Mercurial > hg > orthanc
view OrthancServer/ServerContext.cpp @ 2277:c6defdc4c611 issue-46-anonymization
updated list of fields to remove during anonymization following PS 3.15-2011 Table E.1-1
author | amazy |
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date | Wed, 10 May 2017 22:40:59 +0200 |
parents | a3a65de1840f |
children | 563bf878407a |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, Belgium * Copyright (C) 2017 Osimis, Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU General Public License as * published by the Free Software Foundation, either version 3 of the * License, or (at your option) any later version. * * In addition, as a special exception, the copyright holders of this * program give permission to link the code of its release with the * OpenSSL project's "OpenSSL" library (or with modified versions of it * that use the same license as the "OpenSSL" library), and distribute * the linked executables. You must obey the GNU General Public License * in all respects for all of the code used other than "OpenSSL". If you * modify file(s) with this exception, you may extend this exception to * your version of the file(s), but you are not obligated to do so. If * you do not wish to do so, delete this exception statement from your * version. If you delete this exception statement from all source files * in the program, then also delete it here. * * This program is distributed in the hope that it will be useful, but * WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * General Public License for more details. * * You should have received a copy of the GNU General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ #include "PrecompiledHeadersServer.h" #include "ServerContext.h" #include "../Core/FileStorage/StorageAccessor.h" #include "../Core/HttpServer/FilesystemHttpSender.h" #include "../Core/HttpServer/HttpStreamTranscoder.h" #include "../Core/Logging.h" #include "FromDcmtkBridge.h" #include "ServerToolbox.h" #include "OrthancInitialization.h" #include <EmbeddedResources.h> #include <dcmtk/dcmdata/dcfilefo.h> #include "Scheduler/CallSystemCommand.h" #include "Scheduler/DeleteInstanceCommand.h" #include "Scheduler/ModifyInstanceCommand.h" #include "Scheduler/StoreScuCommand.h" #include "Scheduler/StorePeerCommand.h" #include "OrthancRestApi/OrthancRestApi.h" #include "../Plugins/Engine/OrthancPlugins.h" #include "Search/LookupResource.h" #define ENABLE_DICOM_CACHE 1 static const size_t DICOM_CACHE_SIZE = 2; /** * IMPORTANT: We make the assumption that the same instance of * FileStorage can be accessed from multiple threads. This seems OK * since the filesystem implements the required locking mechanisms, * but maybe a read-writer lock on the "FileStorage" could be * useful. Conversely, "ServerIndex" already implements mutex-based * locking. **/ namespace Orthanc { void ServerContext::ChangeThread(ServerContext* that) { while (!that->done_) { std::auto_ptr<IDynamicObject> obj(that->pendingChanges_.Dequeue(100)); if (obj.get() != NULL) { const ServerIndexChange& change = dynamic_cast<const ServerIndexChange&>(*obj.get()); boost::recursive_mutex::scoped_lock lock(that->listenersMutex_); for (ServerListeners::iterator it = that->listeners_.begin(); it != that->listeners_.end(); ++it) { try { try { it->GetListener().SignalChange(change); } catch (std::bad_alloc&) { LOG(ERROR) << "Not enough memory while signaling a change"; } catch (...) { throw OrthancException(ErrorCode_InternalError); } } catch (OrthancException& e) { LOG(ERROR) << "Error in the " << it->GetDescription() << " callback while signaling a change: " << e.What() << " (code " << e.GetErrorCode() << ")"; } } } } } ServerContext::ServerContext(IDatabaseWrapper& database, IStorageArea& area) : index_(*this, database), area_(area), compressionEnabled_(false), storeMD5_(true), provider_(*this), dicomCache_(provider_, DICOM_CACHE_SIZE), scheduler_(Configuration::GetGlobalUnsignedIntegerParameter("LimitJobs", 10)), lua_(*this), #if ORTHANC_ENABLE_PLUGINS == 1 plugins_(NULL), #endif done_(false), queryRetrieveArchive_(Configuration::GetGlobalUnsignedIntegerParameter("QueryRetrieveSize", 10)), defaultLocalAet_(Configuration::GetGlobalStringParameter("DicomAet", "ORTHANC")) { uint64_t s = Configuration::GetGlobalUnsignedIntegerParameter("DicomAssociationCloseDelay", 5); // In seconds scu_.SetMillisecondsBeforeClose(s * 1000); // Milliseconds are expected here listeners_.push_back(ServerListener(lua_, "Lua")); changeThread_ = boost::thread(ChangeThread, this); } ServerContext::~ServerContext() { if (!done_) { LOG(ERROR) << "INTERNAL ERROR: ServerContext::Stop() should be invoked manually to avoid mess in the destruction order!"; Stop(); } } void ServerContext::Stop() { if (!done_) { { boost::recursive_mutex::scoped_lock lock(listenersMutex_); listeners_.clear(); } done_ = true; if (changeThread_.joinable()) { changeThread_.join(); } scu_.Finalize(); // Do not change the order below! scheduler_.Stop(); index_.Stop(); } } void ServerContext::SetCompressionEnabled(bool enabled) { if (enabled) LOG(WARNING) << "Disk compression is enabled"; else LOG(WARNING) << "Disk compression is disabled"; compressionEnabled_ = enabled; } void ServerContext::RemoveFile(const std::string& fileUuid, FileContentType type) { area_.Remove(fileUuid, type); } StoreStatus ServerContext::Store(std::string& resultPublicId, DicomInstanceToStore& dicom) { try { StorageAccessor accessor(area_); DicomInstanceHasher hasher(dicom.GetSummary()); resultPublicId = hasher.HashInstance(); Json::Value simplifiedTags; ServerToolbox::SimplifyTags(simplifiedTags, dicom.GetJson(), DicomToJsonFormat_Human); // Test if the instance must be filtered out bool accepted = true; { boost::recursive_mutex::scoped_lock lock(listenersMutex_); for (ServerListeners::iterator it = listeners_.begin(); it != listeners_.end(); ++it) { try { if (!it->GetListener().FilterIncomingInstance(dicom, simplifiedTags)) { accepted = false; break; } } catch (OrthancException& e) { LOG(ERROR) << "Error in the " << it->GetDescription() << " callback while receiving an instance: " << e.What() << " (code " << e.GetErrorCode() << ")"; throw; } } } if (!accepted) { LOG(INFO) << "An incoming instance has been discarded by the filter"; return StoreStatus_FilteredOut; } // TODO Should we use "gzip" instead? CompressionType compression = (compressionEnabled_ ? CompressionType_ZlibWithSize : CompressionType_None); FileInfo dicomInfo = accessor.Write(dicom.GetBufferData(), dicom.GetBufferSize(), FileContentType_Dicom, compression, storeMD5_); FileInfo jsonInfo = accessor.Write(dicom.GetJson().toStyledString(), FileContentType_DicomAsJson, compression, storeMD5_); ServerIndex::Attachments attachments; attachments.push_back(dicomInfo); attachments.push_back(jsonInfo); typedef std::map<MetadataType, std::string> InstanceMetadata; InstanceMetadata instanceMetadata; StoreStatus status = index_.Store(instanceMetadata, dicom, attachments); // Only keep the metadata for the "instance" level dicom.GetMetadata().clear(); for (InstanceMetadata::const_iterator it = instanceMetadata.begin(); it != instanceMetadata.end(); ++it) { dicom.GetMetadata().insert(std::make_pair(std::make_pair(ResourceType_Instance, it->first), it->second)); } if (status != StoreStatus_Success) { accessor.Remove(dicomInfo); accessor.Remove(jsonInfo); } switch (status) { case StoreStatus_Success: LOG(INFO) << "New instance stored"; break; case StoreStatus_AlreadyStored: LOG(INFO) << "Already stored"; break; case StoreStatus_Failure: LOG(ERROR) << "Store failure"; break; default: // This should never happen break; } if (status == StoreStatus_Success || status == StoreStatus_AlreadyStored) { boost::recursive_mutex::scoped_lock lock(listenersMutex_); for (ServerListeners::iterator it = listeners_.begin(); it != listeners_.end(); ++it) { try { it->GetListener().SignalStoredInstance(resultPublicId, dicom, simplifiedTags); } catch (OrthancException& e) { LOG(ERROR) << "Error in the " << it->GetDescription() << " callback while receiving an instance: " << e.What() << " (code " << e.GetErrorCode() << ")"; } } } return status; } catch (OrthancException& e) { if (e.GetErrorCode() == ErrorCode_InexistentTag) { ServerToolbox::LogMissingRequiredTag(dicom.GetSummary()); } throw; } } void ServerContext::AnswerAttachment(RestApiOutput& output, const std::string& resourceId, FileContentType content) { FileInfo attachment; if (!index_.LookupAttachment(attachment, resourceId, content)) { throw OrthancException(ErrorCode_UnknownResource); } StorageAccessor accessor(area_); accessor.AnswerFile(output, attachment, GetFileContentMime(content)); } void ServerContext::ChangeAttachmentCompression(const std::string& resourceId, FileContentType attachmentType, CompressionType compression) { LOG(INFO) << "Changing compression type for attachment " << EnumerationToString(attachmentType) << " of resource " << resourceId << " to " << compression; FileInfo attachment; if (!index_.LookupAttachment(attachment, resourceId, attachmentType)) { throw OrthancException(ErrorCode_UnknownResource); } if (attachment.GetCompressionType() == compression) { // Nothing to do return; } std::string content; StorageAccessor accessor(area_); accessor.Read(content, attachment); FileInfo modified = accessor.Write(content.empty() ? NULL : content.c_str(), content.size(), attachmentType, compression, storeMD5_); try { StoreStatus status = index_.AddAttachment(modified, resourceId); if (status != StoreStatus_Success) { accessor.Remove(modified); throw OrthancException(ErrorCode_Database); } } catch (OrthancException&) { accessor.Remove(modified); throw; } } void ServerContext::ReadDicomAsJson(std::string& result, const std::string& instancePublicId) { FileInfo attachment; if (index_.LookupAttachment(attachment, instancePublicId, FileContentType_DicomAsJson)) { ReadAttachment(result, attachment); return; } // The "DICOM as JSON" summary is not available from the Orthanc // store (most probably deleted), reconstruct it from the DICOM file std::string dicom; ReadDicom(dicom, instancePublicId); LOG(INFO) << "Reconstructing the missing DICOM-as-JSON summary for instance: " << instancePublicId; ParsedDicomFile parsed(dicom); Json::Value summary; parsed.DatasetToJson(summary); result = summary.toStyledString(); if (!AddAttachment(instancePublicId, FileContentType_DicomAsJson, result.c_str(), result.size())) { LOG(WARNING) << "Cannot associate the DICOM-as-JSON summary to instance: " << instancePublicId; throw OrthancException(ErrorCode_InternalError); } } void ServerContext::ReadDicomAsJson(Json::Value& result, const std::string& instancePublicId) { std::string tmp; ReadDicomAsJson(tmp, instancePublicId); Json::Reader reader; if (!reader.parse(tmp, result)) { throw OrthancException(ErrorCode_CorruptedFile); } } void ServerContext::ReadAttachment(std::string& result, const std::string& instancePublicId, FileContentType content, bool uncompressIfNeeded) { FileInfo attachment; if (!index_.LookupAttachment(attachment, instancePublicId, content)) { LOG(WARNING) << "Unable to read attachment " << EnumerationToString(content) << " of instance " << instancePublicId; throw OrthancException(ErrorCode_InternalError); } if (uncompressIfNeeded) { ReadAttachment(result, attachment); } else { // Do not interpret the content of the storage area, return the // raw data area_.Read(result, attachment.GetUuid(), content); } } void ServerContext::ReadAttachment(std::string& result, const FileInfo& attachment) { // This will decompress the attachment StorageAccessor accessor(area_); accessor.Read(result, attachment); } IDynamicObject* ServerContext::DicomCacheProvider::Provide(const std::string& instancePublicId) { std::string content; context_.ReadDicom(content, instancePublicId); return new ParsedDicomFile(content); } ServerContext::DicomCacheLocker::DicomCacheLocker(ServerContext& that, const std::string& instancePublicId) : that_(that), lock_(that_.dicomCacheMutex_) { #if ENABLE_DICOM_CACHE == 0 static std::auto_ptr<IDynamicObject> p; p.reset(provider_.Provide(instancePublicId)); dicom_ = dynamic_cast<ParsedDicomFile*>(p.get()); #else dicom_ = &dynamic_cast<ParsedDicomFile&>(that_.dicomCache_.Access(instancePublicId)); #endif } ServerContext::DicomCacheLocker::~DicomCacheLocker() { } void ServerContext::SetStoreMD5ForAttachments(bool storeMD5) { LOG(INFO) << "Storing MD5 for attachments: " << (storeMD5 ? "yes" : "no"); storeMD5_ = storeMD5; } bool ServerContext::AddAttachment(const std::string& resourceId, FileContentType attachmentType, const void* data, size_t size) { LOG(INFO) << "Adding attachment " << EnumerationToString(attachmentType) << " to resource " << resourceId; // TODO Should we use "gzip" instead? CompressionType compression = (compressionEnabled_ ? CompressionType_ZlibWithSize : CompressionType_None); StorageAccessor accessor(area_); FileInfo attachment = accessor.Write(data, size, attachmentType, compression, storeMD5_); StoreStatus status = index_.AddAttachment(attachment, resourceId); if (status != StoreStatus_Success) { accessor.Remove(attachment); return false; } else { return true; } } bool ServerContext::DeleteResource(Json::Value& target, const std::string& uuid, ResourceType expectedType) { return index_.DeleteResource(target, uuid, expectedType); } void ServerContext::SignalChange(const ServerIndexChange& change) { pendingChanges_.Enqueue(change.Clone()); } #if ORTHANC_ENABLE_PLUGINS == 1 void ServerContext::SetPlugins(OrthancPlugins& plugins) { boost::recursive_mutex::scoped_lock lock(listenersMutex_); plugins_ = &plugins; // TODO REFACTOR THIS listeners_.clear(); listeners_.push_back(ServerListener(lua_, "Lua")); listeners_.push_back(ServerListener(plugins, "plugin")); } void ServerContext::ResetPlugins() { boost::recursive_mutex::scoped_lock lock(listenersMutex_); plugins_ = NULL; // TODO REFACTOR THIS listeners_.clear(); listeners_.push_back(ServerListener(lua_, "Lua")); } const OrthancPlugins& ServerContext::GetPlugins() const { if (HasPlugins()) { return *plugins_; } else { throw OrthancException(ErrorCode_InternalError); } } OrthancPlugins& ServerContext::GetPlugins() { if (HasPlugins()) { return *plugins_; } else { throw OrthancException(ErrorCode_InternalError); } } #endif bool ServerContext::HasPlugins() const { #if ORTHANC_ENABLE_PLUGINS == 1 return (plugins_ != NULL); #else return false; #endif } bool ServerContext::Apply(std::list<std::string>& result, const ::Orthanc::LookupResource& lookup, size_t maxResults) { result.clear(); std::vector<std::string> resources, instances; GetIndex().FindCandidates(resources, instances, lookup); assert(resources.size() == instances.size()); for (size_t i = 0; i < instances.size(); i++) { Json::Value dicom; ReadDicomAsJson(dicom, instances[i]); if (lookup.IsMatch(dicom)) { if (maxResults != 0 && result.size() >= maxResults) { return false; // too many results } else { result.push_back(resources[i]); } } } return true; // finished } }