/** {@inheritDoc} not needed in Testserver */
public UriDt post(IResource res) {
log.info(res.getClass().toString());
String resURI = "http://www.test-server.de/" + res.getClass().getSimpleName() + "/" + resNumber;
UriDt setUri = new UriDt(resURI);
log.info("TestSever Created ID: " + resURI);
resMap.put(resURI, res);
resNumber++;
return setUri;
}
private String parseNarrative(
HomeRequest theRequest, EncodingEnum theCtEnum, String theResultBody) {
try {
IBaseResource par = theCtEnum.newParser(getContext(theRequest)).parseResource(theResultBody);
String retVal;
if (par instanceof IResource) {
IResource resource = (IResource) par;
retVal = resource.getText().getDiv().getValueAsString();
} else if (par instanceof IDomainResource) {
retVal = ((IDomainResource) par).getText().getDivAsString();
} else {
retVal = null;
}
return StringUtils.defaultString(retVal);
} catch (Exception e) {
ourLog.error("Failed to parse resource", e);
return "";
}
}
private void encodeResourceToXmlStreamWriter(
IBaseResource theResource, XMLStreamWriter theEventWriter, boolean theIncludedResource)
throws XMLStreamException, DataFormatException {
String resourceId = null;
if (theResource instanceof IResource) {
// HAPI structs
IResource iResource = (IResource) theResource;
if (StringUtils.isNotBlank(iResource.getId().getValue())) {
resourceId = iResource.getId().getIdPart();
}
} else {
// HL7 structs
IAnyResource resource = (IAnyResource) theResource;
if (StringUtils.isNotBlank(resource.getId())) {
resourceId = resource.getId();
}
}
encodeResourceToXmlStreamWriter(theResource, theEventWriter, theIncludedResource, resourceId);
}
@Override
public IDeleteTyped resource(IResource theResource) {
Validate.notNull(theResource, "theResource can not be null");
IdDt id = theResource.getId();
Validate.notNull(id, "theResource.getId() can not be null");
if (id.hasResourceType() == false || id.hasIdPart() == false) {
throw new IllegalArgumentException(
"theResource.getId() must contain a resource type and logical ID at a minimum (e.g. Patient/1234), found: "
+ id.getValue());
}
myId = id;
return this;
}
/**
* @notice In Fhir model, {@link Patient} has a collection of names, while in this extension
* table, {@link PersonComplement}, there is only one name for each {@link Person}.
*/
@Override
public IResourceEntity constructEntityFromResource(IResource resource) {
super.constructEntityFromResource(resource);
if (resource instanceof Patient) {
Patient patient = (Patient) resource;
Iterator<HumanNameDt> iterator = patient.getName().iterator();
// while(iterator.hasNext()){
if (iterator.hasNext()) {
HumanNameDt next = iterator.next();
this.givenName1 =
next.getGiven()
.get(0)
.getValue(); // the next method was not advancing to the next element, then the need
// to use the get(index) method
if (next.getGiven().size()
> 1) // TODO add unit tests, to assure this won't be changed to hasNext
this.givenName2 = next.getGiven().get(1).getValue();
Iterator<StringDt> family = next.getFamily().iterator();
this.familyName = "";
while (family.hasNext()) {
this.familyName = this.familyName.concat(family.next().getValue() + " ");
}
if (next.getSuffix().iterator().hasNext())
this.suffixName = next.getSuffix().iterator().next().getValue();
if (next.getPrefix().iterator().hasNext())
this.prefixName = next.getPrefix().iterator().next().getValue();
}
// }
this.active = patient.getActive();
// MARITAL STATUS
//
// this.maritalStatus.setId(OmopConceptMapping.getInstance().get(OmopConceptMapping.MARITAL_STATUS, patient.getMaritalStatus().getText()));
} else {
ourLog.error(
"There was not possible to construct the entity ? using the resource ?. It should be used the resource ?.",
this.getClass().getSimpleName(),
resource.getResourceName(),
getResourceType());
}
return this;
}
@Override
public MethodOutcome execute() {
if (myResource == null) {
myResource = parseResourceBody(myResourceBody);
}
if (myId == null) {
myId = myResource.getId();
}
if (myId == null || myId.hasIdPart() == false) {
throw new InvalidRequestException(
"No ID supplied for resource to update, can not invoke server");
}
BaseHttpClientInvocation invocation =
MethodUtil.createUpdateInvocation(myResource, myResourceBody, myId, myContext);
RuntimeResourceDefinition def = myContext.getResourceDefinition(myResource);
final String resourceName = def.getName();
OutcomeResponseHandler binding = new OutcomeResponseHandler(resourceName);
Map<String, List<String>> params = new HashMap<String, List<String>>();
return invoke(params, binding, invocation);
}
@SuppressWarnings("unchecked")
@Override
public Object invokeServer(
IRestfulServer theServer, RequestDetails theRequest, Object[] theMethodParams)
throws InvalidRequestException, InternalErrorException {
/*
* The design of HAPI's transaction method for DSTU1 support assumed that a transaction was just an update on a
* bunch of resources (because that's what it was), but in DSTU2 transaction has become much more broad, so we
* no longer hold the user's hand much here.
*/
if (myTransactionParamStyle == ParamStyle.RESOURCE_BUNDLE) {
// This is the DSTU2 style
Object response = invokeServerMethod(theServer, theRequest, theMethodParams);
return response;
}
// Grab the IDs of all of the resources in the transaction
List<IResource> resources;
if (theMethodParams[myTransactionParamIndex] instanceof Bundle) {
resources = ((Bundle) theMethodParams[myTransactionParamIndex]).toListOfResources();
} else {
resources = (List<IResource>) theMethodParams[myTransactionParamIndex];
}
IdentityHashMap<IResource, IdDt> oldIds = new IdentityHashMap<IResource, IdDt>();
for (IResource next : resources) {
oldIds.put(next, next.getId());
}
// Call the server implementation method
Object response = invokeServerMethod(theServer, theRequest, theMethodParams);
IBundleProvider retVal = toResourceList(response);
/*
* int offset = 0; if (retVal.size() != resources.size()) { if (retVal.size() > 0 && retVal.getResources(0,
* 1).get(0) instanceof OperationOutcome) { offset = 1; } else { throw new
* InternalErrorException("Transaction bundle contained " + resources.size() +
* " entries, but server method response contained " + retVal.size() + " entries (must be the same)"); } }
*/
List<IBaseResource> retResources = retVal.getResources(0, retVal.size());
for (int i = 0; i < retResources.size(); i++) {
IdDt oldId = oldIds.get(retResources.get(i));
IBaseResource newRes = retResources.get(i);
if (newRes.getIdElement() == null || newRes.getIdElement().isEmpty()) {
if (!(newRes instanceof BaseOperationOutcome)) {
throw new InternalErrorException(
"Transaction method returned resource at index "
+ i
+ " with no id specified - IResource#setId(IdDt)");
}
}
if (oldId != null && !oldId.isEmpty()) {
if (!oldId.equals(newRes.getIdElement()) && newRes instanceof IResource) {
((IResource) newRes)
.getResourceMetadata()
.put(ResourceMetadataKeyEnum.PREVIOUS_ID, oldId);
}
}
}
return retVal;
}
private void encodeResourceToXmlStreamWriter(
IBaseResource theResource,
XMLStreamWriter theEventWriter,
boolean theContainedResource,
String theResourceId)
throws XMLStreamException {
if (!theContainedResource) {
super.containResourcesForEncoding(theResource);
}
RuntimeResourceDefinition resDef = myContext.getResourceDefinition(theResource);
if (resDef == null) {
throw new ConfigurationException("Unknown resource type: " + theResource.getClass());
}
theEventWriter.writeStartElement(resDef.getName());
theEventWriter.writeDefaultNamespace(FHIR_NS);
if (theResource instanceof IAnyResource) {
// HL7.org Structures
encodeCompositeElementToStreamWriter(
theResource, theResource, theEventWriter, resDef, theContainedResource);
} else {
if (myContext.getVersion().getVersion().isNewerThan(FhirVersionEnum.DSTU1)) {
// DSTU2+
IResource resource = (IResource) theResource;
writeOptionalTagWithValue(theEventWriter, "id", theResourceId);
InstantDt updated =
(InstantDt) resource.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
IdDt resourceId = resource.getId();
String versionIdPart = resourceId.getVersionIdPart();
if (isBlank(versionIdPart)) {
versionIdPart = ResourceMetadataKeyEnum.VERSION.get(resource);
}
List<BaseCodingDt> securityLabels =
extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.SECURITY_LABELS);
List<IdDt> profiles =
extractMetadataListNotNull(resource, ResourceMetadataKeyEnum.PROFILES);
TagList tags = ResourceMetadataKeyEnum.TAG_LIST.get(resource);
if (ElementUtil.isEmpty(versionIdPart, updated, securityLabels, profiles) == false) {
theEventWriter.writeStartElement("meta");
writeOptionalTagWithValue(theEventWriter, "versionId", versionIdPart);
if (updated != null) {
writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
}
for (IdDt profile : profiles) {
theEventWriter.writeStartElement("profile");
theEventWriter.writeAttribute("value", profile.getValue());
theEventWriter.writeEndElement();
}
for (BaseCodingDt securityLabel : securityLabels) {
theEventWriter.writeStartElement("security");
BaseRuntimeElementCompositeDefinition<?> def =
(BaseRuntimeElementCompositeDefinition<?>)
myContext.getElementDefinition(securityLabel.getClass());
encodeCompositeElementChildrenToStreamWriter(
resource, securityLabel, theEventWriter, def.getChildren(), theContainedResource);
theEventWriter.writeEndElement();
}
if (tags != null) {
for (Tag tag : tags) {
theEventWriter.writeStartElement("tag");
writeOptionalTagWithValue(theEventWriter, "system", tag.getScheme());
writeOptionalTagWithValue(theEventWriter, "code", tag.getTerm());
writeOptionalTagWithValue(theEventWriter, "display", tag.getLabel());
theEventWriter.writeEndElement();
}
}
theEventWriter.writeEndElement();
}
if (theResource instanceof IBaseBinary) {
IBaseBinary bin = (IBaseBinary) theResource;
writeOptionalTagWithValue(theEventWriter, "contentType", bin.getContentType());
writeOptionalTagWithValue(theEventWriter, "content", bin.getContentAsBase64());
} else {
encodeResourceToStreamWriterInDstu2Format(
resDef, theResource, theResource, theEventWriter, resDef, theContainedResource);
}
} else {
// DSTU1
if (theResourceId != null && theContainedResource) {
theEventWriter.writeAttribute("id", theResourceId);
}
if (theResource instanceof IBaseBinary) {
IBaseBinary bin = (IBaseBinary) theResource;
if (bin.getContentType() != null) {
theEventWriter.writeAttribute("contentType", bin.getContentType());
}
theEventWriter.writeCharacters(bin.getContentAsBase64());
} else {
encodeCompositeElementToStreamWriter(
theResource, theResource, theEventWriter, resDef, theContainedResource);
}
}
}
theEventWriter.writeEndElement();
}
private void encodeBundleToWriterDstu2(Bundle theBundle, XMLStreamWriter theEventWriter)
throws XMLStreamException {
theEventWriter.writeStartElement("Bundle");
theEventWriter.writeDefaultNamespace(FHIR_NS);
writeOptionalTagWithValue(theEventWriter, "id", theBundle.getId().getIdPart());
InstantDt updated =
(InstantDt) theBundle.getResourceMetadata().get(ResourceMetadataKeyEnum.UPDATED);
IdDt bundleId = theBundle.getId();
if (bundleId != null && isNotBlank(bundleId.getVersionIdPart())
|| (updated != null && !updated.isEmpty())) {
theEventWriter.writeStartElement("meta");
writeOptionalTagWithValue(theEventWriter, "versionId", bundleId.getVersionIdPart());
if (updated != null) {
writeOptionalTagWithValue(theEventWriter, "lastUpdated", updated.getValueAsString());
}
theEventWriter.writeEndElement();
}
String bundleBaseUrl = theBundle.getLinkBase().getValue();
writeOptionalTagWithValue(theEventWriter, "type", theBundle.getType().getValue());
writeOptionalTagWithValue(theEventWriter, "base", bundleBaseUrl);
writeOptionalTagWithValue(
theEventWriter, "total", theBundle.getTotalResults().getValueAsString());
writeBundleResourceLink(theEventWriter, "first", theBundle.getLinkFirst());
writeBundleResourceLink(theEventWriter, "previous", theBundle.getLinkPrevious());
writeBundleResourceLink(theEventWriter, "next", theBundle.getLinkNext());
writeBundleResourceLink(theEventWriter, "last", theBundle.getLinkLast());
writeBundleResourceLink(theEventWriter, "self", theBundle.getLinkSelf());
for (BundleEntry nextEntry : theBundle.getEntries()) {
theEventWriter.writeStartElement("entry");
boolean deleted = false;
if (nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false) {
deleted = true;
}
writeOptionalTagWithValue(
theEventWriter, "base", determineResourceBaseUrl(bundleBaseUrl, nextEntry));
IResource resource = nextEntry.getResource();
if (resource != null && !resource.isEmpty() && !deleted) {
theEventWriter.writeStartElement("resource");
encodeResourceToXmlStreamWriter(resource, theEventWriter, false);
theEventWriter.writeEndElement(); // content
} else {
ourLog.debug("Bundle entry contains null resource");
}
if (nextEntry.getSearchMode().isEmpty() == false || nextEntry.getScore().isEmpty() == false) {
theEventWriter.writeStartElement("search");
writeOptionalTagWithValue(
theEventWriter, "mode", nextEntry.getSearchMode().getValueAsString());
writeOptionalTagWithValue(theEventWriter, "score", nextEntry.getScore().getValueAsString());
theEventWriter.writeEndElement();
// IResource nextResource = nextEntry.getResource();
}
if (nextEntry.getTransactionMethod().isEmpty() == false
|| nextEntry.getLinkSearch().isEmpty() == false) {
theEventWriter.writeStartElement("transaction");
writeOptionalTagWithValue(
theEventWriter, "method", nextEntry.getTransactionMethod().getValue());
writeOptionalTagWithValue(theEventWriter, "url", nextEntry.getLinkSearch().getValue());
theEventWriter.writeEndElement();
}
if (deleted) {
theEventWriter.writeStartElement("deleted");
writeOptionalTagWithValue(theEventWriter, "type", nextEntry.getId().getResourceType());
writeOptionalTagWithValue(theEventWriter, "id", nextEntry.getId().getIdPart());
writeOptionalTagWithValue(
theEventWriter, "versionId", nextEntry.getId().getVersionIdPart());
writeOptionalTagWithValue(
theEventWriter, "instant", nextEntry.getDeletedAt().getValueAsString());
theEventWriter.writeEndElement();
}
theEventWriter.writeEndElement(); // entry
}
theEventWriter.writeEndElement();
theEventWriter.close();
}
private void encodeBundleToWriterDstu1(Bundle theBundle, XMLStreamWriter eventWriter)
throws XMLStreamException {
eventWriter.writeStartElement("feed");
eventWriter.writeDefaultNamespace(ATOM_NS);
writeTagWithTextNode(eventWriter, "title", theBundle.getTitle());
writeTagWithTextNode(eventWriter, "id", theBundle.getBundleId());
writeAtomLink(eventWriter, Constants.LINK_SELF, theBundle.getLinkSelf());
writeAtomLink(eventWriter, Constants.LINK_FIRST, theBundle.getLinkFirst());
writeAtomLink(eventWriter, Constants.LINK_PREVIOUS, theBundle.getLinkPrevious());
writeAtomLink(eventWriter, Constants.LINK_NEXT, theBundle.getLinkNext());
writeAtomLink(eventWriter, Constants.LINK_LAST, theBundle.getLinkLast());
writeAtomLink(eventWriter, Constants.LINK_FHIR_BASE, theBundle.getLinkBase());
if (theBundle.getTotalResults().getValue() != null) {
eventWriter.writeStartElement("os", "totalResults", OPENSEARCH_NS);
eventWriter.writeNamespace("os", OPENSEARCH_NS);
eventWriter.writeCharacters(theBundle.getTotalResults().getValue().toString());
eventWriter.writeEndElement();
}
writeOptionalTagWithTextNode(eventWriter, "updated", theBundle.getUpdated());
if (StringUtils.isNotBlank(theBundle.getAuthorName().getValue())) {
eventWriter.writeStartElement("author");
writeTagWithTextNode(eventWriter, "name", theBundle.getAuthorName());
writeOptionalTagWithTextNode(eventWriter, "uri", theBundle.getAuthorUri());
eventWriter.writeEndElement();
}
writeCategories(eventWriter, theBundle.getCategories());
for (BundleEntry nextEntry : theBundle.getEntries()) {
boolean deleted = false;
if (nextEntry.getDeletedAt() != null && nextEntry.getDeletedAt().isEmpty() == false) {
deleted = true;
eventWriter.writeStartElement("at", "deleted-entry", TOMBSTONES_NS);
eventWriter.writeNamespace("at", TOMBSTONES_NS);
if (nextEntry.getDeletedResourceId().isEmpty()) {
writeOptionalAttribute(eventWriter, "ref", nextEntry.getId().getValueAsString());
} else {
writeOptionalAttribute(
eventWriter, "ref", nextEntry.getDeletedResourceId().getValueAsString());
}
writeOptionalAttribute(eventWriter, "when", nextEntry.getDeletedAt().getValueAsString());
if (nextEntry.getDeletedByEmail().isEmpty() == false
|| nextEntry.getDeletedByName().isEmpty() == false) {
eventWriter.writeStartElement(TOMBSTONES_NS, "by");
if (nextEntry.getDeletedByName().isEmpty() == false) {
eventWriter.writeStartElement(TOMBSTONES_NS, "name");
eventWriter.writeCharacters(nextEntry.getDeletedByName().getValue());
eventWriter.writeEndElement();
}
if (nextEntry.getDeletedByEmail().isEmpty() == false) {
eventWriter.writeStartElement(TOMBSTONES_NS, "email");
eventWriter.writeCharacters(nextEntry.getDeletedByEmail().getValue());
eventWriter.writeEndElement();
}
eventWriter.writeEndElement();
}
if (nextEntry.getDeletedComment().isEmpty() == false) {
eventWriter.writeStartElement(TOMBSTONES_NS, "comment");
eventWriter.writeCharacters(nextEntry.getDeletedComment().getValue());
eventWriter.writeEndElement();
}
} else {
eventWriter.writeStartElement("entry");
}
writeOptionalTagWithTextNode(eventWriter, "title", nextEntry.getTitle());
if (!deleted) {
if (nextEntry.getId().isEmpty() == false) {
writeTagWithTextNode(eventWriter, "id", nextEntry.getId());
} else {
writeTagWithTextNode(eventWriter, "id", nextEntry.getResource().getId());
}
}
writeOptionalTagWithTextNode(eventWriter, "updated", nextEntry.getUpdated());
writeOptionalTagWithTextNode(eventWriter, "published", nextEntry.getPublished());
writeCategories(eventWriter, nextEntry.getCategories());
if (!nextEntry.getLinkSelf().isEmpty()) {
writeAtomLink(eventWriter, "self", nextEntry.getLinkSelf());
}
if (!nextEntry.getLinkAlternate().isEmpty()) {
writeAtomLink(eventWriter, "alternate", nextEntry.getLinkAlternate());
}
if (!nextEntry.getLinkSearch().isEmpty()) {
writeAtomLink(eventWriter, "search", nextEntry.getLinkSearch());
}
IResource resource = nextEntry.getResource();
if (resource != null && !resource.isEmpty() && !deleted) {
eventWriter.writeStartElement("content");
eventWriter.writeAttribute("type", "text/xml");
encodeResourceToXmlStreamWriter(resource, eventWriter, false);
eventWriter.writeEndElement(); // content
} else {
ourLog.debug("Bundle entry contains null resource");
}
if (!nextEntry.getSummary().isEmpty()) {
eventWriter.writeStartElement("summary");
eventWriter.writeAttribute("type", "xhtml");
encodeXhtml(nextEntry.getSummary(), eventWriter);
eventWriter.writeEndElement();
}
eventWriter.writeEndElement(); // entry
}
eventWriter.writeEndElement();
eventWriter.close();
}
@Transactional(propagation = Propagation.REQUIRED)
@Override
public List<IResource> transaction(
RequestDetails theRequestDetails, List<IResource> theResources) {
ourLog.info("Beginning transaction with {} resources", theResources.size());
// Notify interceptors
ActionRequestDetails requestDetails = new ActionRequestDetails(null, null);
notifyInterceptors(RestOperationTypeEnum.TRANSACTION, requestDetails);
long start = System.currentTimeMillis();
Set<IdDt> allIds = new HashSet<IdDt>();
for (int i = 0; i < theResources.size(); i++) {
IResource res = theResources.get(i);
if (res.getId().hasIdPart()
&& !res.getId().hasResourceType()
&& !isPlaceholder(res.getId())) {
res.setId(new IdDt(toResourceName(res.getClass()), res.getId().getIdPart()));
}
/*
* Ensure that the bundle doesn't have any duplicates, since this causes all kinds of weirdness
*/
if (isPlaceholder(res.getId())) {
if (!allIds.add(res.getId())) {
throw new InvalidRequestException(
"Transaction bundle contains multiple resources with ID: " + res.getId());
}
} else if (res.getId().hasResourceType() && res.getId().hasIdPart()) {
IdDt nextId = res.getId().toUnqualifiedVersionless();
if (!allIds.add(nextId)) {
throw new InvalidRequestException(
"Transaction bundle contains multiple resources with ID: " + nextId);
}
}
}
FhirTerser terser = getContext().newTerser();
int creations = 0;
int updates = 0;
Map<IdDt, IdDt> idConversions = new HashMap<IdDt, IdDt>();
List<ResourceTable> persistedResources = new ArrayList<ResourceTable>();
List<IResource> retVal = new ArrayList<IResource>();
OperationOutcome oo = new OperationOutcome();
retVal.add(oo);
Date updateTime = new Date();
for (int resourceIdx = 0; resourceIdx < theResources.size(); resourceIdx++) {
IResource nextResource = theResources.get(resourceIdx);
IdDt nextId = nextResource.getId();
if (nextId == null) {
nextId = new IdDt();
}
String resourceName = toResourceName(nextResource);
BundleEntryTransactionMethodEnum nextResouceOperationIn =
ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get(nextResource);
if (nextResouceOperationIn == null
&& hasValue(ResourceMetadataKeyEnum.DELETED_AT.get(nextResource))) {
nextResouceOperationIn = BundleEntryTransactionMethodEnum.DELETE;
}
String matchUrl = ResourceMetadataKeyEnum.LINK_SEARCH.get(nextResource);
Set<Long> candidateMatches = null;
if (StringUtils.isNotBlank(matchUrl)) {
candidateMatches = processMatchUrl(matchUrl, nextResource.getClass());
}
ResourceTable entity;
if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.POST) {
entity = null;
} else if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.PUT
|| nextResouceOperationIn == BundleEntryTransactionMethodEnum.DELETE) {
if (candidateMatches == null || candidateMatches.size() == 0) {
if (nextId == null || StringUtils.isBlank(nextId.getIdPart())) {
throw new InvalidRequestException(
getContext()
.getLocalizer()
.getMessage(
BaseHapiFhirSystemDao.class,
"transactionOperationFailedNoId",
nextResouceOperationIn.name()));
}
entity = tryToLoadEntity(nextId);
if (entity == null) {
if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.PUT) {
ourLog.debug(
"Attempting to UPDATE resource with unknown ID '{}', will CREATE instead",
nextId);
} else if (candidateMatches == null) {
throw new InvalidRequestException(
getContext()
.getLocalizer()
.getMessage(
BaseHapiFhirSystemDao.class,
"transactionOperationFailedUnknownId",
nextResouceOperationIn.name(),
nextId));
} else {
ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl);
persistedResources.add(null);
retVal.add(nextResource);
continue;
}
}
} else if (candidateMatches.size() == 1) {
entity = loadFirstEntityFromCandidateMatches(candidateMatches);
} else {
throw new InvalidRequestException(
getContext()
.getLocalizer()
.getMessage(
BaseHapiFhirSystemDao.class,
"transactionOperationWithMultipleMatchFailure",
nextResouceOperationIn.name(),
matchUrl,
candidateMatches.size()));
}
} else if (nextId.isEmpty() || isPlaceholder(nextId)) {
entity = null;
} else {
entity = tryToLoadEntity(nextId);
}
BundleEntryTransactionMethodEnum nextResouceOperationOut;
if (entity == null) {
nextResouceOperationOut = BundleEntryTransactionMethodEnum.POST;
entity = toEntity(nextResource);
entity.setUpdated(updateTime);
entity.setPublished(updateTime);
if (nextId.isEmpty() == false && "cid:".equals(nextId.getBaseUrl())) {
ourLog.debug(
"Resource in transaction has ID[{}], will replace with server assigned ID",
nextId.getIdPart());
} else if (nextResouceOperationIn == BundleEntryTransactionMethodEnum.POST) {
if (nextId.isEmpty() == false) {
ourLog.debug(
"Resource in transaction has ID[{}] but is marked for CREATE, will ignore ID",
nextId.getIdPart());
}
if (candidateMatches != null) {
if (candidateMatches.size() == 1) {
ourLog.debug("Resource with match URL [{}] already exists, will be NOOP", matchUrl);
BaseHasResource existingEntity =
loadFirstEntityFromCandidateMatches(candidateMatches);
IResource existing = (IResource) toResource(existingEntity, false);
persistedResources.add(null);
retVal.add(existing);
continue;
}
if (candidateMatches.size() > 1) {
throw new InvalidRequestException(
getContext()
.getLocalizer()
.getMessage(
BaseHapiFhirSystemDao.class,
"transactionOperationWithMultipleMatchFailure",
BundleEntryTransactionMethodEnum.POST.name(),
matchUrl,
candidateMatches.size()));
}
}
} else {
createForcedIdIfNeeded(entity, nextId);
}
myEntityManager.persist(entity);
if (entity.getForcedId() != null) {
myEntityManager.persist(entity.getForcedId());
}
creations++;
ourLog.info(
"Resource Type[{}] with ID[{}] does not exist, creating it", resourceName, nextId);
} else {
nextResouceOperationOut = nextResouceOperationIn;
if (nextResouceOperationOut == null) {
nextResouceOperationOut = BundleEntryTransactionMethodEnum.PUT;
}
updates++;
ourLog.info("Resource Type[{}] with ID[{}] exists, updating it", resourceName, nextId);
}
persistedResources.add(entity);
retVal.add(nextResource);
ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.put(nextResource, nextResouceOperationOut);
}
ourLog.info("Flushing transaction to database");
myEntityManager.flush();
for (int i = 0; i < persistedResources.size(); i++) {
ResourceTable entity = persistedResources.get(i);
String resourceName = toResourceName(theResources.get(i));
IdDt nextId = theResources.get(i).getId();
IdDt newId;
if (entity == null) {
newId = retVal.get(i + 1).getId().toUnqualifiedVersionless();
} else {
newId = entity.getIdDt().toUnqualifiedVersionless();
}
if (nextId == null || nextId.isEmpty()) {
ourLog.info(
"Transaction resource (with no preexisting ID) has been assigned new ID[{}]",
nextId,
newId);
} else {
if (nextId.toUnqualifiedVersionless().equals(newId)) {
ourLog.info("Transaction resource ID[{}] is being updated", newId);
} else {
if (isPlaceholder(nextId)) {
// nextId = new IdDt(resourceName, nextId.getIdPart());
ourLog.info("Transaction resource ID[{}] has been assigned new ID[{}]", nextId, newId);
idConversions.put(nextId, newId);
idConversions.put(new IdDt(resourceName + "/" + nextId.getValue()), newId);
}
}
}
}
for (IResource nextResource : theResources) {
List<BaseResourceReferenceDt> allRefs =
terser.getAllPopulatedChildElementsOfType(nextResource, BaseResourceReferenceDt.class);
for (BaseResourceReferenceDt nextRef : allRefs) {
IdDt nextId = nextRef.getReference();
if (idConversions.containsKey(nextId)) {
IdDt newId = idConversions.get(nextId);
ourLog.info(" * Replacing resource ref {} with {}", nextId, newId);
nextRef.setReference(newId);
} else {
ourLog.debug(" * Reference [{}] does not exist in bundle", nextId);
}
}
}
ourLog.info("Re-flushing updated resource references and extracting search criteria");
for (int i = 0; i < theResources.size(); i++) {
IResource resource = theResources.get(i);
ResourceTable table = persistedResources.get(i);
if (table == null) {
continue;
}
InstantDt deletedInstantOrNull = ResourceMetadataKeyEnum.DELETED_AT.get(resource);
Date deletedTimestampOrNull =
deletedInstantOrNull != null ? deletedInstantOrNull.getValue() : null;
if (deletedInstantOrNull == null
&& ResourceMetadataKeyEnum.ENTRY_TRANSACTION_METHOD.get(resource)
== BundleEntryTransactionMethodEnum.DELETE) {
deletedTimestampOrNull = updateTime;
ResourceMetadataKeyEnum.DELETED_AT.put(resource, new InstantDt(deletedTimestampOrNull));
}
updateEntity(resource, table, table.getId() != null, deletedTimestampOrNull, updateTime);
}
long delay = System.currentTimeMillis() - start;
ourLog.info(
"Transaction completed in {}ms with {} creations and {} updates",
new Object[] {delay, creations, updates});
oo.addIssue()
.setSeverity(IssueSeverityEnum.INFORMATION)
.setDetails(
"Transaction completed in "
+ delay
+ "ms with "
+ creations
+ " creations and "
+ updates
+ " updates");
return retVal;
}
@Override
public Object invokeClient(
String theResponseMimeType,
Reader theResponseReader,
int theResponseStatusCode,
Map<String, List<String>> theHeaders)
throws IOException {
IParser parser =
createAppropriateParserForParsingResponse(
theResponseMimeType, theResponseReader, theResponseStatusCode);
switch (getReturnType()) {
case BUNDLE:
{
Bundle bundle;
if (myResourceType != null) {
bundle = parser.parseBundle(myResourceType, theResponseReader);
} else {
bundle = parser.parseBundle(theResponseReader);
}
switch (getMethodReturnType()) {
case BUNDLE:
return bundle;
case LIST_OF_RESOURCES:
List<IResource> listOfResources;
if (myResourceListCollectionType != null) {
listOfResources = new ArrayList<IResource>();
for (IResource next : bundle.toListOfResources()) {
if (!myResourceListCollectionType.isAssignableFrom(next.getClass())) {
ourLog.debug(
"Not returning resource of type {} because it is not a subclass or instance of {}",
next.getClass(),
myResourceListCollectionType);
continue;
}
listOfResources.add(next);
}
} else {
listOfResources = bundle.toListOfResources();
}
return listOfResources;
case RESOURCE:
List<IResource> list = bundle.toListOfResources();
if (list.size() == 0) {
return null;
} else if (list.size() == 1) {
return list.get(0);
} else {
throw new InvalidResponseException(
theResponseStatusCode,
"FHIR server call returned a bundle with multiple resources, but this method is only able to returns one.");
}
case BUNDLE_PROVIDER:
throw new IllegalStateException(
"Return type of "
+ IBundleProvider.class.getSimpleName()
+ " is not supported in clients");
}
break;
}
case RESOURCE:
{
IResource resource;
if (myResourceType != null) {
resource = parser.parseResource(myResourceType, theResponseReader);
} else {
resource = parser.parseResource(theResponseReader);
}
MethodUtil.parseClientRequestResourceHeaders(null, theHeaders, resource);
switch (getMethodReturnType()) {
case BUNDLE:
return Bundle.withSingleResource(resource);
case LIST_OF_RESOURCES:
return Collections.singletonList(resource);
case RESOURCE:
return resource;
case BUNDLE_PROVIDER:
throw new IllegalStateException(
"Return type of "
+ IBundleProvider.class.getSimpleName()
+ " is not supported in clients");
}
break;
}
}
throw new IllegalStateException("Should not get here!");
}
private String getConditionalUrl(IResource resource, IdentifierDt identifier) {
return resource.getResourceName()
+ "?identifier=".concat(identifier.getSystem()).concat("%7C").concat(identifier.getValue());
}
protected String getPreferredId(IResource theResource, String theId) {
if (isNotBlank(theId)) {
return theId;
}
return theResource.getId().getIdPart();
}