Mercurial > hg > orthanc-databases

annotate MySQL/Plugins/MySQLIndex.cpp @ 522:c49136b34891 large-queries tip

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use a prepared statement for InsertOrUpdateMetadata
author Alain Mazy <am@orthanc.team>
date Fri, 05 Jul 2024 09:15:54 +0200
parents 54d518dcd74a
children
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2023 Osimis S.A., Belgium
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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8 *
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9 * This program is free software: you can redistribute it and/or
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10 * modify it under the terms of the GNU Affero General Public License
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11 * as published by the Free Software Foundation, either version 3 of
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12 * the License, or (at your option) any later version.
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13 *
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14 * This program is distributed in the hope that it will be useful, but
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15 * WITHOUT ANY WARRANTY; without even the implied warranty of
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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17 * Affero General Public License for more details.
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18 *
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19 * You should have received a copy of the GNU Affero General Public License
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20 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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21 **/
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24 #include "MySQLIndex.h"
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25
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26 #include "../../Framework/Plugins/GlobalProperties.h"
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27 #include "../../Framework/MySQL/MySQLDatabase.h"
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28 #include "../../Framework/MySQL/MySQLTransaction.h"
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29 #include "MySQLDefinitions.h"
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31 #include <EmbeddedResources.h> // Auto-generated file
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32
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33 #include <Compatibility.h> // For std::unique_ptr<>
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34 #include <Logging.h>
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35 #include <OrthancException.h>
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36
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37 #include <ctype.h>
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38
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39 namespace OrthancDatabases
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40 {
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41 MySQLIndex::MySQLIndex(OrthancPluginContext* context,
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42 const MySQLParameters& parameters) :
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43 IndexBackend(context),
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44 parameters_(parameters),
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45 clearAll_(false)
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46 {
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47 }
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50 IDatabaseFactory* MySQLIndex::CreateDatabaseFactory()
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51 {
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52 return MySQLDatabase::CreateDatabaseFactory(parameters_);
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53 }
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56 static void ThrowCannotCreateTrigger()
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57 {
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58 LOG(ERROR) << "The MySQL user is not allowed to create triggers => 2 possible solutions:";
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59 LOG(ERROR) << " 1- Give the SUPER privilege to the MySQL database user, or";
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60 LOG(ERROR) << " 2- Run \"set global log_bin_trust_function_creators=1;\" as MySQL root user.";
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61 LOG(ERROR) << "Once you are done, drop and recreate the MySQL database";
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62 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database,
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63 "Need to fix the MySQL permissions for \"CREATE TRIGGER\"");
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64 }
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66
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67 void MySQLIndex::ConfigureDatabase(DatabaseManager& manager,
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68 bool hasIdentifierTags,
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69 const std::list<IdentifierTag>& identifierTags)
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70 {
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71 uint32_t expectedVersion = 6;
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72
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73 if (GetContext()) // "GetContext()" can possibly be NULL in the unit tests
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74 {
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75 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(GetContext());
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76 }
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77
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78 // Check the expected version of the database
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79 if (expectedVersion != 6)
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80 {
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81 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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82 << "expecting the DB schema version " << expectedVersion
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83 << ", but this plugin is only compatible with version 6";
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84 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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85 }
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86
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87 if (!MySQLDatabase::IsValidDatabaseIdentifier(parameters_.GetDatabase()))
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88 {
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89 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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90 }
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91
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92 if (clearAll_)
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93 {
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94 MySQLDatabase::ClearDatabase(parameters_);
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95 }
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96
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97 MySQLDatabase& db = dynamic_cast<MySQLDatabase&>(manager.GetDatabase());
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99 {
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100 MySQLDatabase::TransientAdvisoryLock lock(db, MYSQL_LOCK_DATABASE_SETUP);
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101
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102 /**
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103 * In a first transaction, we create the tables. Such a
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104 * transaction cannot be rollback: "The CREATE TABLE statement
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105 * in InnoDB is processed as a single transaction. This means
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106 * that a ROLLBACK from the user does not undo CREATE TABLE
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107 * statements the user made during that transaction."
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108 * https://dev.mysql.com/doc/refman/8.0/en/implicit-commit.html
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109 *
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110 * As a consequence, we delay the initial population of the
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111 * tables in a sequence of transactions below. This solves the
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112 * error message "MySQL plugin is incompatible with database
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113 * schema version: 0" that was reported in the forum:
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114 * https://groups.google.com/d/msg/orthanc-users/OCFFkm1qm0k/Mbroy8VWAQAJ
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115 **/
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116 {
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117 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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118
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119 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER DATABASE " + parameters_.GetDatabase() +
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120 " CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci");
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121
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122 // This is the first table to be created
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123 if (!t.GetDatabaseTransaction().DoesTableExist("GlobalProperties"))
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124 {
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125 std::string query;
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126
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127 Orthanc::EmbeddedResources::GetFileResource
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128 (query, Orthanc::EmbeddedResources::MYSQL_PREPARE_INDEX);
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129
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130 // Need to escape arobases: Don't use "t.GetDatabaseTransaction().ExecuteMultiLines()" here
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131 db.ExecuteMultiLines(query, true);
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132 }
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133
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134 t.Commit();
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135 }
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136
144
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137 /**
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138 * This is the sequence of transactions that initially populate
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139 * the database. WARNING - As table creation cannot be rollback,
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140 * don't forget to add "IF NOT EXISTS" if some table must be
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141 * created below this point (in order to recover from failed
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142 * transaction).
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143 **/
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145 {
237
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146 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
144
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147
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148 // This is the last table to be created
241
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149 if (!t.GetDatabaseTransaction().DoesTableExist("PatientRecyclingOrder"))
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150 {
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151 LOG(ERROR) << "Corrupted MySQL database";
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152 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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153 }
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154
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155 // This is the last item to be created
241
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156 if (!t.GetDatabaseTransaction().DoesTriggerExist("PatientAdded"))
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157 {
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158 ThrowCannotCreateTrigger();
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159 }
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160
290
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161 int version = 0;
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162
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163 if (!LookupGlobalIntegerProperty(version, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion))
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164 {
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165 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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166 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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167 version = expectedVersion;
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168 }
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169
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170 if (version != 6)
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171 {
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172 LOG(ERROR) << "MySQL plugin is incompatible with database schema version: " << version;
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173 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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174 }
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175
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176 t.Commit();
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177 }
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178
144
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179 int revision = 0;
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180
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181 {
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182 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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183
237
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184 if (!LookupGlobalIntegerProperty(revision, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel))
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185 {
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186 revision = 1;
237
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187 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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188 }
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189
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190 t.Commit();
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191 }
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192
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193 if (revision == 1)
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194 {
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195 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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196
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197 // The serialization of jobs as a global property can lead to
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198 // very long values => switch to the LONGTEXT type that can
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199 // store up to 4GB:
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200 // https://stackoverflow.com/a/13932834/881731
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201 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE GlobalProperties MODIFY value LONGTEXT");
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202
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203 revision = 2;
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204 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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205
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206 t.Commit();
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207 }
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208
87
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209 if (revision == 2)
144
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210 {
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211 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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212
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213 // Install the "GetLastChangeIndex" extension
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214 std::string query;
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215
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216 Orthanc::EmbeddedResources::GetFileResource
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217 (query, Orthanc::EmbeddedResources::MYSQL_GET_LAST_CHANGE_INDEX);
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218
241
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219 // Need to escape arobases: Don't use "t.GetDatabaseTransaction().ExecuteMultiLines()" here
237
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220 db.ExecuteMultiLines(query, true);
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221
241
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222 if (!t.GetDatabaseTransaction().DoesTriggerExist("ChangeAdded"))
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223 {
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224 ThrowCannotCreateTrigger();
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225 }
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226
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227 revision = 3;
237
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228 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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229
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230 t.Commit();
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231 }
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232
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233 if (revision == 3)
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234 {
237
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235 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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236
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237 // Reconfiguration of "Metadata" from TEXT type (up to 64KB)
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238 // to the LONGTEXT type (up to 4GB). This might be important
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239 // for applications such as the Osimis Web viewer that stores
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240 // large amount of metadata.
426
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241 // https://orthanc.uclouvain.be/book/faq/features.html#central-registry-of-metadata-and-attachments
241
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242 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE Metadata MODIFY value LONGTEXT");
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243
109
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244 revision = 4;
237
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245 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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246
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247 t.Commit();
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248 }
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249
110
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250 if (revision == 4)
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251 {
237
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252 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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253
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254 // Install the "CreateInstance" extension
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255 std::string query;
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256
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257 Orthanc::EmbeddedResources::GetFileResource
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258 (query, Orthanc::EmbeddedResources::MYSQL_CREATE_INSTANCE);
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259
241
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260 // Need to escape arobases: Don't use "t.GetDatabaseTransaction().ExecuteMultiLines()" here
237
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261 db.ExecuteMultiLines(query, true);
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262
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263 revision = 5;
237
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264 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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265
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266 t.Commit();
110
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267 }
289
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268
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269 if (revision == 5)
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270 {
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271 // Added new table "ServerProperties" since release 4.0 to deal with multiple writers
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272 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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273
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274 if (t.GetDatabaseTransaction().DoesTableExist("ServerProperties"))
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275 {
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276 /**
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277 * Patch for MySQL plugin 4.0, where the column "value" was
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278 * "TEXT" instead of "LONGTEXT", which prevented
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279 * serialization of large jobs. This was giving error "MySQL
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280 * error (1406,22001): Data too long for column 'value' at
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281 * row 1" after log message "Serializing the content of the
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282 * jobs engine" (in --trace mode).
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283 * https://groups.google.com/g/orthanc-users/c/1Y3nTBdr0uE/m/K7PA5pboAgAJ
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284 **/
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285 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE ServerProperties MODIFY value LONGTEXT");
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286 }
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287 else
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288 {
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289 t.GetDatabaseTransaction().ExecuteMultiLines("CREATE TABLE ServerProperties(server VARCHAR(64) NOT NULL, "
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290 "property INTEGER, value LONGTEXT, PRIMARY KEY(server, property))");
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291 }
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292
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293 // Revision 6 indicates that "value" of "ServerProperties" is
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294 // "LONGTEXT", whereas revision 5 corresponds to "TEXT"
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295 revision = 6;
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296 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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297
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298 t.Commit();
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299 }
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300
400
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301 if (revision == 6)
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302 {
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303 // Added new table "Labels" since release 5.0 to deal with
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304 // labels that were introduced in Orthanc 1.12.0
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305 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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306
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307 t.GetDatabaseTransaction().ExecuteMultiLines(
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308 "CREATE TABLE Labels(id BIGINT NOT NULL,"
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309 "label VARCHAR(64) NOT NULL,"
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310 "PRIMARY KEY(id, label),"
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311 "CONSTRAINT Labels1 FOREIGN KEY (id) REFERENCES Resources(internalId) ON DELETE CASCADE);"
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312 "CREATE INDEX LabelsIndex1 ON Labels(id);"
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313 "CREATE INDEX LabelsIndex2 ON Labels(label);");
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314
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315 revision = 7;
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316 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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317
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318 t.Commit();
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319 }
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320
424
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321 if (revision == 7)
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322 {
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323 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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324
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325 // Install the "CreateInstance" extension
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326 std::string query;
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327
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328 Orthanc::EmbeddedResources::GetFileResource
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329 (query, Orthanc::EmbeddedResources::MYSQL_DELETE_RESOURCES);
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330
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331 // Need to escape arobases: Don't use "t.GetDatabaseTransaction().ExecuteMultiLines()" here
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332 db.ExecuteMultiLines(query, true);
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333
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334 revision = 8;
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335 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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336
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337 t.Commit();
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338 }
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339
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340
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341 if (revision != 8)
0
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342 {
53
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343 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision;
0
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344 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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345 }
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346 }
137
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347
238
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348
137
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349 /**
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350 * WARNING: This lock must be acquired after
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351 * "MYSQL_LOCK_DATABASE_SETUP" is released. Indeed, in MySQL <
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352 * 5.7, it is impossible to acquire more than one lock at a time,
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353 * as calling "SELECT GET_LOCK()" releases all the
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354 * previously-acquired locks.
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355 * https://dev.mysql.com/doc/refman/5.7/en/locking-functions.html
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356 **/
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357 if (parameters_.HasLock())
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358 {
226
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359 db.AdvisoryLock(MYSQL_LOCK_INDEX);
137
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360 }
0
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361 }
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362
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363
225
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364 int64_t MySQLIndex::CreateResource(DatabaseManager& manager,
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365 const char* publicId,
0
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366 OrthancPluginResourceType type)
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367 {
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368 {
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369 DatabaseManager::CachedStatement statement(
225
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370 STATEMENT_FROM_HERE, manager,
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371 "INSERT INTO Resources VALUES(NULL, ${type}, ${id}, NULL)");
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372
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373 statement.SetParameterType("id", ValueType_Utf8String);
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374 statement.SetParameterType("type", ValueType_Integer64);
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375
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376 Dictionary args;
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377 args.SetUtf8Value("id", publicId);
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378 args.SetIntegerValue("type", static_cast<int>(type));
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379
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380 statement.Execute(args);
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381 }
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382
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383 {
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384 DatabaseManager::CachedStatement statement(
225
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385 STATEMENT_FROM_HERE, manager,
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386 "SELECT LAST_INSERT_ID()");
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387
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388 statement.Execute();
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389
263
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390 return statement.ReadInteger64(0);
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391 }
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392 }
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393
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394
203
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395 void MySQLIndex::DeleteResource(IDatabaseBackendOutput& output,
225
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396 DatabaseManager& manager,
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397 int64_t id)
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398 {
305
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399 /**
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400 * Contrarily to PostgreSQL and SQLite, the MySQL dialect doesn't
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401 * support cascaded delete inside the same table. This has to be
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402 * manually reimplemented.
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403 **/
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404
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405 ClearDeletedFiles(manager);
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406
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407 // Recursive exploration of resources to be deleted, from the "id"
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408 // resource to the top of the tree of resources
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409
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410 bool done = false;
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411
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412 while (!done)
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413 {
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414 bool hasSibling = false;
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415 int64_t parentId = -1; // Dummy initialization
307
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416
0
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417 {
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418 DatabaseManager::CachedStatement lookupSiblings(
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419 STATEMENT_FROM_HERE, manager,
0
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420 "SELECT parentId FROM Resources "
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421 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});");
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422
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423 lookupSiblings.SetParameterType("id", ValueType_Integer64);
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424
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425 Dictionary args;
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426 args.SetIntegerValue("id", id);
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427
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428 lookupSiblings.Execute(args);
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429
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430 if (lookupSiblings.IsDone())
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431 {
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432 // "id" is a root node
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433 done = true;
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434 }
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435 else
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436 {
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437 parentId = lookupSiblings.ReadInteger64(0);
0
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438 lookupSiblings.Next();
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439
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440 if (lookupSiblings.IsDone())
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441 {
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442 // "id" has no sibling node, recursively remove
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443 done = false;
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444 id = parentId;
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445 }
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446 else
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447 {
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448 // "id" has at least one sibling node: the parent node is the remaining ancestor
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449 done = true;
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450 hasSibling = true;
0
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451 }
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452 }
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453 }
307
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454
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455 if (hasSibling)
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456 {
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457 // This cannot be executed in the same scope as another
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458 // DatabaseManager::CachedStatement
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459
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460 DatabaseManager::CachedStatement parent(
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461 STATEMENT_FROM_HERE, manager,
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462 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};");
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463
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464 parent.SetParameterType("id", ValueType_Integer64);
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465
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466 Dictionary args2;
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467 args2.SetIntegerValue("id", parentId);
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468
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469 parent.Execute(args2);
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470
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471 output.SignalRemainingAncestor(
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472 parent.ReadString(0),
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473 static_cast<OrthancPluginResourceType>(parent.ReadInteger32(1)));
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474 }
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475 }
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476
455
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477 {
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478 DatabaseManager::CachedStatement dropTemporaryTable(
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479 STATEMENT_FROM_HERE, manager,
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480 "DROP TEMPORARY TABLE IF EXISTS DeletedResources");
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481 dropTemporaryTable.Execute();
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482 }
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483
455
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484 {
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485 DatabaseManager::CachedStatement lookupResourcesToDelete(
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486 STATEMENT_FROM_HERE, manager,
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487 "CREATE TEMPORARY TABLE DeletedResources SELECT * FROM (SELECT internalId, resourceType, publicId FROM Resources WHERE internalId=${id} OR parentId=${id} OR parentId IN (SELECT internalId FROM Resources WHERE parentId=${id}) OR parentId IN (SELECT internalId FROM Resources WHERE parentId IN (SELECT internalId FROM Resources WHERE parentId=${id}))) AS t");
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488 lookupResourcesToDelete.SetParameterType("id", ValueType_Integer64);
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489
455
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490 Dictionary args;
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491 args.SetIntegerValue("id", id);
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492 lookupResourcesToDelete.Execute(args);
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493 }
424
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494
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495 // {
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496 // DatabaseManager::CachedStatement deleteHierarchy(
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497 // STATEMENT_FROM_HERE, manager,
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498 // "DELETE FROM Resources WHERE internalId IN (SELECT internalId FROM DeletedResources)");
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499 // deleteHierarchy.Execute();
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500 // }
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501
307
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502
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503 {
424
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504 DatabaseManager::CachedStatement deleteResources(
307
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diff changeset
505 STATEMENT_FROM_HERE, manager,
424
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diff changeset
506 "CALL DeleteResources(${id})");
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parents: 403
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507
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508 deleteResources.SetParameterType("id", ValueType_Integer64);
307
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509
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510 Dictionary args;
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511 args.SetIntegerValue("id", id);
424
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parents: 403
diff changeset
512
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513 deleteResources.Execute(args);
0
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parents:
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514 }
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515
307
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516 SignalDeletedResources(output, manager);
225
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diff changeset
517 SignalDeletedFiles(output, manager);
0
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518 }
87
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519
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diff changeset
520
225
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diff changeset
521 int64_t MySQLIndex::GetLastChangeIndex(DatabaseManager& manager)
87
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522 {
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523 DatabaseManager::CachedStatement statement(
225
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524 STATEMENT_FROM_HERE, manager,
87
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diff changeset
525 "SELECT value FROM GlobalIntegers WHERE property = 0");
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parents: 84
diff changeset
526
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parents: 84
diff changeset
527 statement.SetReadOnly(true);
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diff changeset
528 statement.Execute();
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529
263
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530 return statement.ReadInteger64(0);
87
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parents: 84
diff changeset
531 }
110
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parents: 109
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532
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parents: 109
diff changeset
533
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diff changeset
534 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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diff changeset
535 void MySQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
225
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536 DatabaseManager& manager,
110
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diff changeset
537 const char* hashPatient,
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538 const char* hashStudy,
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diff changeset
539 const char* hashSeries,
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diff changeset
540 const char* hashInstance)
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diff changeset
541 {
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parents: 109
diff changeset
542 {
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parents: 109
diff changeset
543 DatabaseManager::CachedStatement statement(
225
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parents: 221
diff changeset
544 STATEMENT_FROM_HERE, manager,
110
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parents: 109
diff changeset
545 "CALL CreateInstance(${patient}, ${study}, ${series}, ${instance}, "
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parents: 109
diff changeset
546 "@isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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parents: 109
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547 "@patientKey, @studyKey, @seriesKey, @instanceKey)");
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548
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549 statement.SetParameterType("patient", ValueType_Utf8String);
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550 statement.SetParameterType("study", ValueType_Utf8String);
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551 statement.SetParameterType("series", ValueType_Utf8String);
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552 statement.SetParameterType("instance", ValueType_Utf8String);
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553
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554 Dictionary args;
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555 args.SetUtf8Value("patient", hashPatient);
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556 args.SetUtf8Value("study", hashStudy);
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557 args.SetUtf8Value("series", hashSeries);
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558 args.SetUtf8Value("instance", hashInstance);
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559
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560 statement.Execute(args);
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561
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562 if (!statement.IsDone())
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563 {
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564 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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565 }
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566 }
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567
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568 {
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569 DatabaseManager::CachedStatement statement(
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570 STATEMENT_FROM_HERE, manager,
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571 "SELECT @isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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572 "@patientKey, @studyKey, @seriesKey, @instanceKey");
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573
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574 statement.Execute();
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575
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576 for (size_t i = 0; i < 8; i++)
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577 {
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578 statement.SetResultFieldType(i, ValueType_Integer64);
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579 }
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580
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581 result.isNewInstance = (statement.ReadInteger64(3) == 1);
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582 result.instanceId = statement.ReadInteger64(7);
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583
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584 if (result.isNewInstance)
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585 {
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586 result.isNewPatient = (statement.ReadInteger64(0) == 1);
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587 result.isNewStudy = (statement.ReadInteger64(1) == 1);
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588 result.isNewSeries = (statement.ReadInteger64(2) == 1);
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589 result.patientId = statement.ReadInteger64(4);
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590 result.studyId = statement.ReadInteger64(5);
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591 result.seriesId = statement.ReadInteger64(6);
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592 }
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593 }
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594 }
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595 #endif
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596 }