Mercurial > hg > orthanc-databases
view Framework/Plugins/IndexBackend.cpp @ 261:34e2b93a7ac1
implementing interface for revisions in attachments
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 19 Apr 2021 18:47:50 +0200 |
parents | e184dcadf163 |
children | b0c65094b299 |
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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) 2017-2021 Osimis S.A., Belgium * * This program is free software: you can redistribute it and/or * modify it under the terms of the GNU Affero 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 * Affero General Public License for more details. * * You should have received a copy of the GNU Affero General Public License * along with this program. If not, see <http://www.gnu.org/licenses/>. **/ #include "IndexBackend.h" #include "../../Resources/Orthanc/Databases/ISqlLookupFormatter.h" #include "../Common/BinaryStringValue.h" #include "../Common/Integer64Value.h" #include "../Common/Utf8StringValue.h" #include "DatabaseBackendAdapterV2.h" #include "DatabaseBackendAdapterV3.h" #include "GlobalProperties.h" #include <Compatibility.h> // For std::unique_ptr<> #include <Logging.h> #include <OrthancException.h> namespace OrthancDatabases { static std::string ConvertWildcardToLike(const std::string& query) { std::string s = query; for (size_t i = 0; i < s.size(); i++) { if (s[i] == '*') { s[i] = '%'; } else if (s[i] == '?') { s[i] = '_'; } } // TODO Escape underscores and percents return s; } int64_t IndexBackend::ReadInteger64(const DatabaseManager::StatementBase& statement, size_t field) { if (statement.IsDone()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); } const IValue& value = statement.GetResultField(field); switch (value.GetType()) { case ValueType_Integer64: return dynamic_cast<const Integer64Value&>(value).GetValue(); default: //LOG(ERROR) << value.Format(); throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } int32_t IndexBackend::ReadInteger32(const DatabaseManager::StatementBase& statement, size_t field) { if (statement.IsDone()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); } int64_t value = ReadInteger64(statement, field); if (value != static_cast<int64_t>(static_cast<int32_t>(value))) { LOG(ERROR) << "Integer overflow"; throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } else { return static_cast<int32_t>(value); } } std::string IndexBackend::ReadString(const DatabaseManager::StatementBase& statement, size_t field) { const IValue& value = statement.GetResultField(field); switch (value.GetType()) { case ValueType_BinaryString: return dynamic_cast<const BinaryStringValue&>(value).GetContent(); case ValueType_Utf8String: return dynamic_cast<const Utf8StringValue&>(value).GetContent(); default: //LOG(ERROR) << value.Format(); throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } template <typename T> void IndexBackend::ReadListOfIntegers(std::list<T>& target, DatabaseManager::CachedStatement& statement, const Dictionary& args) { statement.Execute(args); target.clear(); if (!statement.IsDone()) { if (statement.GetResultFieldsCount() != 1) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } statement.SetResultFieldType(0, ValueType_Integer64); while (!statement.IsDone()) { target.push_back(static_cast<T>(ReadInteger64(statement, 0))); statement.Next(); } } } void IndexBackend::ReadListOfStrings(std::list<std::string>& target, DatabaseManager::CachedStatement& statement, const Dictionary& args) { statement.Execute(args); target.clear(); if (!statement.IsDone()) { if (statement.GetResultFieldsCount() != 1) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } while (!statement.IsDone()) { target.push_back(ReadString(statement, 0)); statement.Next(); } } } void IndexBackend::ReadChangesInternal(IDatabaseBackendOutput& output, bool& done, DatabaseManager& manager, DatabaseManager::CachedStatement& statement, const Dictionary& args, uint32_t maxResults) { statement.Execute(args); uint32_t count = 0; while (count < maxResults && !statement.IsDone()) { output.AnswerChange( ReadInteger64(statement, 0), ReadInteger32(statement, 1), static_cast<OrthancPluginResourceType>(ReadInteger32(statement, 3)), GetPublicId(manager, ReadInteger64(statement, 2)), ReadString(statement, 4)); statement.Next(); count++; } done = (count < maxResults || statement.IsDone()); } void IndexBackend::ReadExportedResourcesInternal(IDatabaseBackendOutput& output, bool& done, DatabaseManager::CachedStatement& statement, const Dictionary& args, uint32_t maxResults) { statement.Execute(args); uint32_t count = 0; while (count < maxResults && !statement.IsDone()) { int64_t seq = ReadInteger64(statement, 0); OrthancPluginResourceType resourceType = static_cast<OrthancPluginResourceType>(ReadInteger32(statement, 1)); std::string publicId = ReadString(statement, 2); output.AnswerExportedResource(seq, resourceType, publicId, ReadString(statement, 3), // modality ReadString(statement, 8), // date ReadString(statement, 4), // patient ID ReadString(statement, 5), // study instance UID ReadString(statement, 6), // series instance UID ReadString(statement, 7)); // sop instance UID statement.Next(); count++; } done = (count < maxResults || statement.IsDone()); } void IndexBackend::ClearDeletedFiles(DatabaseManager& manager) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM DeletedFiles"); statement.Execute(); } void IndexBackend::ClearDeletedResources(DatabaseManager& manager) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM DeletedResources"); statement.Execute(); } void IndexBackend::SignalDeletedFiles(IDatabaseBackendOutput& output, DatabaseManager& manager) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM DeletedFiles"); statement.SetReadOnly(true); statement.Execute(); while (!statement.IsDone()) { std::string a = ReadString(statement, 0); std::string b = ReadString(statement, 5); std::string c = ReadString(statement, 6); output.SignalDeletedAttachment(a.c_str(), ReadInteger32(statement, 1), ReadInteger64(statement, 3), b.c_str(), ReadInteger32(statement, 4), ReadInteger64(statement, 2), c.c_str()); statement.Next(); } } void IndexBackend::SignalDeletedResources(IDatabaseBackendOutput& output, DatabaseManager& manager) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM DeletedResources"); statement.SetReadOnly(true); statement.Execute(); while (!statement.IsDone()) { output.SignalDeletedResource( ReadString(statement, 1), static_cast<OrthancPluginResourceType>(ReadInteger32(statement, 0))); statement.Next(); } } IndexBackend::IndexBackend(OrthancPluginContext* context) : context_(context) { } void IndexBackend::SetOutputFactory(IDatabaseBackendOutput::IFactory* factory) { boost::unique_lock<boost::shared_mutex> lock(outputFactoryMutex_); if (factory == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } else if (outputFactory_.get() != NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } else { outputFactory_.reset(factory); } } IDatabaseBackendOutput* IndexBackend::CreateOutput() { boost::shared_lock<boost::shared_mutex> lock(outputFactoryMutex_); if (outputFactory_.get() == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_BadSequenceOfCalls); } else { return outputFactory_->CreateOutput(); } } void IndexBackend::AddAttachment(DatabaseManager& manager, int64_t id, const OrthancPluginAttachment& attachment, int64_t revision) { // TODO - REVISIONS DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT INTO AttachedFiles VALUES(${id}, ${type}, ${uuid}, " "${compressed}, ${uncompressed}, ${compression}, ${hash}, ${hash-compressed})"); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); statement.SetParameterType("uuid", ValueType_Utf8String); statement.SetParameterType("compressed", ValueType_Integer64); statement.SetParameterType("uncompressed", ValueType_Integer64); statement.SetParameterType("compression", ValueType_Integer64); statement.SetParameterType("hash", ValueType_Utf8String); statement.SetParameterType("hash-compressed", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", attachment.contentType); args.SetUtf8Value("uuid", attachment.uuid); args.SetIntegerValue("compressed", attachment.compressedSize); args.SetIntegerValue("uncompressed", attachment.uncompressedSize); args.SetIntegerValue("compression", attachment.compressionType); args.SetUtf8Value("hash", attachment.uncompressedHash); args.SetUtf8Value("hash-compressed", attachment.compressedHash); statement.Execute(args); } void IndexBackend::AttachChild(DatabaseManager& manager, int64_t parent, int64_t child) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "UPDATE Resources SET parentId = ${parent} WHERE internalId = ${child}"); statement.SetParameterType("parent", ValueType_Integer64); statement.SetParameterType("child", ValueType_Integer64); Dictionary args; args.SetIntegerValue("parent", parent); args.SetIntegerValue("child", child); statement.Execute(args); } void IndexBackend::ClearChanges(DatabaseManager& manager) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM Changes"); statement.Execute(); } void IndexBackend::ClearExportedResources(DatabaseManager& manager) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM ExportedResources"); statement.Execute(); } void IndexBackend::DeleteAttachment(IDatabaseBackendOutput& output, DatabaseManager& manager, int64_t id, int32_t attachment) { ClearDeletedFiles(manager); { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM AttachedFiles WHERE id=${id} AND fileType=${type}"); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", static_cast<int>(attachment)); statement.Execute(args); } SignalDeletedFiles(output, manager); } void IndexBackend::DeleteMetadata(DatabaseManager& manager, int64_t id, int32_t metadataType) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM Metadata WHERE id=${id} and type=${type}"); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", static_cast<int>(metadataType)); statement.Execute(args); } void IndexBackend::DeleteResource(IDatabaseBackendOutput& output, DatabaseManager& manager, int64_t id) { assert(manager.GetDialect() != Dialect_MySQL); ClearDeletedFiles(manager); ClearDeletedResources(manager); { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM RemainingAncestor"); statement.Execute(); } { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM Resources WHERE internalId=${id}"); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); statement.Execute(args); } { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM RemainingAncestor"); statement.Execute(); if (!statement.IsDone()) { output.SignalRemainingAncestor( ReadString(statement, 1), static_cast<OrthancPluginResourceType>(ReadInteger32(statement, 0))); // There is at most 1 remaining ancestor assert((statement.Next(), statement.IsDone())); } } SignalDeletedFiles(output, manager); SignalDeletedResources(output, manager); } void IndexBackend::GetAllInternalIds(std::list<int64_t>& target, DatabaseManager& manager, OrthancPluginResourceType resourceType) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT internalId FROM Resources WHERE resourceType=${type}"); statement.SetReadOnly(true); statement.SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("type", static_cast<int>(resourceType)); ReadListOfIntegers<int64_t>(target, statement, args); } void IndexBackend::GetAllPublicIds(std::list<std::string>& target, DatabaseManager& manager, OrthancPluginResourceType resourceType) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT publicId FROM Resources WHERE resourceType=${type}"); statement.SetReadOnly(true); statement.SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("type", static_cast<int>(resourceType)); ReadListOfStrings(target, statement, args); } void IndexBackend::GetAllPublicIds(std::list<std::string>& target, DatabaseManager& manager, OrthancPluginResourceType resourceType, uint64_t since, uint64_t limit) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT publicId FROM (SELECT publicId FROM Resources " "WHERE resourceType=${type}) AS tmp " "ORDER BY tmp.publicId LIMIT ${limit} OFFSET ${since}"); statement.SetReadOnly(true); statement.SetParameterType("type", ValueType_Integer64); statement.SetParameterType("limit", ValueType_Integer64); statement.SetParameterType("since", ValueType_Integer64); Dictionary args; args.SetIntegerValue("type", static_cast<int>(resourceType)); args.SetIntegerValue("limit", limit); args.SetIntegerValue("since", since); ReadListOfStrings(target, statement, args); } /* Use GetOutput().AnswerChange() */ void IndexBackend::GetChanges(IDatabaseBackendOutput& output, bool& done /*out*/, DatabaseManager& manager, int64_t since, uint32_t maxResults) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM Changes WHERE seq>${since} ORDER BY seq LIMIT ${limit}"); statement.SetReadOnly(true); statement.SetParameterType("limit", ValueType_Integer64); statement.SetParameterType("since", ValueType_Integer64); Dictionary args; args.SetIntegerValue("limit", maxResults + 1); args.SetIntegerValue("since", since); ReadChangesInternal(output, done, manager, statement, args, maxResults); } void IndexBackend::GetChildrenInternalId(std::list<int64_t>& target /*out*/, DatabaseManager& manager, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT a.internalId FROM Resources AS a, Resources AS b " "WHERE a.parentId = b.internalId AND b.internalId = ${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); ReadListOfIntegers<int64_t>(target, statement, args); } void IndexBackend::GetChildrenPublicId(std::list<std::string>& target /*out*/, DatabaseManager& manager, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT a.publicId FROM Resources AS a, Resources AS b " "WHERE a.parentId = b.internalId AND b.internalId = ${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); ReadListOfStrings(target, statement, args); } /* Use GetOutput().AnswerExportedResource() */ void IndexBackend::GetExportedResources(IDatabaseBackendOutput& output, bool& done /*out*/, DatabaseManager& manager, int64_t since, uint32_t maxResults) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM ExportedResources WHERE seq>${since} ORDER BY seq LIMIT ${limit}"); statement.SetReadOnly(true); statement.SetParameterType("limit", ValueType_Integer64); statement.SetParameterType("since", ValueType_Integer64); Dictionary args; args.SetIntegerValue("limit", maxResults + 1); args.SetIntegerValue("since", since); ReadExportedResourcesInternal(output, done, statement, args, maxResults); } /* Use GetOutput().AnswerChange() */ void IndexBackend::GetLastChange(IDatabaseBackendOutput& output, DatabaseManager& manager) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM Changes ORDER BY seq DESC LIMIT 1"); statement.SetReadOnly(true); Dictionary args; bool done; // Ignored ReadChangesInternal(output, done, manager, statement, args, 1); } /* Use GetOutput().AnswerExportedResource() */ void IndexBackend::GetLastExportedResource(IDatabaseBackendOutput& output, DatabaseManager& manager) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM ExportedResources ORDER BY seq DESC LIMIT 1"); statement.SetReadOnly(true); Dictionary args; bool done; // Ignored ReadExportedResourcesInternal(output, done, statement, args, 1); } /* Use GetOutput().AnswerDicomTag() */ void IndexBackend::GetMainDicomTags(IDatabaseBackendOutput& output, DatabaseManager& manager, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM MainDicomTags WHERE id=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); statement.Execute(args); while (!statement.IsDone()) { output.AnswerDicomTag(static_cast<uint16_t>(ReadInteger64(statement, 1)), static_cast<uint16_t>(ReadInteger64(statement, 2)), ReadString(statement, 3)); statement.Next(); } } std::string IndexBackend::GetPublicId(DatabaseManager& manager, int64_t resourceId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT publicId FROM Resources WHERE internalId=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", resourceId); statement.Execute(args); if (statement.IsDone()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); } else { return ReadString(statement, 0); } } uint64_t IndexBackend::GetResourcesCount(DatabaseManager& manager, OrthancPluginResourceType resourceType) { std::unique_ptr<DatabaseManager::CachedStatement> statement; switch (manager.GetDialect()) { case Dialect_MySQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT CAST(COUNT(*) AS UNSIGNED INT) FROM Resources WHERE resourceType=${type}")); break; case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT CAST(COUNT(*) AS BIGINT) FROM Resources WHERE resourceType=${type}")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT COUNT(*) FROM Resources WHERE resourceType=${type}")); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } statement->SetReadOnly(true); statement->SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("type", resourceType); statement->Execute(args); return static_cast<uint64_t>(ReadInteger64(*statement, 0)); } OrthancPluginResourceType IndexBackend::GetResourceType(DatabaseManager& manager, int64_t resourceId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT resourceType FROM Resources WHERE internalId=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", resourceId); statement.Execute(args); if (statement.IsDone()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); } else { return static_cast<OrthancPluginResourceType>(ReadInteger32(statement, 0)); } } uint64_t IndexBackend::GetTotalCompressedSize(DatabaseManager& manager) { std::unique_ptr<DatabaseManager::CachedStatement> statement; // NB: "COALESCE" is used to replace "NULL" by "0" if the number of rows is empty switch (manager.GetDialect()) { case Dialect_MySQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT CAST(COALESCE(SUM(compressedSize), 0) AS UNSIGNED INTEGER) FROM AttachedFiles")); break; case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT CAST(COALESCE(SUM(compressedSize), 0) AS BIGINT) FROM AttachedFiles")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT COALESCE(SUM(compressedSize), 0) FROM AttachedFiles")); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } statement->SetReadOnly(true); statement->Execute(); return static_cast<uint64_t>(ReadInteger64(*statement, 0)); } uint64_t IndexBackend::GetTotalUncompressedSize(DatabaseManager& manager) { std::unique_ptr<DatabaseManager::CachedStatement> statement; // NB: "COALESCE" is used to replace "NULL" by "0" if the number of rows is empty switch (manager.GetDialect()) { case Dialect_MySQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT CAST(COALESCE(SUM(uncompressedSize), 0) AS UNSIGNED INTEGER) FROM AttachedFiles")); break; case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT CAST(COALESCE(SUM(uncompressedSize), 0) AS BIGINT) FROM AttachedFiles")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT COALESCE(SUM(uncompressedSize), 0) FROM AttachedFiles")); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } statement->SetReadOnly(true); statement->Execute(); return static_cast<uint64_t>(ReadInteger64(*statement, 0)); } bool IndexBackend::IsExistingResource(DatabaseManager& manager, int64_t internalId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM Resources WHERE internalId=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", internalId); statement.Execute(args); return !statement.IsDone(); } bool IndexBackend::IsProtectedPatient(DatabaseManager& manager, int64_t internalId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM PatientRecyclingOrder WHERE patientId = ${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", internalId); statement.Execute(args); return statement.IsDone(); } void IndexBackend::ListAvailableMetadata(std::list<int32_t>& target /*out*/, DatabaseManager& manager, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT type FROM Metadata WHERE id=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); ReadListOfIntegers<int32_t>(target, statement, args); } void IndexBackend::ListAvailableAttachments(std::list<int32_t>& target /*out*/, DatabaseManager& manager, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT fileType FROM AttachedFiles WHERE id=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); ReadListOfIntegers<int32_t>(target, statement, args); } void IndexBackend::LogChange(DatabaseManager& manager, int32_t changeType, int64_t resourceId, OrthancPluginResourceType resourceType, const char* date) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT INTO Changes VALUES(${}, ${changeType}, ${id}, ${resourceType}, ${date})"); statement.SetParameterType("changeType", ValueType_Integer64); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("resourceType", ValueType_Integer64); statement.SetParameterType("date", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("changeType", changeType); args.SetIntegerValue("id", resourceId); args.SetIntegerValue("resourceType", resourceType); args.SetUtf8Value("date", date); statement.Execute(args); } void IndexBackend::LogExportedResource(DatabaseManager& manager, const OrthancPluginExportedResource& resource) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT INTO ExportedResources VALUES(${}, ${type}, ${publicId}, " "${modality}, ${patient}, ${study}, ${series}, ${instance}, ${date})"); statement.SetParameterType("type", ValueType_Integer64); statement.SetParameterType("publicId", ValueType_Utf8String); statement.SetParameterType("modality", ValueType_Utf8String); statement.SetParameterType("patient", ValueType_Utf8String); statement.SetParameterType("study", ValueType_Utf8String); statement.SetParameterType("series", ValueType_Utf8String); statement.SetParameterType("instance", ValueType_Utf8String); statement.SetParameterType("date", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("type", resource.resourceType); args.SetUtf8Value("publicId", resource.publicId); args.SetUtf8Value("modality", resource.modality); args.SetUtf8Value("patient", resource.patientId); args.SetUtf8Value("study", resource.studyInstanceUid); args.SetUtf8Value("series", resource.seriesInstanceUid); args.SetUtf8Value("instance", resource.sopInstanceUid); args.SetUtf8Value("date", resource.date); statement.Execute(args); } /* Use GetOutput().AnswerAttachment() */ bool IndexBackend::LookupAttachment(IDatabaseBackendOutput& output, int64_t& revision /*out*/, DatabaseManager& manager, int64_t id, int32_t contentType) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT uuid, uncompressedSize, compressionType, compressedSize, " "uncompressedHash, compressedHash FROM AttachedFiles WHERE id=${id} AND fileType=${type}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", static_cast<int>(contentType)); statement.Execute(args); if (statement.IsDone()) { return false; } else { output.AnswerAttachment(ReadString(statement, 0), contentType, ReadInteger64(statement, 1), ReadString(statement, 4), ReadInteger32(statement, 2), ReadInteger64(statement, 3), ReadString(statement, 5)); revision = 0; // TODO - REVISIONS return true; } } static bool ReadGlobalProperty(std::string& target, DatabaseManager::CachedStatement& statement, const Dictionary& args) { statement.Execute(args); statement.SetResultFieldType(0, ValueType_Utf8String); if (statement.IsDone()) { return false; } else { ValueType type = statement.GetResultField(0).GetType(); if (type == ValueType_Null) { return false; } else if (type != ValueType_Utf8String) { throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); } else { target = dynamic_cast<const Utf8StringValue&>(statement.GetResultField(0)).GetContent(); return true; } } } bool IndexBackend::LookupGlobalProperty(std::string& target /*out*/, DatabaseManager& manager, const char* serverIdentifier, int32_t property) { if (serverIdentifier == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } else { if (strlen(serverIdentifier) == 0) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT value FROM GlobalProperties WHERE property=${property}"); statement.SetReadOnly(true); statement.SetParameterType("property", ValueType_Integer64); Dictionary args; args.SetIntegerValue("property", property); return ReadGlobalProperty(target, statement, args); } else { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT value FROM ServerProperties WHERE server=${server} AND property=${property}"); statement.SetReadOnly(true); statement.SetParameterType("server", ValueType_Utf8String); statement.SetParameterType("property", ValueType_Integer64); Dictionary args; args.SetUtf8Value("server", serverIdentifier); args.SetIntegerValue("property", property); return ReadGlobalProperty(target, statement, args); } } } void IndexBackend::LookupIdentifier(std::list<int64_t>& target /*out*/, DatabaseManager& manager, OrthancPluginResourceType resourceType, uint16_t group, uint16_t element, OrthancPluginIdentifierConstraint constraint, const char* value) { std::unique_ptr<DatabaseManager::CachedStatement> statement; std::string header = "SELECT d.id FROM DicomIdentifiers AS d, Resources AS r WHERE " "d.id = r.internalId AND r.resourceType=${type} AND d.tagGroup=${group} " "AND d.tagElement=${element} AND "; switch (constraint) { case OrthancPluginIdentifierConstraint_Equal: header += "d.value = ${value}"; statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, header.c_str())); break; case OrthancPluginIdentifierConstraint_SmallerOrEqual: header += "d.value <= ${value}"; statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, header.c_str())); break; case OrthancPluginIdentifierConstraint_GreaterOrEqual: header += "d.value >= ${value}"; statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, header.c_str())); break; case OrthancPluginIdentifierConstraint_Wildcard: header += "d.value LIKE ${value}"; statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, header.c_str())); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); } statement->SetReadOnly(true); statement->SetParameterType("type", ValueType_Integer64); statement->SetParameterType("group", ValueType_Integer64); statement->SetParameterType("element", ValueType_Integer64); statement->SetParameterType("value", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("type", resourceType); args.SetIntegerValue("group", group); args.SetIntegerValue("element", element); if (constraint == OrthancPluginIdentifierConstraint_Wildcard) { args.SetUtf8Value("value", ConvertWildcardToLike(value)); } else { args.SetUtf8Value("value", value); } statement->Execute(args); target.clear(); while (!statement->IsDone()) { target.push_back(ReadInteger64(*statement, 0)); statement->Next(); } } void IndexBackend::LookupIdentifierRange(std::list<int64_t>& target /*out*/, DatabaseManager& manager, OrthancPluginResourceType resourceType, uint16_t group, uint16_t element, const char* start, const char* end) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT d.id FROM DicomIdentifiers AS d, Resources AS r WHERE " "d.id = r.internalId AND r.resourceType=${type} AND d.tagGroup=${group} " "AND d.tagElement=${element} AND d.value>=${start} AND d.value<=${end}"); statement.SetReadOnly(true); statement.SetParameterType("type", ValueType_Integer64); statement.SetParameterType("group", ValueType_Integer64); statement.SetParameterType("element", ValueType_Integer64); statement.SetParameterType("start", ValueType_Utf8String); statement.SetParameterType("end", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("type", resourceType); args.SetIntegerValue("group", group); args.SetIntegerValue("element", element); args.SetUtf8Value("start", start); args.SetUtf8Value("end", end); statement.Execute(args); target.clear(); while (!statement.IsDone()) { target.push_back(ReadInteger64(statement, 0)); statement.Next(); } } bool IndexBackend::LookupMetadata(std::string& target /*out*/, int64_t& revision /*out*/, DatabaseManager& manager, int64_t id, int32_t metadataType) { std::unique_ptr<DatabaseManager::CachedStatement> statement; switch (manager.GetDialect()) { case Dialect_MySQL: case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT value FROM Metadata WHERE id=${id} and type=${type}")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT value, revision FROM Metadata WHERE id=${id} and type=${type}")); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } statement->SetReadOnly(true); statement->SetParameterType("id", ValueType_Integer64); statement->SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", metadataType); statement->Execute(args); if (statement->IsDone()) { return false; } else { target = ReadString(*statement, 0); if (manager.GetDialect() == Dialect_SQLite) { revision = ReadInteger64(*statement, 1); } else { revision = 0; // TODO - REVISIONS } return true; } } bool IndexBackend::LookupParent(int64_t& parentId /*out*/, DatabaseManager& manager, int64_t resourceId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT parentId FROM Resources WHERE internalId=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", resourceId); statement.Execute(args); if (statement.IsDone() || statement.GetResultField(0).GetType() == ValueType_Null) { return false; } else { parentId = ReadInteger64(statement, 0); return true; } } bool IndexBackend::LookupResource(int64_t& id /*out*/, OrthancPluginResourceType& type /*out*/, DatabaseManager& manager, const char* publicId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT internalId, resourceType FROM Resources WHERE publicId=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Utf8String); Dictionary args; args.SetUtf8Value("id", publicId); statement.Execute(args); if (statement.IsDone()) { return false; } else { id = ReadInteger64(statement, 0); type = static_cast<OrthancPluginResourceType>(ReadInteger32(statement, 1)); return true; } } bool IndexBackend::SelectPatientToRecycle(int64_t& internalId /*out*/, DatabaseManager& manager) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT patientId FROM PatientRecyclingOrder ORDER BY seq ASC LIMIT 1"); statement.SetReadOnly(true); statement.Execute(); if (statement.IsDone()) { return false; } else { internalId = ReadInteger64(statement, 0); return true; } } bool IndexBackend::SelectPatientToRecycle(int64_t& internalId /*out*/, DatabaseManager& manager, int64_t patientIdToAvoid) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT patientId FROM PatientRecyclingOrder " "WHERE patientId != ${id} ORDER BY seq ASC LIMIT 1"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", patientIdToAvoid); statement.Execute(args); if (statement.IsDone()) { return false; } else { internalId = ReadInteger64(statement, 0); return true; } } static void RunSetGlobalPropertyStatement(DatabaseManager::CachedStatement& statement, bool hasServer, bool hasValue, const char* serverIdentifier, int32_t property, const char* utf8) { Dictionary args; statement.SetParameterType("property", ValueType_Integer64); args.SetIntegerValue("property", static_cast<int>(property)); if (hasValue) { assert(utf8 != NULL); statement.SetParameterType("value", ValueType_Utf8String); args.SetUtf8Value("value", utf8); } else { assert(utf8 == NULL); } if (hasServer) { assert(serverIdentifier != NULL && strlen(serverIdentifier) > 0); statement.SetParameterType("server", ValueType_Utf8String); args.SetUtf8Value("server", serverIdentifier); } else { assert(serverIdentifier == NULL); } statement.Execute(args); } void IndexBackend::SetGlobalProperty(DatabaseManager& manager, const char* serverIdentifier, int32_t property, const char* utf8) { if (serverIdentifier == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } else if (manager.GetDialect() == Dialect_SQLite) { bool hasServer = (strlen(serverIdentifier) != 0); if (hasServer) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT OR REPLACE INTO ServerProperties VALUES (${server}, ${property}, ${value})"); RunSetGlobalPropertyStatement(statement, true, true, serverIdentifier, property, utf8); } else { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT OR REPLACE INTO GlobalProperties VALUES (${property}, ${value})"); RunSetGlobalPropertyStatement(statement, false, true, NULL, property, utf8); } } else { bool hasServer = (strlen(serverIdentifier) != 0); if (hasServer) { { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM ServerProperties WHERE server=${server} AND property=${property}"); RunSetGlobalPropertyStatement(statement, true, false, serverIdentifier, property, NULL); } { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT INTO ServerProperties VALUES (${server}, ${property}, ${value})"); RunSetGlobalPropertyStatement(statement, true, true, serverIdentifier, property, utf8); } } else { { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM GlobalProperties WHERE property=${property}"); RunSetGlobalPropertyStatement(statement, false, false, NULL, property, NULL); } { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT INTO GlobalProperties VALUES (${property}, ${value})"); RunSetGlobalPropertyStatement(statement, false, true, NULL, property, utf8); } } } } static void ExecuteSetTag(DatabaseManager::CachedStatement& statement, int64_t id, uint16_t group, uint16_t element, const char* value) { statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("group", ValueType_Integer64); statement.SetParameterType("element", ValueType_Integer64); statement.SetParameterType("value", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("group", group); args.SetIntegerValue("element", element); args.SetUtf8Value("value", value); statement.Execute(args); } void IndexBackend::SetMainDicomTag(DatabaseManager& manager, int64_t id, uint16_t group, uint16_t element, const char* value) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT INTO MainDicomTags VALUES(${id}, ${group}, ${element}, ${value})"); ExecuteSetTag(statement, id, group, element, value); } void IndexBackend::SetIdentifierTag(DatabaseManager& manager, int64_t id, uint16_t group, uint16_t element, const char* value) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT INTO DicomIdentifiers VALUES(${id}, ${group}, ${element}, ${value})"); ExecuteSetTag(statement, id, group, element, value); } void IndexBackend::SetMetadata(DatabaseManager& manager, int64_t id, int32_t metadataType, const char* value, int64_t revision) { if (manager.GetDialect() == Dialect_SQLite) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT OR REPLACE INTO Metadata VALUES (${id}, ${type}, ${value}, ${revision})"); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); statement.SetParameterType("value", ValueType_Utf8String); statement.SetParameterType("revision", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", metadataType); args.SetUtf8Value("value", value); args.SetIntegerValue("revision", revision); statement.Execute(args); } else { // TODO - REVISIONS { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM Metadata WHERE id=${id} AND type=${type}"); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", metadataType); statement.Execute(args); } { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT INTO Metadata VALUES (${id}, ${type}, ${value})"); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); statement.SetParameterType("value", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", metadataType); args.SetUtf8Value("value", value); statement.Execute(args); } } } void IndexBackend::SetProtectedPatient(DatabaseManager& manager, int64_t internalId, bool isProtected) { if (isProtected) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM PatientRecyclingOrder WHERE patientId=${id}"); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", internalId); statement.Execute(args); } else if (IsProtectedPatient(manager, internalId)) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT INTO PatientRecyclingOrder VALUES(${}, ${id})"); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", internalId); statement.Execute(args); } else { // Nothing to do: The patient is already unprotected } } uint32_t IndexBackend::GetDatabaseVersion(DatabaseManager& manager) { // Create a read-only, explicit transaction to read the database // version (this was a read-write, implicit transaction in // PostgreSQL plugin <= 3.3 and MySQL plugin <= 3.0) DatabaseManager::Transaction transaction(manager, TransactionType_ReadOnly); std::string version = "unknown"; if (LookupGlobalProperty(version, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion)) { try { return boost::lexical_cast<unsigned int>(version); } catch (boost::bad_lexical_cast&) { } } LOG(ERROR) << "The database is corrupted. Drop it manually for Orthanc to recreate it"; throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); } /** * Upgrade the database to the specified version of the database * schema. The upgrade script is allowed to make calls to * OrthancPluginReconstructMainDicomTags(). **/ void IndexBackend::UpgradeDatabase(DatabaseManager& manager, uint32_t targetVersion, OrthancPluginStorageArea* storageArea) { LOG(ERROR) << "Upgrading database is not implemented by this plugin"; throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } void IndexBackend::ClearMainDicomTags(DatabaseManager& manager, int64_t internalId) { { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM MainDicomTags WHERE id=${id}"); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", internalId); statement.Execute(args); } { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM DicomIdentifiers WHERE id=${id}"); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", internalId); statement.Execute(args); } } // For unit testing only! uint64_t IndexBackend::GetAllResourcesCount(DatabaseManager& manager) { std::unique_ptr<DatabaseManager::CachedStatement> statement; switch (manager.GetDialect()) { case Dialect_MySQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT CAST(COUNT(*) AS UNSIGNED INT) FROM Resources")); break; case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT CAST(COUNT(*) AS BIGINT) FROM Resources")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT COUNT(*) FROM Resources")); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } statement->SetReadOnly(true); statement->Execute(); return static_cast<uint64_t>(ReadInteger64(*statement, 0)); } // For unit testing only! uint64_t IndexBackend::GetUnprotectedPatientsCount(DatabaseManager& manager) { std::unique_ptr<DatabaseManager::CachedStatement> statement; switch (manager.GetDialect()) { case Dialect_MySQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT CAST(COUNT(*) AS UNSIGNED INT) FROM PatientRecyclingOrder")); break; case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT CAST(COUNT(*) AS BIGINT) FROM PatientRecyclingOrder")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager, "SELECT COUNT(*) FROM PatientRecyclingOrder")); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } statement->SetReadOnly(true); statement->Execute(); return static_cast<uint64_t>(ReadInteger64(*statement, 0)); } // For unit testing only! bool IndexBackend::GetParentPublicId(std::string& target, DatabaseManager& manager, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT a.publicId FROM Resources AS a, Resources AS b " "WHERE a.internalId = b.parentId AND b.internalId = ${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); statement.Execute(args); if (statement.IsDone()) { return false; } else { target = ReadString(statement, 0); return true; } } // For unit tests only! void IndexBackend::GetChildren(std::list<std::string>& childrenPublicIds, DatabaseManager& manager, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT publicId FROM Resources WHERE parentId=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); ReadListOfStrings(childrenPublicIds, statement, args); } #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1 class IndexBackend::LookupFormatter : public Orthanc::ISqlLookupFormatter { private: Dialect dialect_; size_t count_; Dictionary dictionary_; static std::string FormatParameter(size_t index) { return "p" + boost::lexical_cast<std::string>(index); } public: LookupFormatter(Dialect dialect) : dialect_(dialect), count_(0) { } virtual std::string GenerateParameter(const std::string& value) { const std::string key = FormatParameter(count_); count_ ++; dictionary_.SetUtf8Value(key, value); return "${" + key + "}"; } virtual std::string FormatResourceType(Orthanc::ResourceType level) { return boost::lexical_cast<std::string>(Orthanc::Plugins::Convert(level)); } virtual std::string FormatWildcardEscape() { switch (dialect_) { case Dialect_SQLite: case Dialect_PostgreSQL: return "ESCAPE '\\'"; case Dialect_MySQL: return "ESCAPE '\\\\'"; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } } void PrepareStatement(DatabaseManager::StandaloneStatement& statement) const { statement.SetReadOnly(true); for (size_t i = 0; i < count_; i++) { statement.SetParameterType(FormatParameter(i), ValueType_Utf8String); } } const Dictionary& GetDictionary() const { return dictionary_; } }; #endif #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1 // New primitive since Orthanc 1.5.2 void IndexBackend::LookupResources(IDatabaseBackendOutput& output, DatabaseManager& manager, const std::vector<Orthanc::DatabaseConstraint>& lookup, OrthancPluginResourceType queryLevel, uint32_t limit, bool requestSomeInstance) { LookupFormatter formatter(manager.GetDialect()); std::string sql; Orthanc::ISqlLookupFormatter::Apply(sql, formatter, lookup, Orthanc::Plugins::Convert(queryLevel), limit); if (requestSomeInstance) { // Composite query to find some instance if requested switch (queryLevel) { case OrthancPluginResourceType_Patient: sql = ("SELECT patients.publicId, MIN(instances.publicId) FROM (" + sql + ") patients " "INNER JOIN Resources studies ON studies.parentId = patients.internalId " "INNER JOIN Resources series ON series.parentId = studies.internalId " "INNER JOIN Resources instances ON instances.parentId = series.internalId " "GROUP BY patients.publicId"); break; case OrthancPluginResourceType_Study: sql = ("SELECT studies.publicId, MIN(instances.publicId) FROM (" + sql + ") studies " "INNER JOIN Resources series ON series.parentId = studies.internalId " "INNER JOIN Resources instances ON instances.parentId = series.internalId " "GROUP BY studies.publicId"); break; case OrthancPluginResourceType_Series: sql = ("SELECT series.publicId, MIN(instances.publicId) FROM (" + sql + ") series " "INNER JOIN Resources instances ON instances.parentId = series.internalId " "GROUP BY series.publicId"); break; case OrthancPluginResourceType_Instance: sql = ("SELECT instances.publicId, instances.publicId FROM (" + sql + ") instances"); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } } DatabaseManager::StandaloneStatement statement(manager, sql); formatter.PrepareStatement(statement); statement.Execute(formatter.GetDictionary()); while (!statement.IsDone()) { if (requestSomeInstance) { output.AnswerMatchingResource(ReadString(statement, 0), ReadString(statement, 1)); } else { output.AnswerMatchingResource(ReadString(statement, 0)); } statement.Next(); } } #endif #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1 static void ExecuteSetResourcesContentTags( DatabaseManager& manager, const std::string& table, const std::string& variablePrefix, uint32_t count, const OrthancPluginResourcesContentTags* tags) { std::string sql; Dictionary args; for (uint32_t i = 0; i < count; i++) { std::string name = variablePrefix + boost::lexical_cast<std::string>(i); args.SetUtf8Value(name, tags[i].value); std::string insert = ("(" + boost::lexical_cast<std::string>(tags[i].resource) + ", " + boost::lexical_cast<std::string>(tags[i].group) + ", " + boost::lexical_cast<std::string>(tags[i].element) + ", " + "${" + name + "})"); if (sql.empty()) { sql = "INSERT INTO " + table + " VALUES " + insert; } else { sql += ", " + insert; } } if (!sql.empty()) { DatabaseManager::StandaloneStatement statement(manager, sql); for (uint32_t i = 0; i < count; i++) { statement.SetParameterType(variablePrefix + boost::lexical_cast<std::string>(i), ValueType_Utf8String); } statement.Execute(args); } } #endif #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1 static void ExecuteSetResourcesContentMetadata( DatabaseManager& manager, uint32_t count, const OrthancPluginResourcesContentMetadata* metadata) { std::string sqlRemove; // To overwrite std::string sqlInsert; Dictionary args; for (uint32_t i = 0; i < count; i++) { std::string name = "m" + boost::lexical_cast<std::string>(i); args.SetUtf8Value(name, metadata[i].value); std::string revisionSuffix; if (manager.GetDialect() == Dialect_SQLite) { revisionSuffix = ", 0"; // TODO - REVISIONS } std::string insert = ("(" + boost::lexical_cast<std::string>(metadata[i].resource) + ", " + boost::lexical_cast<std::string>(metadata[i].metadata) + ", " + "${" + name + "}" + revisionSuffix + ")"); std::string remove = ("(id=" + boost::lexical_cast<std::string>(metadata[i].resource) + " AND type=" + boost::lexical_cast<std::string>(metadata[i].metadata) + ")"); if (sqlInsert.empty()) { sqlInsert = "INSERT INTO Metadata VALUES " + insert; } else { sqlInsert += ", " + insert; } if (sqlRemove.empty()) { sqlRemove = "DELETE FROM Metadata WHERE " + remove; } else { sqlRemove += " OR " + remove; } } if (!sqlRemove.empty()) { DatabaseManager::StandaloneStatement statement(manager, sqlRemove); statement.Execute(); } if (!sqlInsert.empty()) { DatabaseManager::StandaloneStatement statement(manager, sqlInsert); for (uint32_t i = 0; i < count; i++) { statement.SetParameterType("m" + boost::lexical_cast<std::string>(i), ValueType_Utf8String); } statement.Execute(args); } } #endif #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1 // New primitive since Orthanc 1.5.2 void IndexBackend::SetResourcesContent( DatabaseManager& manager, uint32_t countIdentifierTags, const OrthancPluginResourcesContentTags* identifierTags, uint32_t countMainDicomTags, const OrthancPluginResourcesContentTags* mainDicomTags, uint32_t countMetadata, const OrthancPluginResourcesContentMetadata* metadata) { /** * TODO - PostgreSQL doesn't allow multiple commands in a prepared * statement, so we execute 3 separate commands (for identifiers, * main tags and metadata). Maybe MySQL does not suffer from the * same limitation, to check. **/ ExecuteSetResourcesContentTags(manager, "DicomIdentifiers", "i", countIdentifierTags, identifierTags); ExecuteSetResourcesContentTags(manager, "MainDicomTags", "t", countMainDicomTags, mainDicomTags); ExecuteSetResourcesContentMetadata(manager, countMetadata, metadata); } #endif // New primitive since Orthanc 1.5.2 void IndexBackend::GetChildrenMetadata(std::list<std::string>& target, DatabaseManager& manager, int64_t resourceId, int32_t metadata) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT value FROM Metadata WHERE type=${metadata} AND " "id IN (SELECT internalId FROM Resources WHERE parentId=${id})"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("metadata", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", static_cast<int>(resourceId)); args.SetIntegerValue("metadata", static_cast<int>(metadata)); ReadListOfStrings(target, statement, args); } // New primitive since Orthanc 1.5.2 void IndexBackend::TagMostRecentPatient(DatabaseManager& manager, int64_t patient) { int64_t seq; { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT * FROM PatientRecyclingOrder WHERE seq >= " "(SELECT seq FROM PatientRecyclingOrder WHERE patientid=${id}) ORDER BY seq LIMIT 2"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", patient); statement.Execute(args); if (statement.IsDone()) { // The patient is protected, don't add it to the recycling order return; } seq = ReadInteger64(statement, 0); statement.Next(); if (statement.IsDone()) { // The patient is already at the end of the recycling order // (because of the "LIMIT 2" above), no need to modify the table return; } } // Delete the old position of the patient in the recycling order { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "DELETE FROM PatientRecyclingOrder WHERE seq=${seq}"); statement.SetParameterType("seq", ValueType_Integer64); Dictionary args; args.SetIntegerValue("seq", seq); statement.Execute(args); } // Add the patient to the end of the recycling order { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "INSERT INTO PatientRecyclingOrder VALUES(${}, ${id})"); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", patient); statement.Execute(args); } } #if defined(ORTHANC_PLUGINS_VERSION_IS_ABOVE) // Macro introduced in 1.3.1 # if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 5, 4) // New primitive since Orthanc 1.5.4 bool IndexBackend::LookupResourceAndParent(int64_t& id, OrthancPluginResourceType& type, std::string& parentPublicId, DatabaseManager& manager, const char* publicId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT resource.internalId, resource.resourceType, parent.publicId " "FROM Resources AS resource LEFT JOIN Resources parent ON parent.internalId=resource.parentId " "WHERE resource.publicId=${id}"); statement.SetParameterType("id", ValueType_Utf8String); Dictionary args; args.SetUtf8Value("id", publicId); statement.Execute(args); if (statement.IsDone()) { return false; } else { if (statement.GetResultFieldsCount() != 3) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } statement.SetResultFieldType(0, ValueType_Integer64); statement.SetResultFieldType(1, ValueType_Integer64); statement.SetResultFieldType(2, ValueType_Utf8String); id = ReadInteger64(statement, 0); type = static_cast<OrthancPluginResourceType>(ReadInteger32(statement, 1)); const IValue& value = statement.GetResultField(2); switch (value.GetType()) { case ValueType_Null: parentPublicId.clear(); break; case ValueType_Utf8String: parentPublicId = dynamic_cast<const Utf8StringValue&>(value).GetContent(); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } assert((statement.Next(), statement.IsDone())); return true; } } # endif #endif #if defined(ORTHANC_PLUGINS_VERSION_IS_ABOVE) // Macro introduced in 1.3.1 # if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 5, 4) // New primitive since Orthanc 1.5.4 void IndexBackend::GetAllMetadata(std::map<int32_t, std::string>& result, DatabaseManager& manager, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager, "SELECT type, value FROM Metadata WHERE id=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); statement.Execute(args); result.clear(); if (!statement.IsDone()) { if (statement.GetResultFieldsCount() != 2) { throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); } statement.SetResultFieldType(0, ValueType_Integer64); statement.SetResultFieldType(1, ValueType_Utf8String); while (!statement.IsDone()) { result[ReadInteger32(statement, 0)] = ReadString(statement, 1); statement.Next(); } } } # endif #endif void IndexBackend::CreateInstanceGeneric(OrthancPluginCreateInstanceResult& result, DatabaseManager& manager, const char* hashPatient, const char* hashStudy, const char* hashSeries, const char* hashInstance) { // Check out "OrthancServer/Sources/Database/Compatibility/ICreateInstance.cpp" { OrthancPluginResourceType type; int64_t tmp; if (LookupResource(tmp, type, manager, hashInstance)) { // The instance already exists assert(type == OrthancPluginResourceType_Instance); result.instanceId = tmp; result.isNewInstance = false; return; } } result.instanceId = CreateResource(manager, hashInstance, OrthancPluginResourceType_Instance); result.isNewInstance = true; result.isNewPatient = false; result.isNewStudy = false; result.isNewSeries = false; result.patientId = -1; result.studyId = -1; result.seriesId = -1; // Detect up to which level the patient/study/series/instance // hierarchy must be created { OrthancPluginResourceType dummy; if (LookupResource(result.seriesId, dummy, manager, hashSeries)) { assert(dummy == OrthancPluginResourceType_Series); // The patient, the study and the series already exist bool ok = (LookupResource(result.patientId, dummy, manager, hashPatient) && LookupResource(result.studyId, dummy, manager, hashStudy)); (void) ok; // Remove warning about unused variable in release builds assert(ok); } else if (LookupResource(result.studyId, dummy, manager, hashStudy)) { assert(dummy == OrthancPluginResourceType_Study); // New series: The patient and the study already exist result.isNewSeries = true; bool ok = LookupResource(result.patientId, dummy, manager, hashPatient); (void) ok; // Remove warning about unused variable in release builds assert(ok); } else if (LookupResource(result.patientId, dummy, manager, hashPatient)) { assert(dummy == OrthancPluginResourceType_Patient); // New study and series: The patient already exist result.isNewStudy = true; result.isNewSeries = true; } else { // New patient, study and series: Nothing exists result.isNewPatient = true; result.isNewStudy = true; result.isNewSeries = true; } } // Create the series if needed if (result.isNewSeries) { result.seriesId = CreateResource(manager, hashSeries, OrthancPluginResourceType_Series); } // Create the study if needed if (result.isNewStudy) { result.studyId = CreateResource(manager, hashStudy, OrthancPluginResourceType_Study); } // Create the patient if needed if (result.isNewPatient) { result.patientId = CreateResource(manager, hashPatient, OrthancPluginResourceType_Patient); } // Create the parent-to-child links AttachChild(manager, result.seriesId, result.instanceId); if (result.isNewSeries) { AttachChild(manager, result.studyId, result.seriesId); } if (result.isNewStudy) { AttachChild(manager, result.patientId, result.studyId); } TagMostRecentPatient(manager, result.patientId); // Sanity checks assert(result.patientId != -1); assert(result.studyId != -1); assert(result.seriesId != -1); assert(result.instanceId != -1); } void IndexBackend::Register(IndexBackend* backend, size_t countConnections, unsigned int maxDatabaseRetries) { if (backend == NULL) { throw Orthanc::OrthancException(Orthanc::ErrorCode_NullPointer); } bool hasLoadedV3 = false; #if defined(ORTHANC_PLUGINS_VERSION_IS_ABOVE) // Macro introduced in Orthanc 1.3.1 # if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 9, 2) if (OrthancPluginCheckVersionAdvanced(backend->GetContext(), 1, 9, 2) == 1) { LOG(WARNING) << "The index plugin will use " << countConnections << " connection(s) to the database, " << "and will retry up to " << maxDatabaseRetries << " time(s) in the case of a collision"; OrthancDatabases::DatabaseBackendAdapterV3::Register(backend, countConnections, maxDatabaseRetries); hasLoadedV3 = true; } # endif #endif if (!hasLoadedV3) { LOG(WARNING) << "Performance warning: Your version of the Orthanc SDK doesn't support multiple readers/writers"; OrthancDatabases::DatabaseBackendAdapterV2::Register(backend); } } bool IndexBackend::LookupGlobalIntegerProperty(int& target, DatabaseManager& manager, const char* serverIdentifier, int32_t property) { std::string value; if (LookupGlobalProperty(value, manager, serverIdentifier, property)) { try { target = boost::lexical_cast<int>(value); return true; } catch (boost::bad_lexical_cast&) { LOG(ERROR) << "Corrupted PostgreSQL database"; throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); } } else { return false; } } void IndexBackend::SetGlobalIntegerProperty(DatabaseManager& manager, const char* serverIdentifier, int32_t property, int value) { std::string s = boost::lexical_cast<std::string>(value); SetGlobalProperty(manager, serverIdentifier, property, s.c_str()); } void IndexBackend::Finalize() { OrthancDatabases::DatabaseBackendAdapterV2::Finalize(); #if defined(ORTHANC_PLUGINS_VERSION_IS_ABOVE) // Macro introduced in Orthanc 1.3.1 # if ORTHANC_PLUGINS_VERSION_IS_ABOVE(1, 9, 2) OrthancDatabases::DatabaseBackendAdapterV3::Finalize(); # endif #endif } DatabaseManager* IndexBackend::CreateSingleDatabaseManager(IDatabaseBackend& backend) { std::unique_ptr<DatabaseManager> manager(new DatabaseManager(backend.CreateDatabaseFactory())); backend.ConfigureDatabase(*manager); return manager.release(); } }