private String checkPatientIDs(
ProvideAndRegisterDocumentSetRequestType req,
RegistryPackageType submissionSet,
List<ExtrinsicObjectType> extrObjs)
throws XDSException {
String submissionPatId =
InfosetUtil.getExternalIdentifierValue(
XDSConstants.UUID_XDSSubmissionSet_patientId, submissionSet);
String docPatId;
ExtrinsicObjectType eo;
for (int i = 0, len = extrObjs.size(); i < len; i++) {
eo = extrObjs.get(i);
docPatId =
InfosetUtil.getExternalIdentifierValue(XDSConstants.UUID_XDSDocumentEntry_patientId, eo);
if (docPatId != null && !docPatId.equals(submissionPatId)) {
String msg =
"XDSDocumentEntry.patientId ("
+ docPatId
+ ")and XDSSubmissionSet.patientId ("
+ submissionPatId
+ ") doesn't match! ExtrinsicObject.Id:"
+ eo.getId();
log.warn(msg);
throw new XDSException(XDSException.XDS_ERR_PATID_DOESNOT_MATCH, msg, null);
}
}
RegistryPackageType folder =
InfosetUtil.getRegistryPackage(req.getSubmitObjectsRequest(), XDSConstants.UUID_XDSFolder);
String folderPatId =
folder == null
? null
: InfosetUtil.getExternalIdentifierValue(XDSConstants.UUID_XDSFolder_patientId, folder);
if (folderPatId != null && !folderPatId.equals(submissionPatId)) {
String msg =
"XDSFolder.patientId ("
+ folderPatId
+ ")and XDSSubmissionSet.patientId ("
+ submissionPatId
+ ") doesn't match!";
log.warn(msg);
throw new XDSException(XDSException.XDS_ERR_PATID_DOESNOT_MATCH, msg, null);
}
return submissionPatId;
}
public static void logQuery(
EventTypeCode eventTypeCode,
AdhocQueryRequest req,
String srcUserID,
String altSrcUserID,
String srcHostName,
String destUserID,
String altDestUserID,
String destHostName,
boolean success) {
if (logger != null && logger.isInstalled()) {
try {
AdhocQueryType qry = req.getAdhocQuery();
String patID = XDSUtil.getQueryPatID(qry.getSlot());
String homeCommunityID =
InfosetUtil.getSlotValue(qry.getSlot(), XDSConstants.QRY_HOME_COMMUNITY_ID, null);
if (srcHostName == null) srcHostName = AuditLogger.localHost().getHostName();
Calendar timeStamp = logger.timeStamp();
AuditMessage msg =
XDSAudit.createQuery(
eventTypeCode,
qry.getId(),
patID,
homeCommunityID,
InfosetUtil.marshallObject(req, true).getBytes("UTF-8"),
srcUserID,
altSrcUserID,
srcHostName,
destUserID,
altDestUserID,
destHostName,
timeStamp,
success ? EventOutcomeIndicator.Success : EventOutcomeIndicator.MinorFailure);
sendAuditMessage(timeStamp, msg);
} catch (Exception e) {
log.warn("Audit log of Stored Query failed!");
log.debug("AuditLog Exception:", e);
}
}
}
private List<ExtrinsicObjectType> checkRequest(ProvideAndRegisterDocumentSetRequestType req)
throws XDSException {
SubmitObjectsRequest sor = req.getSubmitObjectsRequest();
RegistryPackageType submissionSet =
InfosetUtil.getRegistryPackage(sor, XDSConstants.UUID_XDSSubmissionSet);
if (submissionSet == null) {
log.error("No RegistryPackage id=SubmissionSet found!");
throw new XDSException(
XDSException.XDS_ERR_REPOSITORY_ERROR,
XDSException.XDS_ERR_MISSING_REGISTRY_PACKAGE,
null);
} else if (submissionSet.getId() == null || submissionSet.getId().trim().length() == 0) {
throw new XDSException(
XDSException.XDS_ERR_REPOSITORY_METADATA_ERROR,
"Missing XDSSubmissionSet.entryUUID!",
null);
}
List<ExtrinsicObjectType> extrObjs =
InfosetUtil.getExtrinsicObjects(req.getSubmitObjectsRequest());
checkPatientIDs(req, submissionSet, extrObjs);
Map<String, Document> docs = InfosetUtil.getDocuments(req);
if (extrObjs.size() > docs.size()) {
log.warn(
"Missing Documents! Found more ExtrinsicObjects("
+ extrObjs.size()
+ ") than Documents("
+ docs.size()
+ ")!");
throw new XDSException(XDSException.XDS_ERR_MISSING_DOCUMENT, "", null);
} else if (extrObjs.size() < docs.size()) {
log.warn(
"Missing Document Metadata! Found less ExtrinsicObjects("
+ extrObjs.size()
+ ") than Documents("
+ docs.size()
+ ")!");
throw new XDSException(XDSException.XDS_ERR_MISSING_DOCUMENT_METADATA, "", null);
}
return extrObjs;
}
private String getSourceID(ProvideAndRegisterDocumentSetRequestType req) throws XDSException {
List<JAXBElement<? extends IdentifiableType>> objs =
req.getSubmitObjectsRequest().getRegistryObjectList().getIdentifiable();
IdentifiableType obj;
for (int i = 0, len = objs.size(); i < len; i++) {
obj = objs.get(i).getValue();
if (obj instanceof RegistryPackageType) {
return InfosetUtil.getExternalIdentifierValue(
XDSConstants.UUID_XDSSubmissionSet_sourceId, (RegistryPackageType) obj);
}
}
throw new XDSException(
XDSException.XDS_ERR_REPOSITORY_METADATA_ERROR, "Missing XDSSubmissionSet.sourceId!", null);
}
private XDSDocument[] storeDocuments(
ProvideAndRegisterDocumentSetRequestType req,
List<ExtrinsicObjectType> extrObjs,
String groupID)
throws XDSException {
Map<String, Document> docs = InfosetUtil.getDocuments(req);
Document doc;
ExtrinsicObjectType eo;
String docUID;
XDSDocument[] storedDocs = new XDSDocument[extrObjs.size()];
String[] mimetypes = cfg.isCheckMimetype() ? cfg.getAcceptedMimeTypes() : null;
for (int i = 0, len = extrObjs.size(); i < len; i++) {
eo = extrObjs.get(i);
if (eo.getId() == null || eo.getId().trim().length() == 0)
throw new XDSException(
XDSException.XDS_ERR_REPOSITORY_METADATA_ERROR,
"Missing XDSDocumentEntry.entryUUID!",
null);
doc = docs.get(eo.getId());
docUID =
InfosetUtil.getExternalIdentifierValue(XDSConstants.UUID_XDSDocumentEntry_uniqueId, eo);
if (docUID == null)
throw new XDSException(
XDSException.XDS_ERR_REPOSITORY_METADATA_ERROR,
"Missing XDSDocumentEntry.uniqueId!",
null);
if (mimetypes != null) {
boolean unsupportedMimetype = true;
for (int j = 0; j < mimetypes.length; j++) {
if (mimetypes[j].equals(eo.getMimeType())) {
unsupportedMimetype = false;
break;
}
}
if (unsupportedMimetype)
throw new XDSException(
XDSException.XDS_ERR_REPOSITORY_METADATA_ERROR,
"Mimetype not supported:" + eo.getMimeType(),
null);
}
try {
storedDocs[i] = storage.storeDocument(groupID, docUID, doc.getValue(), eo.getMimeType());
if (storedDocs[i].isCommitted()) {
log.warn("Document already exists! docUid:" + docUID);
}
Map<String, SlotType1> slots =
InfosetUtil.addOrOverwriteSlot(
eo, XDSConstants.SLOT_NAME_REPOSITORY_UNIQUE_ID, getRepositoryUniqueId());
String oldValue =
InfosetUtil.addOrCheckedOverwriteSlot(
eo,
slots,
XDSConstants.SLOT_NAME_SIZE,
String.valueOf(storedDocs[i].getSize()),
false);
if (oldValue != null) {
throw new XDSException(
XDSException.XDS_ERR_REPOSITORY_METADATA_ERROR,
"Slot 'size' already exists but has different value! old:"
+ oldValue
+ " new:"
+ storedDocs[i].getSize(),
null);
}
oldValue =
InfosetUtil.addOrCheckedOverwriteSlot(
eo, slots, XDSConstants.SLOT_NAME_HASH, storedDocs[i].getDigest(), true);
if (oldValue != null) {
throw new XDSException(
XDSException.XDS_ERR_REPOSITORY_METADATA_ERROR,
"Slot 'hash' already exists but has different value! old:"
+ oldValue
+ " new:"
+ storedDocs[i].getDigest(),
null);
}
} catch (XDSException x) {
this.commit(storedDocs, false);
throw x;
} catch (Exception x) {
log.error("Storage of document failed! docUID:" + docUID, x);
this.commit(storedDocs, false);
throw new XDSException(
XDSException.XDS_ERR_REPOSITORY_ERROR,
"Storage of document " + docUID + " failed! : " + x.getMessage(),
x);
}
}
return storedDocs;
}