Mercurial > hg > orthanc
view OrthancServer/ServerIndex.cpp @ 1559:1e6fbb2dcc6f
ParseDoseReport.lua
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 21 Aug 2015 10:12:56 +0200 |
parents | d6a93e12b1c1 |
children | de1413733c97 |
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/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics * Department, University Hospital of Liege, 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 "ServerIndex.h" #ifndef NOMINMAX #define NOMINMAX #endif #include "ServerIndexChange.h" #include "EmbeddedResources.h" #include "OrthancInitialization.h" #include "../Core/Toolbox.h" #include "../Core/Logging.h" #include "../Core/Uuid.h" #include "../Core/DicomFormat/DicomArray.h" #include "FromDcmtkBridge.h" #include "ServerContext.h" #include <boost/lexical_cast.hpp> #include <stdio.h> static const uint64_t MEGA_BYTES = 1024 * 1024; namespace Orthanc { class ServerIndex::Listener : public IDatabaseListener { private: struct FileToRemove { private: std::string uuid_; FileContentType type_; public: FileToRemove(const FileInfo& info) : uuid_(info.GetUuid()), type_(info.GetContentType()) { } const std::string& GetUuid() const { return uuid_; } FileContentType GetContentType() const { return type_; } }; ServerContext& context_; bool hasRemainingLevel_; ResourceType remainingType_; std::string remainingPublicId_; std::list<FileToRemove> pendingFilesToRemove_; std::list<ServerIndexChange> pendingChanges_; uint64_t sizeOfFilesToRemove_; bool insideTransaction_; void Reset() { sizeOfFilesToRemove_ = 0; hasRemainingLevel_ = false; pendingFilesToRemove_.clear(); pendingChanges_.clear(); } public: Listener(ServerContext& context) : context_(context), insideTransaction_(false) { Reset(); assert(ResourceType_Patient < ResourceType_Study && ResourceType_Study < ResourceType_Series && ResourceType_Series < ResourceType_Instance); } void StartTransaction() { Reset(); insideTransaction_ = true; } void EndTransaction() { insideTransaction_ = false; } uint64_t GetSizeOfFilesToRemove() { return sizeOfFilesToRemove_; } void CommitFilesToRemove() { for (std::list<FileToRemove>::const_iterator it = pendingFilesToRemove_.begin(); it != pendingFilesToRemove_.end(); ++it) { context_.RemoveFile(it->GetUuid(), it->GetContentType()); } } void CommitChanges() { for (std::list<ServerIndexChange>::const_iterator it = pendingChanges_.begin(); it != pendingChanges_.end(); ++it) { context_.SignalChange(*it); } } virtual void SignalRemainingAncestor(ResourceType parentType, const std::string& publicId) { VLOG(1) << "Remaining ancestor \"" << publicId << "\" (" << parentType << ")"; if (hasRemainingLevel_) { if (parentType < remainingType_) { remainingType_ = parentType; remainingPublicId_ = publicId; } } else { hasRemainingLevel_ = true; remainingType_ = parentType; remainingPublicId_ = publicId; } } virtual void SignalFileDeleted(const FileInfo& info) { assert(Toolbox::IsUuid(info.GetUuid())); pendingFilesToRemove_.push_back(FileToRemove(info)); sizeOfFilesToRemove_ += info.GetCompressedSize(); } virtual void SignalChange(const ServerIndexChange& change) { VLOG(1) << "Change related to resource " << change.GetPublicId() << " of type " << EnumerationToString(change.GetResourceType()) << ": " << EnumerationToString(change.GetChangeType()); if (insideTransaction_) { pendingChanges_.push_back(change); } else { context_.SignalChange(change); } } bool HasRemainingLevel() const { return hasRemainingLevel_; } ResourceType GetRemainingType() const { assert(HasRemainingLevel()); return remainingType_; } const std::string& GetRemainingPublicId() const { assert(HasRemainingLevel()); return remainingPublicId_; } }; class ServerIndex::Transaction { private: ServerIndex& index_; std::auto_ptr<SQLite::ITransaction> transaction_; bool isCommitted_; public: Transaction(ServerIndex& index) : index_(index), isCommitted_(false) { transaction_.reset(index_.db_.StartTransaction()); transaction_->Begin(); assert(index_.currentStorageSize_ == index_.db_.GetTotalCompressedSize()); index_.listener_->StartTransaction(); } ~Transaction() { index_.listener_->EndTransaction(); if (!isCommitted_) { transaction_->Rollback(); } } void Commit(uint64_t sizeOfAddedFiles) { if (!isCommitted_) { transaction_->Commit(); // We can remove the files once the SQLite transaction has // been successfully committed. Some files might have to be // deleted because of recycling. index_.listener_->CommitFilesToRemove(); index_.currentStorageSize_ += sizeOfAddedFiles; assert(index_.currentStorageSize_ >= index_.listener_->GetSizeOfFilesToRemove()); index_.currentStorageSize_ -= index_.listener_->GetSizeOfFilesToRemove(); // Send all the pending changes to the Orthanc plugins index_.listener_->CommitChanges(); isCommitted_ = true; } } }; class ServerIndex::UnstableResourcePayload { private: ResourceType type_; std::string publicId_; boost::posix_time::ptime time_; public: UnstableResourcePayload() : type_(ResourceType_Instance) { } UnstableResourcePayload(Orthanc::ResourceType type, const std::string& publicId) : type_(type), publicId_(publicId) { time_ = boost::posix_time::second_clock::local_time(); } unsigned int GetAge() const { return (boost::posix_time::second_clock::local_time() - time_).total_seconds(); } ResourceType GetResourceType() const { return type_; } const std::string& GetPublicId() const { return publicId_; } }; bool ServerIndex::DeleteResource(Json::Value& target, const std::string& uuid, ResourceType expectedType) { boost::mutex::scoped_lock lock(mutex_); Transaction t(*this); int64_t id; ResourceType type; if (!db_.LookupResource(id, type, uuid) || expectedType != type) { return false; } db_.DeleteResource(id); if (listener_->HasRemainingLevel()) { ResourceType type = listener_->GetRemainingType(); const std::string& uuid = listener_->GetRemainingPublicId(); target["RemainingAncestor"] = Json::Value(Json::objectValue); target["RemainingAncestor"]["Path"] = GetBasePath(type, uuid); target["RemainingAncestor"]["Type"] = EnumerationToString(type); target["RemainingAncestor"]["ID"] = uuid; } else { target["RemainingAncestor"] = Json::nullValue; } t.Commit(0); return true; } void ServerIndex::FlushThread(ServerIndex* that) { // By default, wait for 10 seconds before flushing unsigned int sleep = 10; try { boost::mutex::scoped_lock lock(that->mutex_); std::string sleepString; if (that->db_.LookupGlobalProperty(sleepString, GlobalProperty_FlushSleep) && Toolbox::IsInteger(sleepString)) { sleep = boost::lexical_cast<unsigned int>(sleepString); } } catch (boost::bad_lexical_cast&) { } LOG(INFO) << "Starting the database flushing thread (sleep = " << sleep << ")"; unsigned int count = 0; while (!that->done_) { boost::this_thread::sleep(boost::posix_time::seconds(1)); count++; if (count < sleep) { continue; } boost::mutex::scoped_lock lock(that->mutex_); that->db_.FlushToDisk(); count = 0; } LOG(INFO) << "Stopping the database flushing thread"; } static void ComputeExpectedNumberOfInstances(IDatabaseWrapper& db, int64_t series, const DicomMap& dicomSummary) { try { const DicomValue* value; const DicomValue* value2; if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL && (value2 = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS)) != NULL) { // Patch for series with temporal positions thanks to Will Ryder int64_t imagesInAcquisition = boost::lexical_cast<int64_t>(value->AsString()); int64_t countTemporalPositions = boost::lexical_cast<int64_t>(value2->AsString()); std::string expected = boost::lexical_cast<std::string>(imagesInAcquisition * countTemporalPositions); db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, expected); } else if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL && (value2 = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_TIME_SLICES)) != NULL) { // Support of Cardio-PET images int64_t numberOfSlices = boost::lexical_cast<int64_t>(value->AsString()); int64_t numberOfTimeSlices = boost::lexical_cast<int64_t>(value2->AsString()); std::string expected = boost::lexical_cast<std::string>(numberOfSlices * numberOfTimeSlices); db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, expected); } else if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL) { db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, value->AsString()); } } catch (boost::bad_lexical_cast) { } } bool ServerIndex::GetMetadataAsInteger(int64_t& result, int64_t id, MetadataType type) { std::string s; if (!db_.LookupMetadata(s, id, type)) { return false; } try { result = boost::lexical_cast<int64_t>(s); return true; } catch (boost::bad_lexical_cast&) { return false; } } void ServerIndex::LogChange(int64_t internalId, ChangeType changeType, ResourceType resourceType, const std::string& publicId) { ServerIndexChange change(changeType, resourceType, publicId); if (changeType <= ChangeType_INTERNAL_LastLogged) { db_.LogChange(internalId, change); } assert(listener_.get() != NULL); listener_->SignalChange(change); } uint64_t ServerIndex::IncrementGlobalSequenceInternal(GlobalProperty property) { std::string oldValue; if (db_.LookupGlobalProperty(oldValue, property)) { uint64_t oldNumber; try { oldNumber = boost::lexical_cast<uint64_t>(oldValue); db_.SetGlobalProperty(property, boost::lexical_cast<std::string>(oldNumber + 1)); return oldNumber + 1; } catch (boost::bad_lexical_cast&) { throw OrthancException(ErrorCode_InternalError); } } else { // Initialize the sequence at "1" db_.SetGlobalProperty(property, "1"); return 1; } } void ServerIndex::SetMainDicomTags(int64_t resource, const DicomMap& tags) { DicomArray flattened(tags); for (size_t i = 0; i < flattened.GetSize(); i++) { const DicomElement& element = flattened.GetElement(i); db_.SetMainDicomTag(resource, element.GetTag(), element.GetValue().AsString()); } } int64_t ServerIndex::CreateResource(const std::string& publicId, ResourceType type) { int64_t id = db_.CreateResource(publicId, type); ChangeType changeType; switch (type) { case ResourceType_Patient: changeType = ChangeType_NewPatient; break; case ResourceType_Study: changeType = ChangeType_NewStudy; break; case ResourceType_Series: changeType = ChangeType_NewSeries; break; case ResourceType_Instance: changeType = ChangeType_NewInstance; break; default: throw OrthancException(ErrorCode_InternalError); } ServerIndexChange change(changeType, type, publicId); db_.LogChange(id, change); assert(listener_.get() != NULL); listener_->SignalChange(change); return id; } ServerIndex::ServerIndex(ServerContext& context, IDatabaseWrapper& db) : done_(false), db_(db), maximumStorageSize_(0), maximumPatients_(0) { listener_.reset(new Listener(context)); db_.SetListener(*listener_); currentStorageSize_ = db_.GetTotalCompressedSize(); // Initial recycling if the parameters have changed since the last // execution of Orthanc StandaloneRecycling(); if (db.HasFlushToDisk()) { flushThread_ = boost::thread(FlushThread, this); } unstableResourcesMonitorThread_ = boost::thread(UnstableResourcesMonitorThread, this); } ServerIndex::~ServerIndex() { if (!done_) { LOG(ERROR) << "INTERNAL ERROR: ServerIndex::Stop() should be invoked manually to avoid mess in the destruction order!"; Stop(); } } void ServerIndex::Stop() { if (!done_) { done_ = true; if (db_.HasFlushToDisk() && flushThread_.joinable()) { flushThread_.join(); } if (unstableResourcesMonitorThread_.joinable()) { unstableResourcesMonitorThread_.join(); } } } StoreStatus ServerIndex::Store(std::map<MetadataType, std::string>& instanceMetadata, const DicomMap& dicomSummary, const Attachments& attachments, const std::string& remoteAet, const MetadataMap& metadata) { boost::mutex::scoped_lock lock(mutex_); instanceMetadata.clear(); DicomInstanceHasher hasher(dicomSummary); try { Transaction t(*this); // Do nothing if the instance already exists { ResourceType type; int64_t tmp; if (db_.LookupResource(tmp, type, hasher.HashInstance())) { assert(type == ResourceType_Instance); db_.GetAllMetadata(instanceMetadata, tmp); return StoreStatus_AlreadyStored; } } // Ensure there is enough room in the storage for the new instance uint64_t instanceSize = 0; for (Attachments::const_iterator it = attachments.begin(); it != attachments.end(); ++it) { instanceSize += it->GetCompressedSize(); } Recycle(instanceSize, hasher.HashPatient()); // Create the instance int64_t instance = CreateResource(hasher.HashInstance(), ResourceType_Instance); DicomMap dicom; dicomSummary.ExtractInstanceInformation(dicom); SetMainDicomTags(instance, dicom); // Detect up to which level the patient/study/series/instance // hierarchy must be created int64_t patient = -1, study = -1, series = -1; bool isNewPatient = false; bool isNewStudy = false; bool isNewSeries = false; { ResourceType dummy; if (db_.LookupResource(series, dummy, hasher.HashSeries())) { assert(dummy == ResourceType_Series); // The patient, the study and the series already exist bool ok = (db_.LookupResource(patient, dummy, hasher.HashPatient()) && db_.LookupResource(study, dummy, hasher.HashStudy())); assert(ok); } else if (db_.LookupResource(study, dummy, hasher.HashStudy())) { assert(dummy == ResourceType_Study); // New series: The patient and the study already exist isNewSeries = true; bool ok = db_.LookupResource(patient, dummy, hasher.HashPatient()); assert(ok); } else if (db_.LookupResource(patient, dummy, hasher.HashPatient())) { assert(dummy == ResourceType_Patient); // New study and series: The patient already exist isNewStudy = true; isNewSeries = true; } else { // New patient, study and series: Nothing exists isNewPatient = true; isNewStudy = true; isNewSeries = true; } } // Create the series if needed if (isNewSeries) { series = CreateResource(hasher.HashSeries(), ResourceType_Series); dicomSummary.ExtractSeriesInformation(dicom); SetMainDicomTags(series, dicom); } // Create the study if needed if (isNewStudy) { study = CreateResource(hasher.HashStudy(), ResourceType_Study); dicomSummary.ExtractStudyInformation(dicom); SetMainDicomTags(study, dicom); } // Create the patient if needed if (isNewPatient) { patient = CreateResource(hasher.HashPatient(), ResourceType_Patient); dicomSummary.ExtractPatientInformation(dicom); SetMainDicomTags(patient, dicom); } // Create the parent-to-child links db_.AttachChild(series, instance); if (isNewSeries) { db_.AttachChild(study, series); } if (isNewStudy) { db_.AttachChild(patient, study); } // Sanity checks assert(patient != -1); assert(study != -1); assert(series != -1); assert(instance != -1); // Attach the files to the newly created instance for (Attachments::const_iterator it = attachments.begin(); it != attachments.end(); ++it) { db_.AddAttachment(instance, *it); } // Attach the user-specified metadata for (MetadataMap::const_iterator it = metadata.begin(); it != metadata.end(); ++it) { switch (it->first.first) { case ResourceType_Patient: db_.SetMetadata(patient, it->first.second, it->second); break; case ResourceType_Study: db_.SetMetadata(study, it->first.second, it->second); break; case ResourceType_Series: db_.SetMetadata(series, it->first.second, it->second); break; case ResourceType_Instance: db_.SetMetadata(instance, it->first.second, it->second); instanceMetadata[it->first.second] = it->second; break; default: throw OrthancException(ErrorCode_ParameterOutOfRange); } } // Attach the auto-computed metadata for the patient/study/series levels std::string now = Toolbox::GetNowIsoString(); db_.SetMetadata(series, MetadataType_LastUpdate, now); db_.SetMetadata(study, MetadataType_LastUpdate, now); db_.SetMetadata(patient, MetadataType_LastUpdate, now); // Attach the auto-computed metadata for the instance level, // reflecting these additions into the input metadata map db_.SetMetadata(instance, MetadataType_Instance_ReceptionDate, now); instanceMetadata[MetadataType_Instance_ReceptionDate] = now; db_.SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); instanceMetadata[MetadataType_Instance_RemoteAet] = remoteAet; const DicomValue* value; if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) { db_.SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->AsString()); instanceMetadata[MetadataType_Instance_IndexInSeries] = value->AsString(); } // Check whether the series of this new instance is now completed if (isNewSeries) { ComputeExpectedNumberOfInstances(db_, series, dicomSummary); } SeriesStatus seriesStatus = GetSeriesStatus(series); if (seriesStatus == SeriesStatus_Complete) { LogChange(series, ChangeType_CompletedSeries, ResourceType_Series, hasher.HashSeries()); } // Mark the parent resources of this instance as unstable MarkAsUnstable(series, ResourceType_Series, hasher.HashSeries()); MarkAsUnstable(study, ResourceType_Study, hasher.HashStudy()); MarkAsUnstable(patient, ResourceType_Patient, hasher.HashPatient()); t.Commit(instanceSize); return StoreStatus_Success; } catch (OrthancException& e) { LOG(ERROR) << "EXCEPTION [" << e.What() << "]"; } return StoreStatus_Failure; } void ServerIndex::ComputeStatistics(Json::Value& target) { boost::mutex::scoped_lock lock(mutex_); target = Json::objectValue; uint64_t cs = currentStorageSize_; assert(cs == db_.GetTotalCompressedSize()); uint64_t us = db_.GetTotalUncompressedSize(); target["TotalDiskSize"] = boost::lexical_cast<std::string>(cs); target["TotalUncompressedSize"] = boost::lexical_cast<std::string>(us); target["TotalDiskSizeMB"] = static_cast<unsigned int>(cs / MEGA_BYTES); target["TotalUncompressedSizeMB"] = static_cast<unsigned int>(us / MEGA_BYTES); target["CountPatients"] = static_cast<unsigned int>(db_.GetResourceCount(ResourceType_Patient)); target["CountStudies"] = static_cast<unsigned int>(db_.GetResourceCount(ResourceType_Study)); target["CountSeries"] = static_cast<unsigned int>(db_.GetResourceCount(ResourceType_Series)); target["CountInstances"] = static_cast<unsigned int>(db_.GetResourceCount(ResourceType_Instance)); } SeriesStatus ServerIndex::GetSeriesStatus(int64_t id) { // Get the expected number of instances in this series (from the metadata) int64_t expected; if (!GetMetadataAsInteger(expected, id, MetadataType_Series_ExpectedNumberOfInstances)) { return SeriesStatus_Unknown; } // Loop over the instances of this series std::list<int64_t> children; db_.GetChildrenInternalId(children, id); std::set<int64_t> instances; for (std::list<int64_t>::const_iterator it = children.begin(); it != children.end(); ++it) { // Get the index of this instance in the series int64_t index; if (!GetMetadataAsInteger(index, *it, MetadataType_Instance_IndexInSeries)) { return SeriesStatus_Unknown; } if (!(index > 0 && index <= expected)) { // Out-of-range instance index return SeriesStatus_Inconsistent; } if (instances.find(index) != instances.end()) { // Twice the same instance index return SeriesStatus_Inconsistent; } instances.insert(index); } if (static_cast<int64_t>(instances.size()) == expected) { return SeriesStatus_Complete; } else { return SeriesStatus_Missing; } } void ServerIndex::MainDicomTagsToJson(Json::Value& target, int64_t resourceId) { DicomMap tags; db_.GetMainDicomTags(tags, resourceId); target["MainDicomTags"] = Json::objectValue; FromDcmtkBridge::ToJson(target["MainDicomTags"], tags, true); } bool ServerIndex::LookupResource(Json::Value& result, const std::string& publicId, ResourceType expectedType) { result = Json::objectValue; boost::mutex::scoped_lock lock(mutex_); // Lookup for the requested resource int64_t id; ResourceType type; if (!db_.LookupResource(id, type, publicId) || type != expectedType) { return false; } // Find the parent resource (if it exists) if (type != ResourceType_Patient) { int64_t parentId; if (!db_.LookupParent(parentId, id)) { throw OrthancException(ErrorCode_InternalError); } std::string parent = db_.GetPublicId(parentId); switch (type) { case ResourceType_Study: result["ParentPatient"] = parent; break; case ResourceType_Series: result["ParentStudy"] = parent; break; case ResourceType_Instance: result["ParentSeries"] = parent; break; default: throw OrthancException(ErrorCode_InternalError); } } // List the children resources std::list<std::string> children; db_.GetChildrenPublicId(children, id); if (type != ResourceType_Instance) { Json::Value c = Json::arrayValue; for (std::list<std::string>::const_iterator it = children.begin(); it != children.end(); ++it) { c.append(*it); } switch (type) { case ResourceType_Patient: result["Studies"] = c; break; case ResourceType_Study: result["Series"] = c; break; case ResourceType_Series: result["Instances"] = c; break; default: throw OrthancException(ErrorCode_InternalError); } } // Set the resource type switch (type) { case ResourceType_Patient: result["Type"] = "Patient"; break; case ResourceType_Study: result["Type"] = "Study"; break; case ResourceType_Series: { result["Type"] = "Series"; result["Status"] = EnumerationToString(GetSeriesStatus(id)); int64_t i; if (GetMetadataAsInteger(i, id, MetadataType_Series_ExpectedNumberOfInstances)) result["ExpectedNumberOfInstances"] = static_cast<int>(i); else result["ExpectedNumberOfInstances"] = Json::nullValue; break; } case ResourceType_Instance: { result["Type"] = "Instance"; FileInfo attachment; if (!db_.LookupAttachment(attachment, id, FileContentType_Dicom)) { throw OrthancException(ErrorCode_InternalError); } result["FileSize"] = static_cast<unsigned int>(attachment.GetUncompressedSize()); result["FileUuid"] = attachment.GetUuid(); int64_t i; if (GetMetadataAsInteger(i, id, MetadataType_Instance_IndexInSeries)) result["IndexInSeries"] = static_cast<int>(i); else result["IndexInSeries"] = Json::nullValue; break; } default: throw OrthancException(ErrorCode_InternalError); } // Record the remaining information result["ID"] = publicId; MainDicomTagsToJson(result, id); std::string tmp; if (db_.LookupMetadata(tmp, id, MetadataType_AnonymizedFrom)) { result["AnonymizedFrom"] = tmp; } if (db_.LookupMetadata(tmp, id, MetadataType_ModifiedFrom)) { result["ModifiedFrom"] = tmp; } if (type == ResourceType_Patient || type == ResourceType_Study || type == ResourceType_Series) { result["IsStable"] = !unstableResources_.Contains(id); if (db_.LookupMetadata(tmp, id, MetadataType_LastUpdate)) { result["LastUpdate"] = tmp; } } return true; } bool ServerIndex::LookupAttachment(FileInfo& attachment, const std::string& instanceUuid, FileContentType contentType) { boost::mutex::scoped_lock lock(mutex_); int64_t id; ResourceType type; if (!db_.LookupResource(id, type, instanceUuid)) { throw OrthancException(ErrorCode_UnknownResource); } if (db_.LookupAttachment(attachment, id, contentType)) { assert(attachment.GetContentType() == contentType); return true; } else { return false; } } void ServerIndex::GetAllUuids(std::list<std::string>& target, ResourceType resourceType) { boost::mutex::scoped_lock lock(mutex_); db_.GetAllPublicIds(target, resourceType); } void ServerIndex::GetAllUuids(std::list<std::string>& target, ResourceType resourceType, size_t since, size_t limit) { if (limit == 0) { target.clear(); return; } boost::mutex::scoped_lock lock(mutex_); db_.GetAllPublicIds(target, resourceType, since, limit); } template <typename T> static void FormatLog(Json::Value& target, const std::list<T>& log, const std::string& name, bool done, int64_t since) { Json::Value items = Json::arrayValue; for (typename std::list<T>::const_iterator it = log.begin(); it != log.end(); ++it) { Json::Value item; it->Format(item); items.append(item); } target = Json::objectValue; target[name] = items; target["Done"] = done; int64_t last = (log.empty() ? since : log.back().GetSeq()); target["Last"] = static_cast<int>(last); } void ServerIndex::GetChanges(Json::Value& target, int64_t since, unsigned int maxResults) { std::list<ServerIndexChange> changes; bool done; { boost::mutex::scoped_lock lock(mutex_); db_.GetChanges(changes, done, since, maxResults); } FormatLog(target, changes, "Changes", done, since); } void ServerIndex::GetLastChange(Json::Value& target) { std::list<ServerIndexChange> changes; { boost::mutex::scoped_lock lock(mutex_); db_.GetLastChange(changes); } FormatLog(target, changes, "Changes", true, 0); } void ServerIndex::LogExportedResource(const std::string& publicId, const std::string& remoteModality) { boost::mutex::scoped_lock lock(mutex_); Transaction transaction(*this); int64_t id; ResourceType type; if (!db_.LookupResource(id, type, publicId)) { throw OrthancException(ErrorCode_InternalError); } std::string patientId; std::string studyInstanceUid; std::string seriesInstanceUid; std::string sopInstanceUid; int64_t currentId = id; ResourceType currentType = type; // Iteratively go up inside the patient/study/series/instance hierarchy bool done = false; while (!done) { DicomMap map; db_.GetMainDicomTags(map, currentId); switch (currentType) { case ResourceType_Patient: patientId = map.GetValue(DICOM_TAG_PATIENT_ID).AsString(); done = true; break; case ResourceType_Study: studyInstanceUid = map.GetValue(DICOM_TAG_STUDY_INSTANCE_UID).AsString(); currentType = ResourceType_Patient; break; case ResourceType_Series: seriesInstanceUid = map.GetValue(DICOM_TAG_SERIES_INSTANCE_UID).AsString(); currentType = ResourceType_Study; break; case ResourceType_Instance: sopInstanceUid = map.GetValue(DICOM_TAG_SOP_INSTANCE_UID).AsString(); currentType = ResourceType_Series; break; default: throw OrthancException(ErrorCode_InternalError); } // If we have not reached the Patient level, find the parent of // the current resource if (!done) { bool ok = db_.LookupParent(currentId, currentId); assert(ok); } } ExportedResource resource(-1, type, publicId, remoteModality, Toolbox::GetNowIsoString(), patientId, studyInstanceUid, seriesInstanceUid, sopInstanceUid); db_.LogExportedResource(resource); transaction.Commit(0); } void ServerIndex::GetExportedResources(Json::Value& target, int64_t since, unsigned int maxResults) { std::list<ExportedResource> exported; bool done; { boost::mutex::scoped_lock lock(mutex_); db_.GetExportedResources(exported, done, since, maxResults); } FormatLog(target, exported, "Exports", done, since); } void ServerIndex::GetLastExportedResource(Json::Value& target) { std::list<ExportedResource> exported; { boost::mutex::scoped_lock lock(mutex_); db_.GetLastExportedResource(exported); } FormatLog(target, exported, "Exports", true, 0); } bool ServerIndex::IsRecyclingNeeded(uint64_t instanceSize) { if (maximumStorageSize_ != 0) { uint64_t currentSize = currentStorageSize_ - listener_->GetSizeOfFilesToRemove(); assert(db_.GetTotalCompressedSize() == currentSize); if (currentSize + instanceSize > maximumStorageSize_) { return true; } } if (maximumPatients_ != 0) { uint64_t patientCount = db_.GetResourceCount(ResourceType_Patient); if (patientCount > maximumPatients_) { return true; } } return false; } void ServerIndex::Recycle(uint64_t instanceSize, const std::string& newPatientId) { if (!IsRecyclingNeeded(instanceSize)) { return; } // Check whether other DICOM instances from this patient are // already stored int64_t patientToAvoid; ResourceType type; bool hasPatientToAvoid = db_.LookupResource(patientToAvoid, type, newPatientId); if (hasPatientToAvoid && type != ResourceType_Patient) { throw OrthancException(ErrorCode_InternalError); } // Iteratively select patient to remove until there is enough // space in the DICOM store int64_t patientToRecycle; while (true) { // If other instances of this patient are already in the store, // we must avoid to recycle them bool ok = hasPatientToAvoid ? db_.SelectPatientToRecycle(patientToRecycle, patientToAvoid) : db_.SelectPatientToRecycle(patientToRecycle); if (!ok) { throw OrthancException(ErrorCode_FullStorage); } VLOG(1) << "Recycling one patient"; db_.DeleteResource(patientToRecycle); if (!IsRecyclingNeeded(instanceSize)) { // OK, we're done break; } } } void ServerIndex::SetMaximumPatientCount(unsigned int count) { boost::mutex::scoped_lock lock(mutex_); maximumPatients_ = count; if (count == 0) { LOG(WARNING) << "No limit on the number of stored patients"; } else { LOG(WARNING) << "At most " << count << " patients will be stored"; } StandaloneRecycling(); } void ServerIndex::SetMaximumStorageSize(uint64_t size) { boost::mutex::scoped_lock lock(mutex_); maximumStorageSize_ = size; if (size == 0) { LOG(WARNING) << "No limit on the size of the storage area"; } else { LOG(WARNING) << "At most " << (size / MEGA_BYTES) << "MB will be used for the storage area"; } StandaloneRecycling(); } void ServerIndex::StandaloneRecycling() { // WARNING: No mutex here, do not include this as a public method Transaction t(*this); Recycle(0, ""); t.Commit(0); } bool ServerIndex::IsProtectedPatient(const std::string& publicId) { boost::mutex::scoped_lock lock(mutex_); // Lookup for the requested resource int64_t id; ResourceType type; if (!db_.LookupResource(id, type, publicId) || type != ResourceType_Patient) { throw OrthancException(ErrorCode_ParameterOutOfRange); } return db_.IsProtectedPatient(id); } void ServerIndex::SetProtectedPatient(const std::string& publicId, bool isProtected) { boost::mutex::scoped_lock lock(mutex_); Transaction transaction(*this); // Lookup for the requested resource int64_t id; ResourceType type; if (!db_.LookupResource(id, type, publicId) || type != ResourceType_Patient) { throw OrthancException(ErrorCode_ParameterOutOfRange); } db_.SetProtectedPatient(id, isProtected); transaction.Commit(0); if (isProtected) LOG(INFO) << "Patient " << publicId << " has been protected"; else LOG(INFO) << "Patient " << publicId << " has been unprotected"; } void ServerIndex::GetChildren(std::list<std::string>& result, const std::string& publicId) { result.clear(); boost::mutex::scoped_lock lock(mutex_); ResourceType type; int64_t resource; if (!db_.LookupResource(resource, type, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } if (type == ResourceType_Instance) { // An instance cannot have a child throw OrthancException(ErrorCode_BadParameterType); } std::list<int64_t> tmp; db_.GetChildrenInternalId(tmp, resource); for (std::list<int64_t>::const_iterator it = tmp.begin(); it != tmp.end(); ++it) { result.push_back(db_.GetPublicId(*it)); } } void ServerIndex::GetChildInstances(std::list<std::string>& result, const std::string& publicId) { result.clear(); boost::mutex::scoped_lock lock(mutex_); ResourceType type; int64_t top; if (!db_.LookupResource(top, type, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } if (type == ResourceType_Instance) { // The resource is already an instance: Do not go down the hierarchy result.push_back(publicId); return; } std::stack<int64_t> toExplore; toExplore.push(top); std::list<int64_t> tmp; while (!toExplore.empty()) { // Get the internal ID of the current resource int64_t resource = toExplore.top(); toExplore.pop(); if (db_.GetResourceType(resource) == ResourceType_Instance) { result.push_back(db_.GetPublicId(resource)); } else { // Tag all the children of this resource as to be explored db_.GetChildrenInternalId(tmp, resource); for (std::list<int64_t>::const_iterator it = tmp.begin(); it != tmp.end(); ++it) { toExplore.push(*it); } } } } void ServerIndex::SetMetadata(const std::string& publicId, MetadataType type, const std::string& value) { boost::mutex::scoped_lock lock(mutex_); ResourceType rtype; int64_t id; if (!db_.LookupResource(id, rtype, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } db_.SetMetadata(id, type, value); } void ServerIndex::DeleteMetadata(const std::string& publicId, MetadataType type) { boost::mutex::scoped_lock lock(mutex_); ResourceType rtype; int64_t id; if (!db_.LookupResource(id, rtype, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } db_.DeleteMetadata(id, type); } bool ServerIndex::LookupMetadata(std::string& target, const std::string& publicId, MetadataType type) { boost::mutex::scoped_lock lock(mutex_); ResourceType rtype; int64_t id; if (!db_.LookupResource(id, rtype, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } return db_.LookupMetadata(target, id, type); } void ServerIndex::ListAvailableMetadata(std::list<MetadataType>& target, const std::string& publicId) { boost::mutex::scoped_lock lock(mutex_); ResourceType rtype; int64_t id; if (!db_.LookupResource(id, rtype, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } db_.ListAvailableMetadata(target, id); } void ServerIndex::ListAvailableAttachments(std::list<FileContentType>& target, const std::string& publicId, ResourceType expectedType) { boost::mutex::scoped_lock lock(mutex_); ResourceType type; int64_t id; if (!db_.LookupResource(id, type, publicId) || expectedType != type) { throw OrthancException(ErrorCode_UnknownResource); } db_.ListAvailableAttachments(target, id); } bool ServerIndex::LookupParent(std::string& target, const std::string& publicId) { boost::mutex::scoped_lock lock(mutex_); ResourceType type; int64_t id; if (!db_.LookupResource(id, type, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } int64_t parentId; if (db_.LookupParent(parentId, id)) { target = db_.GetPublicId(parentId); return true; } else { return false; } } uint64_t ServerIndex::IncrementGlobalSequence(GlobalProperty sequence) { boost::mutex::scoped_lock lock(mutex_); Transaction transaction(*this); uint64_t seq = IncrementGlobalSequenceInternal(sequence); transaction.Commit(0); return seq; } void ServerIndex::LogChange(ChangeType changeType, const std::string& publicId) { boost::mutex::scoped_lock lock(mutex_); Transaction transaction(*this); int64_t id; ResourceType type; if (!db_.LookupResource(id, type, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } LogChange(id, changeType, type, publicId); transaction.Commit(0); } void ServerIndex::DeleteChanges() { boost::mutex::scoped_lock lock(mutex_); db_.ClearChanges(); } void ServerIndex::DeleteExportedResources() { boost::mutex::scoped_lock lock(mutex_); db_.ClearExportedResources(); } void ServerIndex::GetStatisticsInternal(/* out */ uint64_t& compressedSize, /* out */ uint64_t& uncompressedSize, /* out */ unsigned int& countStudies, /* out */ unsigned int& countSeries, /* out */ unsigned int& countInstances, /* in */ int64_t id, /* in */ ResourceType type) { std::stack<int64_t> toExplore; toExplore.push(id); countInstances = 0; countSeries = 0; countStudies = 0; compressedSize = 0; uncompressedSize = 0; while (!toExplore.empty()) { // Get the internal ID of the current resource int64_t resource = toExplore.top(); toExplore.pop(); ResourceType thisType = db_.GetResourceType(resource); std::list<FileContentType> f; db_.ListAvailableAttachments(f, resource); for (std::list<FileContentType>::const_iterator it = f.begin(); it != f.end(); ++it) { FileInfo attachment; if (db_.LookupAttachment(attachment, resource, *it)) { compressedSize += attachment.GetCompressedSize(); uncompressedSize += attachment.GetUncompressedSize(); } } if (thisType == ResourceType_Instance) { countInstances++; } else { switch (thisType) { case ResourceType_Study: countStudies++; break; case ResourceType_Series: countSeries++; break; default: break; } // Tag all the children of this resource as to be explored std::list<int64_t> tmp; db_.GetChildrenInternalId(tmp, resource); for (std::list<int64_t>::const_iterator it = tmp.begin(); it != tmp.end(); ++it) { toExplore.push(*it); } } } if (countStudies == 0) { countStudies = 1; } if (countSeries == 0) { countSeries = 1; } } void ServerIndex::GetStatistics(Json::Value& target, const std::string& publicId) { boost::mutex::scoped_lock lock(mutex_); ResourceType type; int64_t top; if (!db_.LookupResource(top, type, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } uint64_t uncompressedSize; uint64_t compressedSize; unsigned int countStudies; unsigned int countSeries; unsigned int countInstances; GetStatisticsInternal(compressedSize, uncompressedSize, countStudies, countSeries, countInstances, top, type); target = Json::objectValue; target["DiskSize"] = boost::lexical_cast<std::string>(compressedSize); target["DiskSizeMB"] = static_cast<unsigned int>(compressedSize / MEGA_BYTES); target["UncompressedSize"] = boost::lexical_cast<std::string>(uncompressedSize); target["UncompressedSizeMB"] = static_cast<unsigned int>(uncompressedSize / MEGA_BYTES); switch (type) { // Do NOT add "break" below this point! case ResourceType_Patient: target["CountStudies"] = countStudies; case ResourceType_Study: target["CountSeries"] = countSeries; case ResourceType_Series: target["CountInstances"] = countInstances; case ResourceType_Instance: default: break; } } void ServerIndex::GetStatistics(/* out */ uint64_t& compressedSize, /* out */ uint64_t& uncompressedSize, /* out */ unsigned int& countStudies, /* out */ unsigned int& countSeries, /* out */ unsigned int& countInstances, const std::string& publicId) { boost::mutex::scoped_lock lock(mutex_); ResourceType type; int64_t top; if (!db_.LookupResource(top, type, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } GetStatisticsInternal(compressedSize, uncompressedSize, countStudies, countSeries, countInstances, top, type); } void ServerIndex::UnstableResourcesMonitorThread(ServerIndex* that) { int stableAge = Configuration::GetGlobalIntegerParameter("StableAge", 60); if (stableAge <= 0) { stableAge = 60; } LOG(INFO) << "Starting the monitor for stable resources (stable age = " << stableAge << ")"; while (!that->done_) { // Check for stable resources each second boost::this_thread::sleep(boost::posix_time::seconds(1)); boost::mutex::scoped_lock lock(that->mutex_); while (!that->unstableResources_.IsEmpty() && that->unstableResources_.GetOldestPayload().GetAge() > static_cast<unsigned int>(stableAge)) { // This DICOM resource has not received any new instance for // some time. It can be considered as stable. UnstableResourcePayload payload; int64_t id = that->unstableResources_.RemoveOldest(payload); // Ensure that the resource is still existing before logging the change if (that->db_.IsExistingResource(id)) { switch (payload.GetResourceType()) { case ResourceType_Patient: that->LogChange(id, ChangeType_StablePatient, ResourceType_Patient, payload.GetPublicId()); break; case ResourceType_Study: that->LogChange(id, ChangeType_StableStudy, ResourceType_Study, payload.GetPublicId()); break; case ResourceType_Series: that->LogChange(id, ChangeType_StableSeries, ResourceType_Series, payload.GetPublicId()); break; default: throw OrthancException(ErrorCode_InternalError); } //LOG(INFO) << "Stable resource: " << EnumerationToString(payload.type_) << " " << id; } } } LOG(INFO) << "Closing the monitor thread for stable resources"; } void ServerIndex::MarkAsUnstable(int64_t id, Orthanc::ResourceType type, const std::string& publicId) { // WARNING: Before calling this method, "mutex_" must be locked. assert(type == Orthanc::ResourceType_Patient || type == Orthanc::ResourceType_Study || type == Orthanc::ResourceType_Series); UnstableResourcePayload payload(type, publicId); unstableResources_.AddOrMakeMostRecent(id, payload); //LOG(INFO) << "Unstable resource: " << EnumerationToString(type) << " " << id; LogChange(id, ChangeType_NewChildInstance, type, publicId); } void ServerIndex::LookupIdentifier(std::list<std::string>& result, const DicomTag& tag, const std::string& value, ResourceType type) { result.clear(); boost::mutex::scoped_lock lock(mutex_); std::list<int64_t> id; db_.LookupIdentifier(id, tag, value); for (std::list<int64_t>::const_iterator it = id.begin(); it != id.end(); ++it) { if (db_.GetResourceType(*it) == type) { result.push_back(db_.GetPublicId(*it)); } } } void ServerIndex::LookupIdentifier(std::list<std::string>& result, const DicomTag& tag, const std::string& value) { result.clear(); boost::mutex::scoped_lock lock(mutex_); std::list<int64_t> id; db_.LookupIdentifier(id, tag, value); for (std::list<int64_t>::const_iterator it = id.begin(); it != id.end(); ++it) { result.push_back(db_.GetPublicId(*it)); } } void ServerIndex::LookupIdentifier(std::list< std::pair<ResourceType, std::string> >& result, const std::string& value) { result.clear(); boost::mutex::scoped_lock lock(mutex_); std::list<int64_t> id; db_.LookupIdentifier(id, value); for (std::list<int64_t>::const_iterator it = id.begin(); it != id.end(); ++it) { result.push_back(std::make_pair(db_.GetResourceType(*it), db_.GetPublicId(*it))); } } StoreStatus ServerIndex::AddAttachment(const FileInfo& attachment, const std::string& publicId) { boost::mutex::scoped_lock lock(mutex_); Transaction t(*this); ResourceType resourceType; int64_t resourceId; if (!db_.LookupResource(resourceId, resourceType, publicId)) { return StoreStatus_Failure; // Inexistent resource } // Remove possible previous attachment db_.DeleteAttachment(resourceId, attachment.GetContentType()); // Locate the patient of the target resource int64_t patientId = resourceId; for (;;) { int64_t parent; if (db_.LookupParent(parent, patientId)) { // We have not reached the patient level yet patientId = parent; } else { // We have reached the patient level break; } } // Possibly apply the recycling mechanism while preserving this patient assert(db_.GetResourceType(patientId) == ResourceType_Patient); Recycle(attachment.GetCompressedSize(), db_.GetPublicId(patientId)); db_.AddAttachment(resourceId, attachment); t.Commit(attachment.GetCompressedSize()); return StoreStatus_Success; } void ServerIndex::DeleteAttachment(const std::string& publicId, FileContentType type) { boost::mutex::scoped_lock lock(mutex_); Transaction t(*this); ResourceType rtype; int64_t id; if (!db_.LookupResource(id, rtype, publicId)) { throw OrthancException(ErrorCode_UnknownResource); } db_.DeleteAttachment(id, type); t.Commit(0); } bool ServerIndex::GetMetadata(Json::Value& target, const std::string& publicId) { boost::mutex::scoped_lock lock(mutex_); target = Json::objectValue; ResourceType type; int64_t id; if (!db_.LookupResource(id, type, publicId)) { return false; } std::list<MetadataType> metadata; db_.ListAvailableMetadata(metadata, id); for (std::list<MetadataType>::const_iterator it = metadata.begin(); it != metadata.end(); ++it) { std::string key = EnumerationToString(*it); std::string value; if (!db_.LookupMetadata(value, id, *it)) { value.clear(); } target[key] = value; } return true; } void ServerIndex::SetGlobalProperty(GlobalProperty property, const std::string& value) { boost::mutex::scoped_lock lock(mutex_); db_.SetGlobalProperty(property, value); } std::string ServerIndex::GetGlobalProperty(GlobalProperty property, const std::string& defaultValue) { boost::mutex::scoped_lock lock(mutex_); std::string value; if (db_.LookupGlobalProperty(value, property)) { return value; } else { return defaultValue; } } bool ServerIndex::GetMainDicomTags(DicomMap& result, const std::string& publicId, ResourceType expectedType) { result.Clear(); boost::mutex::scoped_lock lock(mutex_); // Lookup for the requested resource int64_t id; ResourceType type; if (!db_.LookupResource(id, type, publicId) || type != expectedType) { return false; } else { db_.GetMainDicomTags(result, id); return true; } } bool ServerIndex::LookupResourceType(ResourceType& type, const std::string& publicId) { boost::mutex::scoped_lock lock(mutex_); int64_t id; return db_.LookupResource(id, type, publicId); } }