Mercurial > hg > orthanc
view OrthancServer/Sources/Database/SQLiteDatabaseWrapper.cpp @ 5117:849000df79b6
fix missing handling of StoreStatus_StorageFull
author | Sebastien Jodogne <s.jodogne@gmail.com> |
---|---|
date | Fri, 02 Dec 2022 15:32:53 +0100 |
parents | cc1a8b3ff319 |
children | 0ea402b4d901 |
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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) 2017-2022 Osimis S.A., Belgium * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, 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. * * 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 "SQLiteDatabaseWrapper.h" #include "../../../OrthancFramework/Sources/DicomFormat/DicomArray.h" #include "../../../OrthancFramework/Sources/Logging.h" #include "../../../OrthancFramework/Sources/SQLite/Transaction.h" #include "../Search/ISqlLookupFormatter.h" #include "../ServerToolbox.h" #include "Compatibility/ICreateInstance.h" #include "Compatibility/IGetChildrenMetadata.h" #include "Compatibility/ILookupResourceAndParent.h" #include "Compatibility/ISetResourcesContent.h" #include "VoidDatabaseListener.h" #include <OrthancServerResources.h> #include <stdio.h> #include <boost/lexical_cast.hpp> namespace Orthanc { class SQLiteDatabaseWrapper::LookupFormatter : public ISqlLookupFormatter { private: std::list<std::string> values_; public: virtual std::string GenerateParameter(const std::string& value) ORTHANC_OVERRIDE { values_.push_back(value); return "?"; } virtual std::string FormatResourceType(ResourceType level) ORTHANC_OVERRIDE { return boost::lexical_cast<std::string>(level); } virtual std::string FormatWildcardEscape() ORTHANC_OVERRIDE { return "ESCAPE '\\'"; } virtual bool IsEscapeBrackets() const ORTHANC_OVERRIDE { return false; } void Bind(SQLite::Statement& statement) const { size_t pos = 0; for (std::list<std::string>::const_iterator it = values_.begin(); it != values_.end(); ++it, pos++) { statement.BindString(pos, *it); } } }; class SQLiteDatabaseWrapper::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 ORTHANC_OVERRIDE { return "SignalRemainingAncestor"; } virtual unsigned int GetCardinality() const ORTHANC_OVERRIDE { return 2; } virtual void Compute(SQLite::FunctionContext& context) ORTHANC_OVERRIDE { CLOG(TRACE, SQLITE) << "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_; } }; class SQLiteDatabaseWrapper::TransactionBase : public SQLiteDatabaseWrapper::UnitTestsTransaction, public Compatibility::ICreateInstance, public Compatibility::IGetChildrenMetadata, public Compatibility::ILookupResourceAndParent, public Compatibility::ISetResourcesContent { private: void AnswerLookup(std::list<std::string>& resourcesId, std::list<std::string>& instancesId, ResourceType level) { resourcesId.clear(); instancesId.clear(); std::unique_ptr<SQLite::Statement> statement; switch (level) { case ResourceType_Patient: { statement.reset( new SQLite::Statement( db_, SQLITE_FROM_HERE, "SELECT patients.publicId, instances.publicID FROM Lookup AS patients " "INNER JOIN Resources studies ON patients.internalId=studies.parentId " "INNER JOIN Resources series ON studies.internalId=series.parentId " "INNER JOIN Resources instances ON series.internalId=instances.parentId " "GROUP BY patients.publicId")); break; } case ResourceType_Study: { statement.reset( new SQLite::Statement( db_, SQLITE_FROM_HERE, "SELECT studies.publicId, instances.publicID FROM Lookup AS studies " "INNER JOIN Resources series ON studies.internalId=series.parentId " "INNER JOIN Resources instances ON series.internalId=instances.parentId " "GROUP BY studies.publicId")); break; } case ResourceType_Series: { statement.reset( new SQLite::Statement( db_, SQLITE_FROM_HERE, "SELECT series.publicId, instances.publicID FROM Lookup AS series " "INNER JOIN Resources instances ON series.internalId=instances.parentId " "GROUP BY series.publicId")); break; } case ResourceType_Instance: { statement.reset( new SQLite::Statement( db_, SQLITE_FROM_HERE, "SELECT publicId, publicId FROM Lookup")); break; } default: throw OrthancException(ErrorCode_InternalError); } assert(statement.get() != NULL); while (statement->Step()) { resourcesId.push_back(statement->ColumnString(0)); instancesId.push_back(statement->ColumnString(1)); } } void ClearTable(const std::string& tableName) { db_.Execute("DELETE FROM " + tableName); } void GetChangesInternal(std::list<ServerIndexChange>& target, bool& done, SQLite::Statement& s, uint32_t maxResults) { target.clear(); while (target.size() < maxResults && s.Step()) { int64_t seq = s.ColumnInt64(0); ChangeType changeType = static_cast<ChangeType>(s.ColumnInt(1)); ResourceType resourceType = static_cast<ResourceType>(s.ColumnInt(3)); const std::string& date = s.ColumnString(4); int64_t internalId = s.ColumnInt64(2); std::string publicId = GetPublicId(internalId); target.push_back(ServerIndexChange(seq, changeType, resourceType, publicId, date)); } done = !(target.size() == maxResults && s.Step()); } void GetExportedResourcesInternal(std::list<ExportedResource>& target, bool& done, SQLite::Statement& s, uint32_t maxResults) { target.clear(); while (target.size() < maxResults && s.Step()) { int64_t seq = s.ColumnInt64(0); ResourceType resourceType = static_cast<ResourceType>(s.ColumnInt(1)); std::string publicId = s.ColumnString(2); ExportedResource resource(seq, resourceType, publicId, s.ColumnString(3), // modality s.ColumnString(8), // date s.ColumnString(4), // patient ID s.ColumnString(5), // study instance UID s.ColumnString(6), // series instance UID s.ColumnString(7)); // sop instance UID target.push_back(resource); } done = !(target.size() == maxResults && s.Step()); } void 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)); } } boost::mutex::scoped_lock lock_; IDatabaseListener& listener_; SignalRemainingAncestor& signalRemainingAncestor_; public: TransactionBase(boost::mutex& mutex, SQLite::Connection& db, IDatabaseListener& listener, SignalRemainingAncestor& signalRemainingAncestor) : UnitTestsTransaction(db), lock_(mutex), listener_(listener), signalRemainingAncestor_(signalRemainingAncestor) { } IDatabaseListener& GetListener() const { return listener_; } virtual void AddAttachment(int64_t id, const FileInfo& attachment, int64_t revision) ORTHANC_OVERRIDE { // TODO - REVISIONS SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO AttachedFiles (id, fileType, uuid, compressedSize, uncompressedSize, compressionType, uncompressedMD5, compressedMD5) VALUES(?, ?, ?, ?, ?, ?, ?, ?)"); s.BindInt64(0, id); s.BindInt(1, attachment.GetContentType()); s.BindString(2, attachment.GetUuid()); s.BindInt64(3, attachment.GetCompressedSize()); s.BindInt64(4, attachment.GetUncompressedSize()); s.BindInt(5, attachment.GetCompressionType()); s.BindString(6, attachment.GetUncompressedMD5()); s.BindString(7, attachment.GetCompressedMD5()); s.Run(); } virtual void ApplyLookupResources(std::list<std::string>& resourcesId, std::list<std::string>* instancesId, const std::vector<DatabaseConstraint>& lookup, ResourceType queryLevel, size_t limit) ORTHANC_OVERRIDE { LookupFormatter formatter; std::string sql; LookupFormatter::Apply(sql, formatter, lookup, queryLevel, limit); sql = "CREATE TEMPORARY TABLE Lookup AS " + sql; { SQLite::Statement s(db_, SQLITE_FROM_HERE, "DROP TABLE IF EXISTS Lookup"); s.Run(); } { SQLite::Statement statement(db_, sql); formatter.Bind(statement); statement.Run(); } if (instancesId != NULL) { AnswerLookup(resourcesId, *instancesId, queryLevel); } else { resourcesId.clear(); SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId FROM Lookup"); while (s.Step()) { resourcesId.push_back(s.ColumnString(0)); } } } // From the "ICreateInstance" interface virtual void AttachChild(int64_t parent, int64_t child) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "UPDATE Resources SET parentId = ? WHERE internalId = ?"); s.BindInt64(0, parent); s.BindInt64(1, child); s.Run(); } virtual void ClearChanges() ORTHANC_OVERRIDE { ClearTable("Changes"); } virtual void ClearExportedResources() ORTHANC_OVERRIDE { ClearTable("ExportedResources"); } virtual void ClearMainDicomTags(int64_t id) ORTHANC_OVERRIDE { { SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM DicomIdentifiers WHERE id=?"); s.BindInt64(0, id); s.Run(); } { SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM MainDicomTags WHERE id=?"); s.BindInt64(0, id); s.Run(); } } virtual bool CreateInstance(CreateInstanceResult& result, int64_t& instanceId, const std::string& patient, const std::string& study, const std::string& series, const std::string& instance) ORTHANC_OVERRIDE { return ICreateInstance::Apply (*this, result, instanceId, patient, study, series, instance); } // From the "ICreateInstance" interface virtual int64_t CreateResource(const std::string& publicId, ResourceType type) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Resources (internalId, resourceType, publicId, parentId) VALUES(NULL, ?, ?, NULL)"); s.BindInt(0, type); s.BindString(1, publicId); s.Run(); return db_.GetLastInsertRowId(); } virtual void DeleteAttachment(int64_t id, FileContentType attachment) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM AttachedFiles WHERE id=? AND fileType=?"); s.BindInt64(0, id); s.BindInt(1, attachment); s.Run(); } virtual void DeleteMetadata(int64_t id, MetadataType type) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM Metadata WHERE id=? and type=?"); s.BindInt64(0, id); s.BindInt(1, type); s.Run(); } virtual void DeleteResource(int64_t id) ORTHANC_OVERRIDE { signalRemainingAncestor_.Reset(); SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM Resources WHERE internalId=?"); s.BindInt64(0, id); s.Run(); if (signalRemainingAncestor_.HasRemainingAncestor()) { listener_.SignalRemainingAncestor(signalRemainingAncestor_.GetRemainingAncestorType(), signalRemainingAncestor_.GetRemainingAncestorId()); } } virtual void GetAllMetadata(std::map<MetadataType, std::string>& target, int64_t id) ORTHANC_OVERRIDE { 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); } } virtual void GetAllPublicIds(std::list<std::string>& target, ResourceType resourceType) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId FROM Resources WHERE resourceType=?"); s.BindInt(0, resourceType); target.clear(); while (s.Step()) { target.push_back(s.ColumnString(0)); } } virtual void GetAllPublicIds(std::list<std::string>& target, ResourceType resourceType, size_t since, size_t limit) ORTHANC_OVERRIDE { if (limit == 0) { target.clear(); return; } SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId FROM Resources WHERE " "resourceType=? LIMIT ? OFFSET ?"); s.BindInt(0, resourceType); s.BindInt64(1, limit); s.BindInt64(2, since); target.clear(); while (s.Step()) { target.push_back(s.ColumnString(0)); } } virtual void GetChanges(std::list<ServerIndexChange>& target /*out*/, bool& done /*out*/, int64_t since, uint32_t maxResults) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM Changes WHERE seq>? ORDER BY seq LIMIT ?"); s.BindInt64(0, since); s.BindInt(1, maxResults + 1); GetChangesInternal(target, done, s, maxResults); } virtual void GetChildrenMetadata(std::list<std::string>& target, int64_t resourceId, MetadataType metadata) ORTHANC_OVERRIDE { IGetChildrenMetadata::Apply(*this, target, resourceId, metadata); } virtual void GetChildrenInternalId(std::list<int64_t>& target, int64_t id) ORTHANC_OVERRIDE { 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.BindInt64(0, id); target.clear(); while (s.Step()) { target.push_back(s.ColumnInt64(0)); } } virtual void GetChildrenPublicId(std::list<std::string>& target, int64_t id) ORTHANC_OVERRIDE { 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.BindInt64(0, id); target.clear(); while (s.Step()) { target.push_back(s.ColumnString(0)); } } virtual void GetExportedResources(std::list<ExportedResource>& target, bool& done, int64_t since, uint32_t maxResults) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM ExportedResources WHERE seq>? ORDER BY seq LIMIT ?"); s.BindInt64(0, since); s.BindInt(1, maxResults + 1); GetExportedResourcesInternal(target, done, s, maxResults); } virtual void GetLastChange(std::list<ServerIndexChange>& target /*out*/) ORTHANC_OVERRIDE { bool done; // Ignored SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM Changes ORDER BY seq DESC LIMIT 1"); GetChangesInternal(target, done, s, 1); } int64_t GetLastChangeIndex() ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT seq FROM sqlite_sequence WHERE name='Changes'"); if (s.Step()) { int64_t c = s.ColumnInt(0); assert(!s.Step()); return c; } else { // No change has been recorded so far in the database return 0; } } virtual void GetLastExportedResource(std::list<ExportedResource>& target) ORTHANC_OVERRIDE { bool done; // Ignored SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM ExportedResources ORDER BY seq DESC LIMIT 1"); GetExportedResourcesInternal(target, done, s, 1); } virtual void GetMainDicomTags(DicomMap& map, int64_t id) ORTHANC_OVERRIDE { map.Clear(); SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM MainDicomTags WHERE id=?"); s.BindInt64(0, id); while (s.Step()) { map.SetValue(s.ColumnInt(1), s.ColumnInt(2), s.ColumnString(3), false); } } virtual std::string GetPublicId(int64_t resourceId) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId FROM Resources WHERE internalId=?"); s.BindInt64(0, resourceId); if (s.Step()) { return s.ColumnString(0); } else { throw OrthancException(ErrorCode_UnknownResource); } } virtual uint64_t GetResourcesCount(ResourceType resourceType) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT COUNT(*) FROM Resources WHERE resourceType=?"); s.BindInt(0, resourceType); if (!s.Step()) { return 0; } else { int64_t c = s.ColumnInt(0); assert(!s.Step()); return c; } } virtual ResourceType GetResourceType(int64_t resourceId) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT resourceType FROM Resources WHERE internalId=?"); s.BindInt64(0, resourceId); if (s.Step()) { return static_cast<ResourceType>(s.ColumnInt(0)); } else { throw OrthancException(ErrorCode_UnknownResource); } } virtual uint64_t GetTotalCompressedSize() ORTHANC_OVERRIDE { // Old SQL query that was used in Orthanc <= 1.5.0: // SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT SUM(compressedSize) FROM AttachedFiles"); SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT value FROM GlobalIntegers WHERE key=0"); s.Run(); return static_cast<uint64_t>(s.ColumnInt64(0)); } virtual uint64_t GetTotalUncompressedSize() ORTHANC_OVERRIDE { // Old SQL query that was used in Orthanc <= 1.5.0: // SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT SUM(uncompressedSize) FROM AttachedFiles"); SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT value FROM GlobalIntegers WHERE key=1"); s.Run(); return static_cast<uint64_t>(s.ColumnInt64(0)); } virtual bool IsDiskSizeAbove(uint64_t threshold) ORTHANC_OVERRIDE { return GetTotalCompressedSize() > threshold; } virtual bool IsExistingResource(int64_t internalId) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM Resources WHERE internalId=?"); s.BindInt64(0, internalId); return s.Step(); } virtual bool IsProtectedPatient(int64_t internalId) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT * FROM PatientRecyclingOrder WHERE patientId = ?"); s.BindInt64(0, internalId); return !s.Step(); } virtual void ListAvailableAttachments(std::set<FileContentType>& target, int64_t id) ORTHANC_OVERRIDE { target.clear(); SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT fileType FROM AttachedFiles WHERE id=?"); s.BindInt64(0, id); while (s.Step()) { target.insert(static_cast<FileContentType>(s.ColumnInt(0))); } } virtual void LogChange(int64_t internalId, const ServerIndexChange& change) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Changes (seq, changeType, internalId, resourceType, date) VALUES(NULL, ?, ?, ?, ?)"); s.BindInt(0, change.GetChangeType()); s.BindInt64(1, internalId); s.BindInt(2, change.GetResourceType()); s.BindString(3, change.GetDate()); s.Run(); } virtual void LogExportedResource(const ExportedResource& resource) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO ExportedResources (seq, resourceType, publicId, remoteModality, patientId, studyInstanceUid, seriesInstanceUid, sopInstanceUid, date) VALUES(NULL, ?, ?, ?, ?, ?, ?, ?, ?)"); s.BindInt(0, resource.GetResourceType()); s.BindString(1, resource.GetPublicId()); s.BindString(2, resource.GetModality()); s.BindString(3, resource.GetPatientId()); s.BindString(4, resource.GetStudyInstanceUid()); s.BindString(5, resource.GetSeriesInstanceUid()); s.BindString(6, resource.GetSopInstanceUid()); s.BindString(7, resource.GetDate()); s.Run(); } virtual bool LookupAttachment(FileInfo& attachment, int64_t& revision, int64_t id, FileContentType contentType) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT uuid, uncompressedSize, compressionType, compressedSize, " "uncompressedMD5, compressedMD5 FROM AttachedFiles WHERE id=? AND fileType=?"); s.BindInt64(0, id); s.BindInt(1, contentType); if (!s.Step()) { return false; } else { attachment = FileInfo(s.ColumnString(0), contentType, s.ColumnInt64(1), s.ColumnString(4), static_cast<CompressionType>(s.ColumnInt(2)), s.ColumnInt64(3), s.ColumnString(5)); revision = 0; // TODO - REVISIONS return true; } } virtual bool LookupGlobalProperty(std::string& target, GlobalProperty property, bool shared) ORTHANC_OVERRIDE { // The "shared" info is not used by the SQLite database, as it // can only be used by one Orthanc server. 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; } } virtual bool LookupMetadata(std::string& target, int64_t& revision, int64_t id, MetadataType type) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT value FROM Metadata WHERE id=? AND type=?"); s.BindInt64(0, id); s.BindInt(1, type); if (!s.Step()) { return false; } else { target = s.ColumnString(0); revision = 0; // TODO - REVISIONS return true; } } virtual bool LookupParent(int64_t& parentId, int64_t resourceId) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT parentId FROM Resources WHERE internalId=?"); s.BindInt64(0, resourceId); if (!s.Step()) { throw OrthancException(ErrorCode_UnknownResource); } if (s.ColumnIsNull(0)) { return false; } else { parentId = s.ColumnInt(0); return true; } } virtual bool LookupResourceAndParent(int64_t& id, ResourceType& type, std::string& parentPublicId, const std::string& publicId) ORTHANC_OVERRIDE { return ILookupResourceAndParent::Apply(*this, id, type, parentPublicId, publicId); } virtual bool LookupResource(int64_t& id, ResourceType& type, const std::string& publicId) ORTHANC_OVERRIDE { 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; } } virtual bool SelectPatientToRecycle(int64_t& internalId) ORTHANC_OVERRIDE { 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; } } virtual bool SelectPatientToRecycle(int64_t& internalId, int64_t patientIdToAvoid) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT patientId FROM PatientRecyclingOrder " "WHERE patientId != ? ORDER BY seq ASC LIMIT 1"); s.BindInt64(0, patientIdToAvoid); if (!s.Step()) { // No patient remaining or all the patients are protected return false; } else { internalId = s.ColumnInt(0); return true; } } virtual void SetGlobalProperty(GlobalProperty property, bool shared, const std::string& value) ORTHANC_OVERRIDE { // The "shared" info is not used by the SQLite database, as it // can only be used by one Orthanc server. SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT OR REPLACE INTO GlobalProperties (property, value) VALUES(?, ?)"); s.BindInt(0, property); s.BindString(1, value); s.Run(); } // From the "ISetResourcesContent" interface virtual void SetIdentifierTag(int64_t id, const DicomTag& tag, const std::string& value) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO DicomIdentifiers (id, tagGroup, tagElement, value) VALUES(?, ?, ?, ?)"); s.BindInt64(0, id); s.BindInt(1, tag.GetGroup()); s.BindInt(2, tag.GetElement()); s.BindString(3, value); s.Run(); } virtual void SetProtectedPatient(int64_t internalId, bool isProtected) ORTHANC_OVERRIDE { if (isProtected) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM PatientRecyclingOrder WHERE patientId=?"); s.BindInt64(0, internalId); s.Run(); } else if (IsProtectedPatient(internalId)) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO PatientRecyclingOrder (seq, patientId) VALUES(NULL, ?)"); s.BindInt64(0, internalId); s.Run(); } else { // Nothing to do: The patient is already unprotected } } // From the "ISetResourcesContent" interface virtual void SetMainDicomTag(int64_t id, const DicomTag& tag, const std::string& value) ORTHANC_OVERRIDE { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO MainDicomTags (id, tagGroup, tagElement, value) VALUES(?, ?, ?, ?)"); s.BindInt64(0, id); s.BindInt(1, tag.GetGroup()); s.BindInt(2, tag.GetElement()); s.BindString(3, value); s.Run(); } virtual void SetMetadata(int64_t id, MetadataType type, const std::string& value, int64_t revision) ORTHANC_OVERRIDE { // TODO - REVISIONS SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT OR REPLACE INTO Metadata (id, type, value) VALUES(?, ?, ?)"); s.BindInt64(0, id); s.BindInt(1, type); s.BindString(2, value); s.Run(); } virtual void SetResourcesContent(const Orthanc::ResourcesContent& content) ORTHANC_OVERRIDE { ISetResourcesContent::Apply(*this, content); } // From the "ICreateInstance" interface virtual void TagMostRecentPatient(int64_t patient) ORTHANC_OVERRIDE { { SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM PatientRecyclingOrder WHERE patientId=?"); s.BindInt64(0, patient); s.Run(); assert(db_.GetLastChangeCount() == 0 || db_.GetLastChangeCount() == 1); if (db_.GetLastChangeCount() == 0) { // The patient was protected, there was nothing to delete from the recycling order return; } } { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO PatientRecyclingOrder (seq, patientId) VALUES(NULL, ?)"); s.BindInt64(0, patient); s.Run(); } } }; class SQLiteDatabaseWrapper::SignalFileDeleted : public SQLite::IScalarFunction { private: SQLiteDatabaseWrapper& sqlite_; public: SignalFileDeleted(SQLiteDatabaseWrapper& sqlite) : sqlite_(sqlite) { } virtual const char* GetName() const ORTHANC_OVERRIDE { return "SignalFileDeleted"; } virtual unsigned int GetCardinality() const ORTHANC_OVERRIDE { return 7; } virtual void Compute(SQLite::FunctionContext& context) ORTHANC_OVERRIDE { if (sqlite_.activeTransaction_ != NULL) { 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); sqlite_.activeTransaction_->GetListener().SignalAttachmentDeleted(info); } } }; class SQLiteDatabaseWrapper::SignalResourceDeleted : public SQLite::IScalarFunction { private: SQLiteDatabaseWrapper& sqlite_; public: SignalResourceDeleted(SQLiteDatabaseWrapper& sqlite) : sqlite_(sqlite) { } virtual const char* GetName() const ORTHANC_OVERRIDE { return "SignalResourceDeleted"; } virtual unsigned int GetCardinality() const ORTHANC_OVERRIDE { return 2; } virtual void Compute(SQLite::FunctionContext& context) ORTHANC_OVERRIDE { if (sqlite_.activeTransaction_ != NULL) { sqlite_.activeTransaction_->GetListener(). SignalResourceDeleted(static_cast<ResourceType>(context.GetIntValue(1)), context.GetStringValue(0)); } } }; class SQLiteDatabaseWrapper::ReadWriteTransaction : public SQLiteDatabaseWrapper::TransactionBase { private: SQLiteDatabaseWrapper& that_; std::unique_ptr<SQLite::Transaction> transaction_; int64_t initialDiskSize_; public: ReadWriteTransaction(SQLiteDatabaseWrapper& that, IDatabaseListener& listener) : TransactionBase(that.mutex_, that.db_, listener, *that.signalRemainingAncestor_), that_(that), transaction_(new SQLite::Transaction(that_.db_)) { if (that_.activeTransaction_ != NULL) { throw OrthancException(ErrorCode_InternalError); } that_.activeTransaction_ = this; #if defined(NDEBUG) // Release mode initialDiskSize_ = 0; #else // Debug mode initialDiskSize_ = static_cast<int64_t>(GetTotalCompressedSize()); #endif } virtual ~ReadWriteTransaction() { assert(that_.activeTransaction_ != NULL); that_.activeTransaction_ = NULL; } void Begin() { transaction_->Begin(); } virtual void Rollback() ORTHANC_OVERRIDE { transaction_->Rollback(); } virtual void Commit(int64_t fileSizeDelta /* only used in debug */) ORTHANC_OVERRIDE { transaction_->Commit(); assert(initialDiskSize_ + fileSizeDelta >= 0 && initialDiskSize_ + fileSizeDelta == static_cast<int64_t>(GetTotalCompressedSize())); } }; class SQLiteDatabaseWrapper::ReadOnlyTransaction : public SQLiteDatabaseWrapper::TransactionBase { private: SQLiteDatabaseWrapper& that_; public: ReadOnlyTransaction(SQLiteDatabaseWrapper& that, IDatabaseListener& listener) : TransactionBase(that.mutex_, that.db_, listener, *that.signalRemainingAncestor_), that_(that) { if (that_.activeTransaction_ != NULL) { throw OrthancException(ErrorCode_InternalError); } that_.activeTransaction_ = this; } virtual ~ReadOnlyTransaction() { assert(that_.activeTransaction_ != NULL); that_.activeTransaction_ = NULL; } virtual void Rollback() ORTHANC_OVERRIDE { } virtual void Commit(int64_t fileSizeDelta /* only used in debug */) ORTHANC_OVERRIDE { if (fileSizeDelta != 0) { throw OrthancException(ErrorCode_InternalError); } } }; SQLiteDatabaseWrapper::SQLiteDatabaseWrapper(const std::string& path) : activeTransaction_(NULL), signalRemainingAncestor_(NULL), version_(0) { db_.Open(path); } SQLiteDatabaseWrapper::SQLiteDatabaseWrapper() : activeTransaction_(NULL), signalRemainingAncestor_(NULL), version_(0) { db_.OpenInMemory(); } SQLiteDatabaseWrapper::~SQLiteDatabaseWrapper() { if (activeTransaction_ != NULL) { LOG(ERROR) << "A SQLite transaction is still active in the SQLiteDatabaseWrapper destructor: Expect a crash"; } } void SQLiteDatabaseWrapper::Open() { { boost::mutex::scoped_lock lock(mutex_); if (signalRemainingAncestor_ != NULL) { throw OrthancException(ErrorCode_BadSequenceOfCalls); // Cannot open twice } signalRemainingAncestor_ = dynamic_cast<SignalRemainingAncestor*>(db_.Register(new SignalRemainingAncestor)); db_.Register(new SignalFileDeleted(*this)); db_.Register(new SignalResourceDeleted(*this)); 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"); // Make "LIKE" case-sensitive in SQLite db_.Execute("PRAGMA case_sensitive_like = true;"); } VoidDatabaseListener listener; { std::unique_ptr<ITransaction> transaction(StartTransaction(TransactionType_ReadOnly, listener)); if (!db_.DoesTableExist("GlobalProperties")) { LOG(INFO) << "Creating the database"; std::string query; ServerResources::GetFileResource(query, ServerResources::PREPARE_DATABASE); db_.Execute(query); } // Check the version of the database std::string tmp; if (!transaction->LookupGlobalProperty(tmp, GlobalProperty_DatabaseSchemaVersion, true /* unused in SQLite */)) { 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) { throw OrthancException(ErrorCode_IncompatibleDatabaseVersion, "Incompatible version of the Orthanc database: " + tmp); } // New in Orthanc 1.5.1 if (version_ == 6) { if (!transaction->LookupGlobalProperty(tmp, GlobalProperty_GetTotalSizeIsFast, true /* unused in SQLite */) || tmp != "1") { LOG(INFO) << "Installing the SQLite triggers to track the size of the attachments"; std::string query; ServerResources::GetFileResource(query, ServerResources::INSTALL_TRACK_ATTACHMENTS_SIZE); db_.Execute(query); } } transaction->Commit(0); } } void SQLiteDatabaseWrapper::Close() { boost::mutex::scoped_lock lock(mutex_); // close and delete the WAL when exiting properly -> the DB is stored in a single file (no more -wal and -shm files) db_.Execute("PRAGMA JOURNAL_MODE=DELETE;"); db_.Close(); } static void ExecuteUpgradeScript(SQLite::Connection& db, ServerResources::FileResourceId script) { std::string upgrade; ServerResources::GetFileResource(upgrade, script); db.BeginTransaction(); db.Execute(upgrade); db.CommitTransaction(); } void SQLiteDatabaseWrapper::Upgrade(unsigned int targetVersion, IStorageArea& storageArea) { boost::mutex::scoped_lock lock(mutex_); 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_, ServerResources::UPGRADE_DATABASE_3_TO_4); version_ = 4; } if (version_ == 4) { LOG(WARNING) << "Upgrading database version from 4 to 5"; ExecuteUpgradeScript(db_, ServerResources::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). VoidDatabaseListener listener; { std::unique_ptr<ITransaction> transaction(StartTransaction(TransactionType_ReadWrite, listener)); ServerToolbox::ReconstructMainDicomTags(*transaction, storageArea, ResourceType_Patient); ServerToolbox::ReconstructMainDicomTags(*transaction, storageArea, ResourceType_Study); ServerToolbox::ReconstructMainDicomTags(*transaction, storageArea, ResourceType_Series); ServerToolbox::ReconstructMainDicomTags(*transaction, storageArea, ResourceType_Instance); db_.Execute("UPDATE GlobalProperties SET value=\"6\" WHERE property=" + boost::lexical_cast<std::string>(GlobalProperty_DatabaseSchemaVersion) + ";"); transaction->Commit(0); } version_ = 6; } } IDatabaseWrapper::ITransaction* SQLiteDatabaseWrapper::StartTransaction(TransactionType type, IDatabaseListener& listener) { switch (type) { case TransactionType_ReadOnly: return new ReadOnlyTransaction(*this, listener); // This is a no-op transaction in SQLite (thanks to mutex) case TransactionType_ReadWrite: { std::unique_ptr<ReadWriteTransaction> transaction; transaction.reset(new ReadWriteTransaction(*this, listener)); transaction->Begin(); return transaction.release(); } default: throw OrthancException(ErrorCode_InternalError); } } void SQLiteDatabaseWrapper::FlushToDisk() { boost::mutex::scoped_lock lock(mutex_); db_.FlushToDisk(); } int64_t SQLiteDatabaseWrapper::UnitTestsTransaction::CreateResource(const std::string& publicId, ResourceType type) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO Resources (internalId, resourceType, publicId, parentId) VALUES(NULL, ?, ?, NULL)"); s.BindInt(0, type); s.BindString(1, publicId); s.Run(); return db_.GetLastInsertRowId(); } void SQLiteDatabaseWrapper::UnitTestsTransaction::AttachChild(int64_t parent, int64_t child) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "UPDATE Resources SET parentId = ? WHERE internalId = ?"); s.BindInt64(0, parent); s.BindInt64(1, child); s.Run(); } void SQLiteDatabaseWrapper::UnitTestsTransaction::SetIdentifierTag(int64_t id, const DicomTag& tag, const std::string& value) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO DicomIdentifiers (id, tagGroup, tagElement, value) VALUES(?, ?, ?, ?)"); s.BindInt64(0, id); s.BindInt(1, tag.GetGroup()); s.BindInt(2, tag.GetElement()); s.BindString(3, value); s.Run(); } void SQLiteDatabaseWrapper::UnitTestsTransaction::SetMainDicomTag(int64_t id, const DicomTag& tag, const std::string& value) { SQLite::Statement s(db_, SQLITE_FROM_HERE, "INSERT INTO MainDicomTags (id, tagGroup, tagElement, value) VALUES(?, ?, ?, ?)"); s.BindInt64(0, id); s.BindInt(1, tag.GetGroup()); s.BindInt(2, tag.GetElement()); s.BindString(3, value); s.Run(); } int64_t SQLiteDatabaseWrapper::UnitTestsTransaction::GetTableRecordCount(const std::string& table) { /** * "Generally one cannot use SQL parameters/placeholders for * database identifiers (tables, columns, views, schemas, etc.) or * database functions (e.g., CURRENT_DATE), but instead only for * binding literal values." => To avoid any SQL injection, we * check that the "table" parameter has only alphabetic * characters. * https://stackoverflow.com/a/1274764/881731 **/ for (size_t i = 0; i < table.size(); i++) { if (!isalpha(table[i])) { throw OrthancException(ErrorCode_ParameterOutOfRange); } } // Don't use "SQLITE_FROM_HERE", otherwise "table" would be cached SQLite::Statement s(db_, "SELECT COUNT(*) FROM " + table); if (s.Step()) { int64_t c = s.ColumnInt(0); assert(!s.Step()); return c; } else { throw OrthancException(ErrorCode_InternalError); } } bool SQLiteDatabaseWrapper::UnitTestsTransaction::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; } } void SQLiteDatabaseWrapper::UnitTestsTransaction::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)); } } }