received External Attachment ID");
}
var externalAttachment = externalAttachmentResult.get();
descriptionString = externalAttachment.getDescription();
}
PatientAttachmentLog fragmentLog = patientAttachmentLogService.findAttachmentLog(messageId, conversationId);
if (fragmentLog != null) {
updateFragmentLog(fragmentLog, parentAttachmentLog, descriptionString, index - 1, parentAttachmentLog.getLargeAttachment());
patientAttachmentLogService.updateAttachmentLog(fragmentLog, conversationId);
} else {
PatientAttachmentLog newFragmentLog = buildPatientAttachmentLog(messageId, descriptionString, parentAttachmentLog.getMid(), migrationRequest.getId(), index - 1, fileUpload, parentAttachmentLog.getLargeAttachment());
patientAttachmentLogService.addAttachmentLog(newFragmentLog);
}
}
}
use of org.hl7.fhir.r4b.model.Attachment in project CRD by HL7-DaVinci.
the class LibraryContentProcessor method processResource.
/**
* Processes the Library to have content pointing to CQL replaced with embedded base64 encoded CQL file.
* Only supports relative paths to files being hosted on this server.
*/
@Override
protected Library processResource(Library inputResource, FileStore fileStore, String baseUrl) {
Library output = inputResource.copy();
List<Attachment> content = inputResource.getContent();
logger.info("Attempt to embed CQL (ELM) into Requested Library");
// if the first value in content is application/elm+json with a url, replace it with base64 encoded data
if (content.size() > 0) {
Attachment attachment = content.get(0);
if (attachment.hasUrl()) {
String url = attachment.getUrl();
// make sure this is a relative path
if (!url.toUpperCase().startsWith("HTTP")) {
// grab the topic, fhir version, and filename from the url
String[] urlParts = url.split("/");
if (urlParts.length >= 4) {
if ((attachment.getContentType().equalsIgnoreCase("application/elm+json")) || (attachment.getContentType().equalsIgnoreCase("text/cql"))) {
// content is CQL (assuming elm/json is actually CQL)
String topic = urlParts[1];
String fhirVersion = urlParts[2].toUpperCase();
String fileName = urlParts[3];
List<Attachment> attachments = new ArrayList<>();
// get the CQL data and base64 encode
FileResource cqlFileResource = fileStore.getFile(topic, fileName, fhirVersion, false);
attachments.add(base64EncodeToAttachment(cqlFileResource, "text/cql"));
// get the ELM data and base64 encode
FileResource elmFileResource = fileStore.getFile(topic, fileName, fhirVersion, true);
attachments.add(base64EncodeToAttachment(elmFileResource, "application/elm+json"));
// insert back into the Library
output.setContent(attachments);
} else {
logger.info("Content is not xml or json elm");
}
} else {
logger.info("URL doesn't split properly: " + url);
}
} else {
logger.info("URL is NOT relative");
}
} else {
logger.info("Content is not a url");
}
} else {
logger.info("No content in library");
}
return output;
}
use of org.hl7.fhir.r4b.model.Attachment 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));
}
}
use of org.hl7.fhir.r4b.model.Attachment 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();
}
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