Mercurial > hg > orthanc
view OrthancServer/DatabaseWrapper.cpp @ 406:fb1d988a978b
news
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Tue, 30 Apr 2013 15:26:34 +0200 |
parents | 4d5f0857ec9c |
children | 47d63c941902 |
line wrap: on
line source
/** * Orthanc - A Lightweight, RESTful DICOM Store * Copyright (C) 2012-2013 Medical Physics Department, CHU 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 "DatabaseWrapper.h" #include "../Core/DicomFormat/DicomArray.h" #include "../Core/Uuid.h" #include "EmbeddedResources.h" #include <glog/logging.h> #include <stdio.h> namespace Orthanc { namespace Internals { class SignalFileDeleted : public SQLite::IScalarFunction { private: IServerIndexListener& listener_; public: SignalFileDeleted(IServerIndexListener& listener) : listener_(listener) { } virtual const char* GetName() const { return "SignalFileDeleted"; } virtual unsigned int GetCardinality() const { return 5; } virtual void Compute(SQLite::FunctionContext& context) { FileInfo info(context.GetStringValue(0), static_cast<FileContentType>(context.GetIntValue(1)), static_cast<uint64_t>(context.GetInt64Value(2)), static_cast<CompressionType>(context.GetIntValue(3)), static_cast<uint64_t>(context.GetInt64Value(4))); listener_.SignalFileDeleted(info); } }; class SignalRemainingAncestor : public SQLite::IScalarFunction { private: bool hasRemainingAncestor_; std::string remainingPublicId_; ResourceType remainingType_; public: void Reset() { hasRemainingAncestor_ = false; } virtual const char* GetName() const { return "SignalRemainingAncestor"; } virtual unsigned int GetCardinality() const { return 2; } virtual void Compute(SQLite::FunctionContext& context) { VLOG(1) << "There exists a remaining ancestor with public ID \"" << context.GetStringValue(0) << "\" of type " << context.GetIntValue(1); if (!hasRemainingAncestor_ || remainingType_ >= context.GetIntValue(1)) { hasRemainingAncestor_ = true; remainingPublicId_ = context.GetStringValue(0); remainingType_ = static_cast<ResourceType>(context.GetIntValue(1)); } } bool HasRemainingAncestor() const { return hasRemainingAncestor_; } const std::string& GetRemainingAncestorId() const { assert(hasRemainingAncestor_); return remainingPublicId_; } ResourceType GetRemainingAncestorType() const { assert(hasRemainingAncestor_); return remainingType_; } }; } void DatabaseWrapper::SetGlobalProperty(GlobalProperty property, const std::string& value) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT OR REPLACE INTO GlobalProperties VALUES(?, ?)"); s.BindInt(0, property); s.BindString(1, value); s.Run(); } bool DatabaseWrapper::LookupGlobalProperty(std::string& target, GlobalProperty property) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT value FROM GlobalProperties WHERE property=?"); s.BindInt(0, property); if (!s.Step()) { return false; } else { target = s.ColumnString(0); return true; } } std::string DatabaseWrapper::GetGlobalProperty(GlobalProperty property, const std::string& defaultValue) { std::string s; if (LookupGlobalProperty(s, property)) { return s; } else { return defaultValue; } } int64_t DatabaseWrapper::CreateResource(const std::string& publicId, ResourceType type) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Resources VALUES(NULL, ?, ?, NULL)"); s.BindInt(0, type); s.BindString(1, publicId); s.Run(); int64_t id = db_.GetLastInsertRowId(); 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); } LogChange(changeType, id, type); return id; } bool DatabaseWrapper::LookupResource(const std::string& publicId, int64_t& id, ResourceType& type) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT internalId, resourceType FROM Resources WHERE publicId=?"); s.BindString(0, publicId); if (!s.Step()) { return false; } else { id = s.ColumnInt(0); type = static_cast<ResourceType>(s.ColumnInt(1)); // Check whether there is a single resource with this public id assert(!s.Step()); return true; } } bool DatabaseWrapper::LookupParent(int64_t& parentId, int64_t resourceId) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT parentId FROM Resources WHERE internalId=?"); s.BindInt(0, resourceId); if (!s.Step()) { throw OrthancException(ErrorCode_UnknownResource); } if (s.ColumnIsNull(0)) { return false; } else { parentId = s.ColumnInt(0); return true; } } std::string DatabaseWrapper::GetPublicId(int64_t resourceId) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId FROM Resources WHERE internalId=?"); s.BindInt(0, resourceId); if (!s.Step()) { throw OrthancException(ErrorCode_UnknownResource); } return s.ColumnString(0); } ResourceType DatabaseWrapper::GetResourceType(int64_t resourceId) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT resourceType FROM Resources WHERE internalId=?"); s.BindInt(0, resourceId); if (!s.Step()) { throw OrthancException(ErrorCode_UnknownResource); } return static_cast<ResourceType>(s.ColumnInt(0)); } void DatabaseWrapper::AttachChild(int64_t parent, int64_t child) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "UPDATE Resources SET parentId = ? WHERE internalId = ?"); s.BindInt(0, parent); s.BindInt(1, child); s.Run(); } void DatabaseWrapper::GetChildren(Json::Value& childrenPublicIds, int64_t id) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId FROM Resources WHERE parentId=?"); s.BindInt(0, id); childrenPublicIds = Json::arrayValue; while (s.Step()) { childrenPublicIds.append(s.ColumnString(0)); } } void DatabaseWrapper::DeleteResource(int64_t id) { signalRemainingAncestor_->Reset(); SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM Resources WHERE internalId=?"); s.BindInt(0, id); s.Run(); if (signalRemainingAncestor_->HasRemainingAncestor()) { listener_.SignalRemainingAncestor(signalRemainingAncestor_->GetRemainingAncestorType(), signalRemainingAncestor_->GetRemainingAncestorId()); } } void DatabaseWrapper::SetMetadata(int64_t id, MetadataType type, const std::string& value) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT OR REPLACE INTO Metadata VALUES(?, ?, ?)"); s.BindInt(0, id); s.BindInt(1, type); s.BindString(2, value); s.Run(); } bool DatabaseWrapper::LookupMetadata(std::string& target, int64_t id, MetadataType type) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT value FROM Metadata WHERE id=? AND type=?"); s.BindInt(0, id); s.BindInt(1, type); if (!s.Step()) { return false; } else { target = s.ColumnString(0); return true; } } std::string DatabaseWrapper::GetMetadata(int64_t id, MetadataType type, const std::string& defaultValue) { std::string s; if (LookupMetadata(s, id, type)) { return s; } else { return defaultValue; } } bool DatabaseWrapper::GetMetadataAsInteger(int& result, int64_t id, MetadataType type) { std::string s = GetMetadata(id, type, ""); if (s.size() == 0) { return false; } try { result = boost::lexical_cast<int>(s); return true; } catch (boost::bad_lexical_cast&) { return false; } } void DatabaseWrapper::AddAttachment(int64_t id, const FileInfo& attachment) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO AttachedFiles VALUES(?, ?, ?, ?, ?, ?)"); s.BindInt(0, id); s.BindInt(1, attachment.GetContentType()); s.BindString(2, attachment.GetUuid()); s.BindInt(3, attachment.GetCompressedSize()); s.BindInt(4, attachment.GetUncompressedSize()); s.BindInt(5, attachment.GetCompressionType()); s.Run(); } bool DatabaseWrapper::LookupAttachment(FileInfo& attachment, int64_t id, FileContentType contentType) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid, uncompressedSize, compressionType, compressedSize FROM AttachedFiles WHERE id=? AND fileType=?"); s.BindInt(0, id); s.BindInt(1, contentType); if (!s.Step()) { return false; } else { attachment = FileInfo(s.ColumnString(0), contentType, s.ColumnInt(1), static_cast<CompressionType>(s.ColumnInt(2)), s.ColumnInt(3)); return true; } } void DatabaseWrapper::SetMainDicomTags(int64_t id, const DicomMap& tags) { DicomArray flattened(tags); for (size_t i = 0; i < flattened.GetSize(); i++) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO MainDicomTags VALUES(?, ?, ?, ?)"); s.BindInt(0, id); s.BindInt(1, flattened.GetElement(i).GetTag().GetGroup()); s.BindInt(2, flattened.GetElement(i).GetTag().GetElement()); s.BindString(3, flattened.GetElement(i).GetValue().AsString()); s.Run(); } } void DatabaseWrapper::GetMainDicomTags(DicomMap& map, int64_t id) { map.Clear(); SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM MainDicomTags WHERE id=?"); s.BindInt(0, id); while (s.Step()) { map.SetValue(s.ColumnInt(1), s.ColumnInt(2), s.ColumnString(3)); } } bool DatabaseWrapper::GetParentPublicId(std::string& result, int64_t id) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT a.publicId FROM Resources AS a, Resources AS b " "WHERE a.internalId = b.parentId AND b.internalId = ?"); s.BindInt(0, id); if (s.Step()) { result = s.ColumnString(0); return true; } else { return false; } } void DatabaseWrapper::GetChildrenPublicId(std::list<std::string>& result, int64_t id) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT a.publicId FROM Resources AS a, Resources AS b " "WHERE a.parentId = b.internalId AND b.internalId = ?"); s.BindInt(0, id); result.clear(); while (s.Step()) { result.push_back(s.ColumnString(0)); } } void DatabaseWrapper::GetChildrenInternalId(std::list<int64_t>& result, int64_t id) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT a.internalId FROM Resources AS a, Resources AS b " "WHERE a.parentId = b.internalId AND b.internalId = ?"); s.BindInt(0, id); result.clear(); while (s.Step()) { result.push_back(s.ColumnInt(0)); } } void DatabaseWrapper::LogChange(ChangeType changeType, int64_t internalId, ResourceType resourceType, const boost::posix_time::ptime& date) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Changes VALUES(NULL, ?, ?, ?, ?)"); s.BindInt(0, changeType); s.BindInt(1, internalId); s.BindInt(2, resourceType); s.BindString(3, boost::posix_time::to_iso_string(date)); s.Run(); } void DatabaseWrapper::GetChangesInternal(Json::Value& target, SQLite::Statement& s, int64_t since, unsigned int maxResults) { Json::Value changes = Json::arrayValue; int64_t last = since; while (changes.size() < maxResults && s.Step()) { int64_t seq = s.ColumnInt(0); ChangeType changeType = static_cast<ChangeType>(s.ColumnInt(1)); int64_t internalId = s.ColumnInt(2); ResourceType resourceType = static_cast<ResourceType>(s.ColumnInt(3)); const std::string& date = s.ColumnString(4); std::string publicId = GetPublicId(internalId); Json::Value item = Json::objectValue; item["Seq"] = static_cast<int>(seq); item["ChangeType"] = ToString(changeType); item["ResourceType"] = ToString(resourceType); item["ID"] = publicId; item["Path"] = GetBasePath(resourceType, publicId); item["Date"] = date; last = seq; changes.append(item); } target = Json::objectValue; target["Changes"] = changes; target["Done"] = !(changes.size() == maxResults && s.Step()); target["Last"] = static_cast<int>(last); } void DatabaseWrapper::GetChanges(Json::Value& target, int64_t since, unsigned int maxResults) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM Changes WHERE seq>? ORDER BY seq LIMIT ?"); s.BindInt(0, since); s.BindInt(1, maxResults + 1); GetChangesInternal(target, s, since, maxResults); } void DatabaseWrapper::GetLastChange(Json::Value& target) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM Changes ORDER BY seq DESC LIMIT 1"); GetChangesInternal(target, s, 0, 1); } void DatabaseWrapper::LogExportedResource(ResourceType resourceType, const std::string& publicId, const std::string& remoteModality, const std::string& patientId, const std::string& studyInstanceUid, const std::string& seriesInstanceUid, const std::string& sopInstanceUid, const boost::posix_time::ptime& date) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO ExportedResources VALUES(NULL, ?, ?, ?, ?, ?, ?, ?, ?)"); s.BindInt(0, resourceType); s.BindString(1, publicId); s.BindString(2, remoteModality); s.BindString(3, patientId); s.BindString(4, studyInstanceUid); s.BindString(5, seriesInstanceUid); s.BindString(6, sopInstanceUid); s.BindString(7, boost::posix_time::to_iso_string(date)); s.Run(); } void DatabaseWrapper::GetExportedResources(Json::Value& target, SQLite::Statement& s, int64_t since, unsigned int maxResults) { Json::Value changes = Json::arrayValue; int64_t last = since; while (changes.size() < maxResults && s.Step()) { int64_t seq = s.ColumnInt(0); ResourceType resourceType = static_cast<ResourceType>(s.ColumnInt(1)); std::string publicId = s.ColumnString(2); Json::Value item = Json::objectValue; item["Seq"] = static_cast<int>(seq); item["ResourceType"] = ToString(resourceType); item["ID"] = publicId; item["Path"] = GetBasePath(resourceType, publicId); item["RemoteModality"] = s.ColumnString(3); item["Date"] = s.ColumnString(8); // WARNING: Do not add "break" below and do not reorder the case items! switch (resourceType) { case ResourceType_Instance: item["SopInstanceUid"] = s.ColumnString(7); case ResourceType_Series: item["SeriesInstanceUid"] = s.ColumnString(6); case ResourceType_Study: item["StudyInstanceUid"] = s.ColumnString(5); case ResourceType_Patient: item["PatientId"] = s.ColumnString(4); break; default: throw OrthancException(ErrorCode_InternalError); } last = seq; changes.append(item); } target = Json::objectValue; target["Exports"] = changes; target["Done"] = !(changes.size() == maxResults && s.Step()); target["Last"] = static_cast<int>(last); } void DatabaseWrapper::GetExportedResources(Json::Value& target, int64_t since, unsigned int maxResults) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM ExportedResources WHERE seq>? ORDER BY seq LIMIT ?"); s.BindInt(0, since); s.BindInt(1, maxResults + 1); GetExportedResources(target, s, since, maxResults); } void DatabaseWrapper::GetLastExportedResource(Json::Value& target) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM ExportedResources ORDER BY seq DESC LIMIT 1"); GetExportedResources(target, s, 0, 1); } int64_t DatabaseWrapper::GetTableRecordCount(const std::string& table) { char buf[128]; sprintf(buf, "SELECT COUNT(*) FROM %s", table.c_str()); SQLite::Statement s(db_, buf); if (!s.Step()) { throw OrthancException(ErrorCode_InternalError); } int64_t c = s.ColumnInt(0); assert(!s.Step()); return c; } uint64_t DatabaseWrapper::GetTotalCompressedSize() { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT SUM(compressedSize) FROM AttachedFiles"); s.Run(); return static_cast<uint64_t>(s.ColumnInt64(0)); } uint64_t DatabaseWrapper::GetTotalUncompressedSize() { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT SUM(uncompressedSize) FROM AttachedFiles"); s.Run(); return static_cast<uint64_t>(s.ColumnInt64(0)); } void DatabaseWrapper::GetAllPublicIds(Json::Value& target, ResourceType resourceType) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId FROM Resources WHERE resourceType=?"); s.BindInt(0, resourceType); target = Json::arrayValue; while (s.Step()) { target.append(s.ColumnString(0)); } } DatabaseWrapper::DatabaseWrapper(const std::string& path, IServerIndexListener& listener) : listener_(listener) { db_.Open(path); Open(); } DatabaseWrapper::DatabaseWrapper(IServerIndexListener& listener) : listener_(listener) { db_.OpenInMemory(); Open(); } void DatabaseWrapper::Open() { // Performance tuning of SQLite with PRAGMAs // http://www.sqlite.org/pragma.html db_.Execute("PRAGMA SYNCHRONOUS=NORMAL;"); db_.Execute("PRAGMA JOURNAL_MODE=WAL;"); db_.Execute("PRAGMA LOCKING_MODE=EXCLUSIVE;"); db_.Execute("PRAGMA WAL_AUTOCHECKPOINT=1000;"); //db_.Execute("PRAGMA TEMP_STORE=memory"); if (!db_.DoesTableExist("GlobalProperties")) { LOG(INFO) << "Creating the database"; std::string query; EmbeddedResources::GetFileResource(query, EmbeddedResources::PREPARE_DATABASE); db_.Execute(query); } // Sanity check of the version of the database std::string version = GetGlobalProperty(GlobalProperty_DatabaseSchemaVersion, "Unknown"); bool ok = false; try { LOG(INFO) << "Version of the Orthanc database: " << version; unsigned int v = boost::lexical_cast<unsigned int>(version); // This version of Orthanc is only compatible with version 3 of // the DB schema (since Orthanc 0.3.2) ok = (v == 3); } catch (boost::bad_lexical_cast&) { } if (!ok) { throw OrthancException(ErrorCode_IncompatibleDatabaseVersion); } signalRemainingAncestor_ = new Internals::SignalRemainingAncestor; db_.Register(signalRemainingAncestor_); db_.Register(new Internals::SignalFileDeleted(listener_)); } uint64_t DatabaseWrapper::GetResourceCount(ResourceType resourceType) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT COUNT(*) FROM Resources WHERE resourceType=?"); s.BindInt(0, resourceType); if (!s.Step()) { throw OrthancException(ErrorCode_InternalError); } int64_t c = s.ColumnInt(0); assert(!s.Step()); return c; } bool DatabaseWrapper::SelectPatientToRecycle(int64_t& internalId) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT patientId FROM PatientRecyclingOrder ORDER BY seq ASC LIMIT 1"); if (!s.Step()) { // No patient remaining or all the patients are protected return false; } else { internalId = s.ColumnInt(0); return true; } } bool DatabaseWrapper::SelectPatientToRecycle(int64_t& internalId, int64_t patientIdToAvoid) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT patientId FROM PatientRecyclingOrder " "WHERE patientId != ? ORDER BY seq ASC LIMIT 1"); s.BindInt(0, patientIdToAvoid); if (!s.Step()) { // No patient remaining or all the patients are protected return false; } else { internalId = s.ColumnInt(0); return true; } } bool DatabaseWrapper::IsProtectedPatient(int64_t internalId) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM PatientRecyclingOrder WHERE patientId = ?"); s.BindInt(0, internalId); return !s.Step(); } void DatabaseWrapper::SetProtectedPatient(int64_t internalId, bool isProtected) { if (isProtected) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM PatientRecyclingOrder WHERE patientId=?"); s.BindInt(0, internalId); s.Run(); } else if (IsProtectedPatient(internalId)) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO PatientRecyclingOrder VALUES(NULL, ?)"); s.BindInt(0, internalId); s.Run(); } else { // Nothing to do: The patient is already unprotected } } uint64_t DatabaseWrapper::IncrementGlobalSequence(GlobalProperty property) { std::string oldValue; if (LookupGlobalProperty(oldValue, property)) { uint64_t oldNumber; try { oldNumber = boost::lexical_cast<uint64_t>(oldValue); 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" SetGlobalProperty(property, "1"); return 1; } } }