Mercurial > hg > orthanc-databases
view Framework/Plugins/IndexBackend.cpp @ 73:aa81c1c80c75 db-changes
fix compatibility with older sdk
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 04 Jan 2019 17:06:34 +0100 |
parents | e6c13ddd26d9 |
children | a4e440e65c68 |
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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) 2017-2019 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 "../Common/BinaryStringValue.h" #include "../Common/Integer64Value.h" #include "../Common/Utf8StringValue.h" #include "GlobalProperties.h" #include <Core/Logging.h> #include <Core/OrthancException.h> #include <OrthancServer/ServerEnumerations.h> #include <OrthancServer/Search/ISqlLookupFormatter.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(bool& done, DatabaseManager::CachedStatement& statement, const Dictionary& args, uint32_t maxResults) { statement.Execute(args); uint32_t count = 0; while (count < maxResults && !statement.IsDone()) { GetOutput().AnswerChange( ReadInteger64(statement, 0), ReadInteger32(statement, 1), static_cast<OrthancPluginResourceType>(ReadInteger32(statement, 3)), GetPublicId(ReadInteger64(statement, 2)), ReadString(statement, 4)); statement.Next(); count++; } done = (count < maxResults || statement.IsDone()); } void IndexBackend::ReadExportedResourcesInternal(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); GetOutput().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::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "DELETE FROM DeletedFiles"); statement.Execute(); } void IndexBackend::ClearDeletedResources() { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "DELETE FROM DeletedResources"); statement.Execute(); } void IndexBackend::SignalDeletedFiles() { 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); GetOutput().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() { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT * FROM DeletedResources"); statement.SetReadOnly(true); statement.Execute(); while (!statement.IsDone()) { GetOutput().SignalDeletedResource( ReadString(statement, 1), static_cast<OrthancPluginResourceType>(ReadInteger32(statement, 0))); statement.Next(); } } IndexBackend::IndexBackend(IDatabaseFactory* factory) : manager_(factory) { } void IndexBackend::AddAttachment(int64_t id, const OrthancPluginAttachment& attachment) { 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(int64_t parent, int64_t child) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "UPDATE Resources SET parentId = ${parent} WHERE internalId = ${child}"); statement.SetParameterType("parent", ValueType_Integer64); statement.SetParameterType("child", ValueType_Integer64); Dictionary args; args.SetIntegerValue("parent", parent); args.SetIntegerValue("child", child); statement.Execute(args); } void IndexBackend::ClearChanges() { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "DELETE FROM Changes"); statement.Execute(); } void IndexBackend::ClearExportedResources() { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "DELETE FROM ExportedResources"); statement.Execute(); } void IndexBackend::DeleteAttachment(int64_t id, int32_t attachment) { ClearDeletedFiles(); { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "DELETE FROM AttachedFiles WHERE id=${id} AND fileType=${type}"); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", static_cast<int>(attachment)); statement.Execute(args); } SignalDeletedFiles(); } void IndexBackend::DeleteMetadata(int64_t id, int32_t metadataType) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "DELETE FROM Metadata WHERE id=${id} and type=${type}"); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", static_cast<int>(metadataType)); statement.Execute(args); } void IndexBackend::DeleteResource(int64_t id) { assert(manager_.GetDialect() != Dialect_MySQL); ClearDeletedFiles(); ClearDeletedResources(); { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, GetManager(), "DELETE FROM RemainingAncestor"); statement.Execute(); } { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, GetManager(), "DELETE FROM Resources WHERE internalId=${id}"); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); statement.Execute(args); } { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, GetManager(), "SELECT * FROM RemainingAncestor"); statement.Execute(); if (!statement.IsDone()) { GetOutput().SignalRemainingAncestor( ReadString(statement, 1), static_cast<OrthancPluginResourceType>(ReadInteger32(statement, 0))); // There is at most 1 remaining ancestor assert((statement.Next(), statement.IsDone())); } } SignalDeletedFiles(); SignalDeletedResources(); } void IndexBackend::GetAllInternalIds(std::list<int64_t>& target, OrthancPluginResourceType resourceType) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT internalId FROM Resources WHERE resourceType=${type}"); statement.SetReadOnly(true); statement.SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("type", static_cast<int>(resourceType)); ReadListOfIntegers<int64_t>(target, statement, args); } void IndexBackend::GetAllPublicIds(std::list<std::string>& target, OrthancPluginResourceType resourceType) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT publicId FROM Resources WHERE resourceType=${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, 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 ${since}"); statement.SetReadOnly(true); statement.SetParameterType("type", ValueType_Integer64); statement.SetParameterType("limit", ValueType_Integer64); statement.SetParameterType("since", ValueType_Integer64); Dictionary args; args.SetIntegerValue("type", static_cast<int>(resourceType)); args.SetIntegerValue("limit", limit); args.SetIntegerValue("since", since); ReadListOfStrings(target, statement, args); } /* Use GetOutput().AnswerChange() */ void IndexBackend::GetChanges(bool& done /*out*/, int64_t since, uint32_t maxResults) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT * FROM Changes WHERE seq>${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(done, statement, args, maxResults); } void IndexBackend::GetChildrenInternalId(std::list<int64_t>& target /*out*/, 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*/, 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 = ${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); ReadListOfStrings(target, statement, args); } /* Use GetOutput().AnswerExportedResource() */ void IndexBackend::GetExportedResources(bool& done /*out*/, int64_t since, uint32_t maxResults) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT * FROM ExportedResources WHERE seq>${since} ORDER BY seq LIMIT ${limit}"); statement.SetReadOnly(true); statement.SetParameterType("limit", ValueType_Integer64); statement.SetParameterType("since", ValueType_Integer64); Dictionary args; args.SetIntegerValue("limit", maxResults + 1); args.SetIntegerValue("since", since); ReadExportedResourcesInternal(done, statement, args, maxResults); } /* Use GetOutput().AnswerChange() */ void IndexBackend::GetLastChange() { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT * FROM Changes ORDER BY seq DESC LIMIT 1"); statement.SetReadOnly(true); Dictionary args; bool done; // Ignored ReadChangesInternal(done, statement, args, 1); } /* Use GetOutput().AnswerExportedResource() */ void IndexBackend::GetLastExportedResource() { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT * FROM ExportedResources ORDER BY seq DESC LIMIT 1"); statement.SetReadOnly(true); Dictionary args; bool done; // Ignored ReadExportedResourcesInternal(done, statement, args, 1); } /* Use GetOutput().AnswerDicomTag() */ void IndexBackend::GetMainDicomTags(int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT * FROM MainDicomTags WHERE id=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); statement.Execute(args); while (!statement.IsDone()) { GetOutput().AnswerDicomTag(static_cast<uint16_t>(ReadInteger64(statement, 1)), static_cast<uint16_t>(ReadInteger64(statement, 2)), ReadString(statement, 3)); statement.Next(); } } std::string IndexBackend::GetPublicId(int64_t resourceId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT publicId FROM Resources WHERE internalId=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", resourceId); statement.Execute(args); if (statement.IsDone()) { throw Orthanc::OrthancException(Orthanc::ErrorCode_UnknownResource); } else { return ReadString(statement, 0); } } uint64_t IndexBackend::GetResourceCount(OrthancPluginResourceType resourceType) { std::auto_ptr<DatabaseManager::CachedStatement> statement; switch (manager_.GetDialect()) { case Dialect_MySQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "SELECT CAST(COUNT(*) AS UNSIGNED INT) FROM Resources WHERE resourceType=${type}")); break; case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "SELECT CAST(COUNT(*) AS BIGINT) FROM Resources WHERE resourceType=${type}")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "SELECT COUNT(*) FROM Resources WHERE resourceType=${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(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() { std::auto_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, GetManager(), "SELECT CAST(COALESCE(SUM(compressedSize), 0) AS UNSIGNED INTEGER) FROM AttachedFiles")); break; case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "SELECT CAST(COALESCE(SUM(compressedSize), 0) AS BIGINT) FROM AttachedFiles")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "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() { std::auto_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, GetManager(), "SELECT CAST(COALESCE(SUM(uncompressedSize), 0) AS UNSIGNED INTEGER) FROM AttachedFiles")); break; case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "SELECT CAST(COALESCE(SUM(uncompressedSize), 0) AS BIGINT) FROM AttachedFiles")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "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(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(int64_t internalId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT * FROM PatientRecyclingOrder WHERE patientId = ${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", internalId); statement.Execute(args); return statement.IsDone(); } void IndexBackend::ListAvailableMetadata(std::list<int32_t>& target /*out*/, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT type FROM Metadata WHERE id=${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*/, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT fileType FROM AttachedFiles WHERE id=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); ReadListOfIntegers<int32_t>(target, statement, args); } void IndexBackend::LogChange(const OrthancPluginChange& change) { int64_t id; OrthancPluginResourceType type; if (!LookupResource(id, type, change.publicId) || type != change.resourceType) { throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); } DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "INSERT INTO Changes VALUES(${}, ${changeType}, ${id}, ${resourceType}, ${date})"); statement.SetParameterType("changeType", ValueType_Integer64); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("resourceType", ValueType_Integer64); statement.SetParameterType("date", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("changeType", change.changeType); args.SetIntegerValue("id", id); args.SetIntegerValue("resourceType", change.resourceType); args.SetUtf8Value("date", change.date); statement.Execute(args); } void IndexBackend::LogExportedResource(const OrthancPluginExportedResource& resource) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "INSERT INTO ExportedResources VALUES(${}, ${type}, ${publicId}, " "${modality}, ${patient}, ${study}, ${series}, ${instance}, ${date})"); statement.SetParameterType("type", ValueType_Integer64); statement.SetParameterType("publicId", ValueType_Utf8String); statement.SetParameterType("modality", ValueType_Utf8String); statement.SetParameterType("patient", ValueType_Utf8String); statement.SetParameterType("study", ValueType_Utf8String); statement.SetParameterType("series", ValueType_Utf8String); statement.SetParameterType("instance", ValueType_Utf8String); statement.SetParameterType("date", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("type", resource.resourceType); args.SetUtf8Value("publicId", resource.publicId); args.SetUtf8Value("modality", resource.modality); args.SetUtf8Value("patient", resource.patientId); args.SetUtf8Value("study", resource.studyInstanceUid); args.SetUtf8Value("series", resource.seriesInstanceUid); args.SetUtf8Value("instance", resource.sopInstanceUid); args.SetUtf8Value("date", resource.date); statement.Execute(args); } /* Use GetOutput().AnswerAttachment() */ bool IndexBackend::LookupAttachment(int64_t id, int32_t contentType) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT uuid, uncompressedSize, compressionType, compressedSize, " "uncompressedHash, compressedHash FROM AttachedFiles WHERE id=${id} AND fileType=${type}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", static_cast<int>(contentType)); statement.Execute(args); if (statement.IsDone()) { return false; } else { GetOutput().AnswerAttachment(ReadString(statement, 0), contentType, ReadInteger64(statement, 1), ReadString(statement, 4), ReadInteger32(statement, 2), ReadInteger64(statement, 3), ReadString(statement, 5)); return true; } } bool IndexBackend::LookupGlobalProperty(std::string& target /*out*/, int32_t property) { return ::OrthancDatabases::LookupGlobalProperty(target, manager_, static_cast<Orthanc::GlobalProperty>(property)); } void IndexBackend::LookupIdentifier(std::list<int64_t>& target /*out*/, OrthancPluginResourceType resourceType, uint16_t group, uint16_t element, OrthancPluginIdentifierConstraint constraint, const char* value) { std::auto_ptr<DatabaseManager::CachedStatement> statement; std::string header = "SELECT d.id FROM DicomIdentifiers AS d, Resources AS r WHERE " "d.id = r.internalId AND r.resourceType=${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 ${value}"; statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, manager_, header.c_str())); break; default: throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); } statement->SetReadOnly(true); statement->SetParameterType("type", ValueType_Integer64); statement->SetParameterType("group", ValueType_Integer64); statement->SetParameterType("element", ValueType_Integer64); statement->SetParameterType("value", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("type", resourceType); args.SetIntegerValue("group", group); args.SetIntegerValue("element", element); if (constraint == OrthancPluginIdentifierConstraint_Wildcard) { args.SetUtf8Value("value", ConvertWildcardToLike(value)); } else { args.SetUtf8Value("value", value); } statement->Execute(args); target.clear(); while (!statement->IsDone()) { target.push_back(ReadInteger64(*statement, 0)); statement->Next(); } } void IndexBackend::LookupIdentifierRange(std::list<int64_t>& target /*out*/, OrthancPluginResourceType resourceType, uint16_t group, uint16_t element, const char* start, const char* end) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT d.id FROM DicomIdentifiers AS d, Resources AS r WHERE " "d.id = r.internalId AND r.resourceType=${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 id, int32_t metadataType) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT value FROM Metadata WHERE id=${id} and type=${type}"); 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); return true; } } bool IndexBackend::LookupParent(int64_t& parentId /*out*/, int64_t resourceId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT parentId FROM Resources WHERE internalId=${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", resourceId); statement.Execute(args); if (statement.IsDone() || statement.GetResultField(0).GetType() == ValueType_Null) { return false; } else { parentId = ReadInteger64(statement, 0); return true; } } bool IndexBackend::LookupResource(int64_t& id /*out*/, OrthancPluginResourceType& type /*out*/, const char* publicId) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT internalId, resourceType FROM Resources WHERE publicId=${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::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*/, int64_t patientIdToAvoid) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "SELECT patientId FROM PatientRecyclingOrder " "WHERE patientId != ${id} ORDER BY seq ASC LIMIT 1"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", patientIdToAvoid); statement.Execute(args); if (statement.IsDone()) { return false; } else { internalId = ReadInteger64(statement, 0); return true; } } void IndexBackend::SetGlobalProperty(int32_t property, const char* value) { return ::OrthancDatabases::SetGlobalProperty(manager_, static_cast<Orthanc::GlobalProperty>(property), value); } static void ExecuteSetTag(DatabaseManager::CachedStatement& statement, int64_t id, uint16_t group, uint16_t element, const char* value) { statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("group", ValueType_Integer64); statement.SetParameterType("element", ValueType_Integer64); statement.SetParameterType("value", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("group", group); args.SetIntegerValue("element", element); args.SetUtf8Value("value", value); statement.Execute(args); } void IndexBackend::SetMainDicomTag(int64_t id, uint16_t group, uint16_t element, const char* value) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "INSERT INTO MainDicomTags VALUES(${id}, ${group}, ${element}, ${value})"); ExecuteSetTag(statement, id, group, element, value); } void IndexBackend::SetIdentifierTag(int64_t id, uint16_t group, uint16_t element, const char* value) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "INSERT INTO DicomIdentifiers VALUES(${id}, ${group}, ${element}, ${value})"); ExecuteSetTag(statement, id, group, element, value); } void IndexBackend::SetMetadata(int64_t id, int32_t metadataType, const char* value) { if (manager_.GetDialect() == Dialect_SQLite) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "INSERT OR REPLACE INTO Metadata VALUES (${id}, ${type}, ${value})"); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); statement.SetParameterType("value", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", metadataType); args.SetUtf8Value("value", value); statement.Execute(args); } else { { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "DELETE FROM Metadata WHERE id=${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}, ${value})"); statement.SetParameterType("id", ValueType_Integer64); statement.SetParameterType("type", ValueType_Integer64); statement.SetParameterType("value", ValueType_Utf8String); Dictionary args; args.SetIntegerValue("id", id); args.SetIntegerValue("type", metadataType); args.SetUtf8Value("value", value); statement.Execute(args); } } } void IndexBackend::SetProtectedPatient(int64_t internalId, bool isProtected) { if (isProtected) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "DELETE FROM PatientRecyclingOrder WHERE patientId=${id}"); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", internalId); statement.Execute(args); } else if (IsProtectedPatient(internalId)) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "INSERT INTO PatientRecyclingOrder VALUES(${}, ${id})"); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", internalId); statement.Execute(args); } else { // Nothing to do: The patient is already unprotected } } uint32_t IndexBackend::GetDatabaseVersion() { std::string version = "unknown"; if (LookupGlobalProperty(version, Orthanc::GlobalProperty_DatabaseSchemaVersion)) { try { return boost::lexical_cast<unsigned int>(version); } catch (boost::bad_lexical_cast&) { } } LOG(ERROR) << "The database is corrupted. Drop it manually for Orthanc to recreate it"; throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); } /** * Upgrade the database to the specified version of the database * schema. The upgrade script is allowed to make calls to * OrthancPluginReconstructMainDicomTags(). **/ void IndexBackend::UpgradeDatabase(uint32_t targetVersion, OrthancPluginStorageArea* storageArea) { LOG(ERROR) << "Upgrading database is not implemented by this plugin"; throw Orthanc::OrthancException(Orthanc::ErrorCode_NotImplemented); } void IndexBackend::ClearMainDicomTags(int64_t internalId) { { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, manager_, "DELETE FROM MainDicomTags WHERE id=${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::GetResourcesCount() { std::auto_ptr<DatabaseManager::CachedStatement> statement; switch (manager_.GetDialect()) { case Dialect_MySQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "SELECT CAST(COUNT(*) AS UNSIGNED INT) FROM Resources")); break; case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "SELECT CAST(COUNT(*) AS BIGINT) FROM Resources")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "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() { std::auto_ptr<DatabaseManager::CachedStatement> statement; switch (manager_.GetDialect()) { case Dialect_MySQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "SELECT CAST(COUNT(*) AS UNSIGNED INT) FROM PatientRecyclingOrder")); break; case Dialect_PostgreSQL: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "SELECT CAST(COUNT(*) AS BIGINT) FROM PatientRecyclingOrder")); break; case Dialect_SQLite: statement.reset(new DatabaseManager::CachedStatement( STATEMENT_FROM_HERE, GetManager(), "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, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, GetManager(), "SELECT a.publicId FROM Resources AS a, Resources AS b " "WHERE a.internalId = b.parentId AND b.internalId = ${id}"); statement.SetReadOnly(true); statement.SetParameterType("id", ValueType_Integer64); Dictionary args; args.SetIntegerValue("id", id); statement.Execute(args); if (statement.IsDone()) { return false; } else { target = ReadString(statement, 0); return true; } } // For unit tests only! void IndexBackend::GetChildren(std::list<std::string>& childrenPublicIds, int64_t id) { DatabaseManager::CachedStatement statement( STATEMENT_FROM_HERE, GetManager(), "SELECT publicId FROM Resources WHERE parentId=${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(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(GetManager(), sql); formatter.PrepareStatement(statement); statement.Execute(formatter.GetDictionary()); while (!statement.IsDone()) { if (requestSomeInstance) { GetOutput().AnswerMatchingResource(ReadString(statement, 0), ReadString(statement, 1)); } else { GetOutput().AnswerMatchingResource(ReadString(statement, 0)); } statement.Next(); } } #endif }