Mercurial > hg > orthanc
view OrthancServer/DatabaseWrapper.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 | 878b59270859 |
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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 "DatabaseWrapper.h" #include "../Core/DicomFormat/DicomArray.h" #include "../Core/Logging.h" #include "EmbeddedResources.h" #include "ServerToolbox.h" #include <stdio.h> #include <boost/lexical_cast.hpp> namespace Orthanc { namespace Internals { class SignalFileDeleted : public SQLite::IScalarFunction { private: IDatabaseListener& listener_; public: SignalFileDeleted(IDatabaseListener& listener) : listener_(listener) { } virtual const char* GetName() const { return "SignalFileDeleted"; } virtual unsigned int GetCardinality() const { return 7; } virtual void Compute(SQLite::FunctionContext& context) { std::string uncompressedMD5, compressedMD5; if (!context.IsNullValue(5)) { uncompressedMD5 = context.GetStringValue(5); } if (!context.IsNullValue(6)) { compressedMD5 = context.GetStringValue(6); } FileInfo info(context.GetStringValue(0), static_cast<FileContentType>(context.GetIntValue(1)), static_cast<uint64_t>(context.GetInt64Value(2)), uncompressedMD5, static_cast<CompressionType>(context.GetIntValue(3)), static_cast<uint64_t>(context.GetInt64Value(4)), compressedMD5); listener_.SignalFileDeleted(info); } }; class SignalResourceDeleted : public SQLite::IScalarFunction { private: IDatabaseListener& listener_; public: SignalResourceDeleted(IDatabaseListener& listener) : listener_(listener) { } virtual const char* GetName() const { return "SignalResourceDeleted"; } virtual unsigned int GetCardinality() const { return 2; } virtual void Compute(SQLite::FunctionContext& context) { ResourceType type = static_cast<ResourceType>(context.GetIntValue(1)); ServerIndexChange change(ChangeType_Deleted, type, context.GetStringValue(0)); listener_.SignalChange(change); } }; class SignalRemainingAncestor : public SQLite::IScalarFunction { private: bool hasRemainingAncestor_; std::string remainingPublicId_; ResourceType remainingType_; public: SignalRemainingAncestor() : hasRemainingAncestor_(false) { } 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::GetChildren(std::list<std::string>& childrenPublicIds, int64_t id) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId FROM Resources WHERE parentId=?"); s.BindInt64(0, id); childrenPublicIds.clear(); while (s.Step()) { childrenPublicIds.push_back(s.ColumnString(0)); } } void DatabaseWrapper::DeleteResource(int64_t id) { signalRemainingAncestor_->Reset(); SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM Resources WHERE internalId=?"); s.BindInt64(0, id); s.Run(); if (signalRemainingAncestor_->HasRemainingAncestor() && listener_ != NULL) { listener_->SignalRemainingAncestor(signalRemainingAncestor_->GetRemainingAncestorType(), signalRemainingAncestor_->GetRemainingAncestorId()); } } bool DatabaseWrapper::GetParentPublicId(std::string& target, 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.BindInt64(0, id); if (s.Step()) { target = s.ColumnString(0); return true; } else { return false; } } 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; } DatabaseWrapper::DatabaseWrapper(const std::string& path) : listener_(NULL), base_(db_), signalRemainingAncestor_(NULL), version_(0) { db_.Open(path); } DatabaseWrapper::DatabaseWrapper() : listener_(NULL), base_(db_), signalRemainingAncestor_(NULL), version_(0) { db_.OpenInMemory(); } void DatabaseWrapper::Open() { db_.Execute("PRAGMA ENCODING=\"UTF-8\";"); // 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); } // Check the version of the database std::string tmp; if (!LookupGlobalProperty(tmp, GlobalProperty_DatabaseSchemaVersion)) { tmp = "Unknown"; } bool ok = false; try { LOG(INFO) << "Version of the Orthanc database: " << tmp; version_ = boost::lexical_cast<unsigned int>(tmp); ok = true; } catch (boost::bad_lexical_cast&) { } if (!ok) { LOG(ERROR) << "Incompatible version of the Orthanc database: " << tmp; throw OrthancException(ErrorCode_IncompatibleDatabaseVersion); } signalRemainingAncestor_ = new Internals::SignalRemainingAncestor; db_.Register(signalRemainingAncestor_); } static void ExecuteUpgradeScript(SQLite::Connection& db, EmbeddedResources::FileResourceId script) { std::string upgrade; EmbeddedResources::GetFileResource(upgrade, script); db.BeginTransaction(); db.Execute(upgrade); db.CommitTransaction(); } void DatabaseWrapper::Upgrade(unsigned int targetVersion, IStorageArea& storageArea) { if (targetVersion != 6) { throw OrthancException(ErrorCode_IncompatibleDatabaseVersion); } // This version of Orthanc is only compatible with versions 3, 4, // 5 and 6 of the DB schema if (version_ != 3 && version_ != 4 && version_ != 5 && version_ != 6) { throw OrthancException(ErrorCode_IncompatibleDatabaseVersion); } if (version_ == 3) { LOG(WARNING) << "Upgrading database version from 3 to 4"; ExecuteUpgradeScript(db_, EmbeddedResources::UPGRADE_DATABASE_3_TO_4); version_ = 4; } if (version_ == 4) { LOG(WARNING) << "Upgrading database version from 4 to 5"; ExecuteUpgradeScript(db_, EmbeddedResources::UPGRADE_DATABASE_4_TO_5); version_ = 5; } if (version_ == 5) { LOG(WARNING) << "Upgrading database version from 5 to 6"; // No change in the DB schema, the step from version 5 to 6 only // consists in reconstructing the main DICOM tags information // (as more tags got included). db_.BeginTransaction(); ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Patient); ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Study); ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Series); ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Instance); db_.Execute("UPDATE GlobalProperties SET value=\"6\" WHERE property=" + boost::lexical_cast<std::string>(GlobalProperty_DatabaseSchemaVersion) + ";"); db_.CommitTransaction(); version_ = 6; } } void DatabaseWrapper::SetListener(IDatabaseListener& listener) { listener_ = &listener; db_.Register(new Internals::SignalFileDeleted(listener)); db_.Register(new Internals::SignalResourceDeleted(listener)); } void DatabaseWrapper::ClearTable(const std::string& tableName) { db_.Execute("DELETE FROM " + tableName); } bool DatabaseWrapper::LookupParent(int64_t& parentId, int64_t resourceId) { bool found; ErrorCode error = base_.LookupParent(found, parentId, resourceId); if (error != ErrorCode_Success) { throw OrthancException(error); } else { return found; } } ResourceType DatabaseWrapper::GetResourceType(int64_t resourceId) { ResourceType result; ErrorCode code = base_.GetResourceType(result, resourceId); if (code == ErrorCode_Success) { return result; } else { throw OrthancException(code); } } std::string DatabaseWrapper::GetPublicId(int64_t resourceId) { std::string id; if (base_.GetPublicId(id, resourceId)) { return id; } else { throw OrthancException(ErrorCode_UnknownResource); } } void DatabaseWrapper::GetChanges(std::list<ServerIndexChange>& target /*out*/, bool& done /*out*/, int64_t since, uint32_t maxResults) { ErrorCode code = base_.GetChanges(target, done, since, maxResults); if (code != ErrorCode_Success) { throw OrthancException(code); } } void DatabaseWrapper::GetLastChange(std::list<ServerIndexChange>& target /*out*/) { ErrorCode code = base_.GetLastChange(target); if (code != ErrorCode_Success) { throw OrthancException(code); } } void DatabaseWrapper::GetAllMetadata(std::map<MetadataType, std::string>& target, int64_t id) { target.clear(); SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT type, value FROM Metadata WHERE id=?"); s.BindInt64(0, id); while (s.Step()) { MetadataType key = static_cast<MetadataType>(s.ColumnInt(0)); target[key] = s.ColumnString(1); } } }