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annotate MySQL/Plugins/MySQLIndex.cpp @ 359:16aac0287485

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copyright upgraded to 2022
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 21 Feb 2022 09:32:46 +0100
parents eb0b04c10bc4
children 3d6886f3e5b3
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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) 2017-2022 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2022 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU Affero General Public License
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10 * as published by the Free Software Foundation, either version 3 of
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11 * the License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * Affero General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU Affero General Public License
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19 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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20 **/
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22
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23 #include "MySQLIndex.h"
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24
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25 #include "../../Framework/Plugins/GlobalProperties.h"
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26 #include "../../Framework/MySQL/MySQLDatabase.h"
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27 #include "../../Framework/MySQL/MySQLTransaction.h"
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28 #include "MySQLDefinitions.h"
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30 #include <EmbeddedResources.h> // Auto-generated file
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31
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32 #include <Compatibility.h> // For std::unique_ptr<>
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33 #include <Logging.h>
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34 #include <OrthancException.h>
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35
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36 #include <ctype.h>
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37
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38 namespace OrthancDatabases
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39 {
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40 MySQLIndex::MySQLIndex(OrthancPluginContext* context,
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41 const MySQLParameters& parameters) :
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42 IndexBackend(context),
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43 parameters_(parameters),
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44 clearAll_(false)
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45 {
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46 }
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48
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49 IDatabaseFactory* MySQLIndex::CreateDatabaseFactory()
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50 {
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51 return MySQLDatabase::CreateDatabaseFactory(parameters_);
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52 }
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54
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55 static void ThrowCannotCreateTrigger()
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56 {
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57 LOG(ERROR) << "The MySQL user is not allowed to create triggers => 2 possible solutions:";
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58 LOG(ERROR) << " 1- Give the SUPER privilege to the MySQL database user, or";
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59 LOG(ERROR) << " 2- Run \"set global log_bin_trust_function_creators=1;\" as MySQL root user.";
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60 LOG(ERROR) << "Once you are done, drop and recreate the MySQL database";
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61 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database,
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62 "Need to fix the MySQL permissions for \"CREATE TRIGGER\"");
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63 }
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65
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66 void MySQLIndex::ConfigureDatabase(DatabaseManager& manager)
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67 {
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68 uint32_t expectedVersion = 6;
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69
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70 if (GetContext()) // "GetContext()" can possibly be NULL in the unit tests
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71 {
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72 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(GetContext());
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73 }
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74
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75 // Check the expected version of the database
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76 if (expectedVersion != 6)
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77 {
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78 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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79 << "expecting the DB schema version " << expectedVersion
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80 << ", but this plugin is only compatible with version 6";
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81 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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82 }
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83
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84 if (!MySQLDatabase::IsValidDatabaseIdentifier(parameters_.GetDatabase()))
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85 {
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86 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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87 }
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88
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89 if (clearAll_)
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90 {
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91 MySQLDatabase::ClearDatabase(parameters_);
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92 }
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93
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94 MySQLDatabase& db = dynamic_cast<MySQLDatabase&>(manager.GetDatabase());
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95
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96 {
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97 MySQLDatabase::TransientAdvisoryLock lock(db, MYSQL_LOCK_DATABASE_SETUP);
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99 /**
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100 * In a first transaction, we create the tables. Such a
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101 * transaction cannot be rollback: "The CREATE TABLE statement
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102 * in InnoDB is processed as a single transaction. This means
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103 * that a ROLLBACK from the user does not undo CREATE TABLE
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104 * statements the user made during that transaction."
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105 * https://dev.mysql.com/doc/refman/8.0/en/implicit-commit.html
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106 *
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107 * As a consequence, we delay the initial population of the
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108 * tables in a sequence of transactions below. This solves the
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109 * error message "MySQL plugin is incompatible with database
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110 * schema version: 0" that was reported in the forum:
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111 * https://groups.google.com/d/msg/orthanc-users/OCFFkm1qm0k/Mbroy8VWAQAJ
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112 **/
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113 {
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114 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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115
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116 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER DATABASE " + parameters_.GetDatabase() +
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117 " CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci");
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118
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119 // This is the first table to be created
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120 if (!t.GetDatabaseTransaction().DoesTableExist("GlobalProperties"))
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121 {
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122 std::string query;
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123
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124 Orthanc::EmbeddedResources::GetFileResource
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125 (query, Orthanc::EmbeddedResources::MYSQL_PREPARE_INDEX);
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126
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127 // Need to escape arobases: Don't use "t.GetDatabaseTransaction().ExecuteMultiLines()" here
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128 db.ExecuteMultiLines(query, true);
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129 }
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131 t.Commit();
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132 }
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133
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134 /**
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135 * This is the sequence of transactions that initially populate
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136 * the database. WARNING - As table creation cannot be rollback,
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137 * don't forget to add "IF NOT EXISTS" if some table must be
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138 * created below this point (in order to recover from failed
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139 * transaction).
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140 **/
0
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141
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142 {
237
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143 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
144
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144
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145 // This is the last table to be created
241
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146 if (!t.GetDatabaseTransaction().DoesTableExist("PatientRecyclingOrder"))
144
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147 {
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148 LOG(ERROR) << "Corrupted MySQL database";
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149 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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150 }
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151
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152 // This is the last item to be created
241
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153 if (!t.GetDatabaseTransaction().DoesTriggerExist("PatientAdded"))
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154 {
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155 ThrowCannotCreateTrigger();
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156 }
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157
290
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158 int version = 0;
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159
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160 if (!LookupGlobalIntegerProperty(version, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion))
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161 {
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162 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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163 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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164 version = expectedVersion;
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165 }
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166
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167 if (version != 6)
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168 {
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169 LOG(ERROR) << "MySQL plugin is incompatible with database schema version: " << version;
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170 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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171 }
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172
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173 t.Commit();
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174 }
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175
144
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176 int revision = 0;
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177
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178 {
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179 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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180
237
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181 if (!LookupGlobalIntegerProperty(revision, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel))
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182 {
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183 revision = 1;
237
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184 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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185 }
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186
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187 t.Commit();
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188 }
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189
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190 if (revision == 1)
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191 {
237
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192 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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193
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194 // The serialization of jobs as a global property can lead to
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195 // very long values => switch to the LONGTEXT type that can
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196 // store up to 4GB:
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197 // https://stackoverflow.com/a/13932834/881731
241
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198 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE GlobalProperties MODIFY value LONGTEXT");
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199
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200 revision = 2;
237
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201 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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202
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203 t.Commit();
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204 }
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205
87
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206 if (revision == 2)
144
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207 {
237
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208 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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209
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210 // Install the "GetLastChangeIndex" extension
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211 std::string query;
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212
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213 Orthanc::EmbeddedResources::GetFileResource
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214 (query, Orthanc::EmbeddedResources::MYSQL_GET_LAST_CHANGE_INDEX);
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215
241
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216 // Need to escape arobases: Don't use "t.GetDatabaseTransaction().ExecuteMultiLines()" here
237
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217 db.ExecuteMultiLines(query, true);
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218
241
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219 if (!t.GetDatabaseTransaction().DoesTriggerExist("ChangeAdded"))
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220 {
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221 ThrowCannotCreateTrigger();
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222 }
87
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223
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224 revision = 3;
237
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225 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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226
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227 t.Commit();
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228 }
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229
109
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230 if (revision == 3)
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231 {
237
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232 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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233
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234 // Reconfiguration of "Metadata" from TEXT type (up to 64KB)
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235 // to the LONGTEXT type (up to 4GB). This might be important
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236 // for applications such as the Osimis Web viewer that stores
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237 // large amount of metadata.
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238 // http://book.orthanc-server.com/faq/features.html#central-registry-of-metadata-and-attachments
241
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239 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE Metadata MODIFY value LONGTEXT");
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240
109
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241 revision = 4;
237
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242 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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243
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244 t.Commit();
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245 }
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246
110
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247 if (revision == 4)
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248 {
237
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249 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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250
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251 // Install the "CreateInstance" extension
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252 std::string query;
144
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253
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254 Orthanc::EmbeddedResources::GetFileResource
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255 (query, Orthanc::EmbeddedResources::MYSQL_CREATE_INSTANCE);
237
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256
241
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257 // Need to escape arobases: Don't use "t.GetDatabaseTransaction().ExecuteMultiLines()" here
237
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258 db.ExecuteMultiLines(query, true);
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259
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260 revision = 5;
237
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261 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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262
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263 t.Commit();
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264 }
289
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265
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266 if (revision == 5)
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267 {
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268 // Added new table "ServerProperties" since release 4.0 to deal with multiple writers
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269 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite);
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270
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271 if (t.GetDatabaseTransaction().DoesTableExist("ServerProperties"))
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272 {
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273 /**
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274 * Patch for MySQL plugin 4.0, where the column "value" was
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275 * "TEXT" instead of "LONGTEXT", which prevented
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276 * serialization of large jobs. This was giving error "MySQL
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277 * error (1406,22001): Data too long for column 'value' at
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278 * row 1" after log message "Serializing the content of the
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279 * jobs engine" (in --trace mode).
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280 * https://groups.google.com/g/orthanc-users/c/1Y3nTBdr0uE/m/K7PA5pboAgAJ
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281 **/
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282 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE ServerProperties MODIFY value LONGTEXT");
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283 }
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284 else
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285 {
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286 t.GetDatabaseTransaction().ExecuteMultiLines("CREATE TABLE ServerProperties(server VARCHAR(64) NOT NULL, "
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287 "property INTEGER, value LONGTEXT, PRIMARY KEY(server, property))");
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288 }
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289
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290 // Revision 6 indicates that "value" of "ServerProperties" is
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291 // "LONGTEXT", whereas revision 5 corresponds to "TEXT"
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292 revision = 6;
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293 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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294
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295 t.Commit();
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296 }
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297
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298 if (revision != 6)
0
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299 {
53
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300 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision;
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301 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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302 }
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303 }
137
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304
238
f033cc039264 new table: "ServerProperties"
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305
137
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306 /**
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307 * WARNING: This lock must be acquired after
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308 * "MYSQL_LOCK_DATABASE_SETUP" is released. Indeed, in MySQL <
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309 * 5.7, it is impossible to acquire more than one lock at a time,
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310 * as calling "SELECT GET_LOCK()" releases all the
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311 * previously-acquired locks.
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312 * https://dev.mysql.com/doc/refman/5.7/en/locking-functions.html
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313 **/
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314 if (parameters_.HasLock())
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315 {
226
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316 db.AdvisoryLock(MYSQL_LOCK_INDEX);
137
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317 }
0
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318 }
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319
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320
225
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321 int64_t MySQLIndex::CreateResource(DatabaseManager& manager,
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322 const char* publicId,
0
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323 OrthancPluginResourceType type)
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324 {
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325 {
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326 DatabaseManager::CachedStatement statement(
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327 STATEMENT_FROM_HERE, manager,
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328 "INSERT INTO Resources VALUES(NULL, ${type}, ${id}, NULL)");
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329
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330 statement.SetParameterType("id", ValueType_Utf8String);
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331 statement.SetParameterType("type", ValueType_Integer64);
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332
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333 Dictionary args;
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334 args.SetUtf8Value("id", publicId);
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335 args.SetIntegerValue("type", static_cast<int>(type));
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336
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337 statement.Execute(args);
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338 }
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339
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340 {
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341 DatabaseManager::CachedStatement statement(
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342 STATEMENT_FROM_HERE, manager,
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343 "SELECT LAST_INSERT_ID()");
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344
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345 statement.Execute();
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346
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347 return statement.ReadInteger64(0);
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348 }
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349 }
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350
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351
203
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352 void MySQLIndex::DeleteResource(IDatabaseBackendOutput& output,
225
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353 DatabaseManager& manager,
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354 int64_t id)
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355 {
305
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356 /**
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357 * Contrarily to PostgreSQL and SQLite, the MySQL dialect doesn't
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358 * support cascaded delete inside the same table. This has to be
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359 * manually reimplemented.
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360 **/
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361
225
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362 ClearDeletedFiles(manager);
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363
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364 // Recursive exploration of resources to be deleted, from the "id"
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365 // resource to the top of the tree of resources
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366
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367 bool done = false;
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368
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369 while (!done)
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370 {
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371 bool hasSibling = false;
321
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372 int64_t parentId = -1; // Dummy initialization
307
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373
0
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374 {
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375 DatabaseManager::CachedStatement lookupSiblings(
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376 STATEMENT_FROM_HERE, manager,
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377 "SELECT parentId FROM Resources "
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378 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});");
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379
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380 lookupSiblings.SetParameterType("id", ValueType_Integer64);
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381
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382 Dictionary args;
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383 args.SetIntegerValue("id", id);
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384
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385 lookupSiblings.Execute(args);
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386
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387 if (lookupSiblings.IsDone())
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388 {
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389 // "id" is a root node
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390 done = true;
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391 }
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392 else
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393 {
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394 parentId = lookupSiblings.ReadInteger64(0);
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395 lookupSiblings.Next();
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396
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397 if (lookupSiblings.IsDone())
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398 {
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399 // "id" has no sibling node, recursively remove
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400 done = false;
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401 id = parentId;
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402 }
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403 else
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404 {
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405 // "id" has at least one sibling node: the parent node is the remaining ancestor
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406 done = true;
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407 hasSibling = true;
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408 }
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409 }
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410 }
307
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411
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412 if (hasSibling)
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413 {
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414 // This cannot be executed in the same scope as another
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415 // DatabaseManager::CachedStatement
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416
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417 DatabaseManager::CachedStatement parent(
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418 STATEMENT_FROM_HERE, manager,
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419 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};");
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420
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421 parent.SetParameterType("id", ValueType_Integer64);
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422
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423 Dictionary args2;
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424 args2.SetIntegerValue("id", parentId);
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425
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426 parent.Execute(args2);
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427
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428 output.SignalRemainingAncestor(
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429 parent.ReadString(0),
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430 static_cast<OrthancPluginResourceType>(parent.ReadInteger32(1)));
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431 }
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432 }
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433
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434 {
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435 DatabaseManager::CachedStatement dropTemporaryTable(
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436 STATEMENT_FROM_HERE, manager,
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437 "DROP TEMPORARY TABLE IF EXISTS DeletedResources");
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438 dropTemporaryTable.Execute();
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439 }
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440
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441 {
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442 DatabaseManager::CachedStatement lookupResourcesToDelete(
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443 STATEMENT_FROM_HERE, manager,
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444 "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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445 lookupResourcesToDelete.SetParameterType("id", ValueType_Integer64);
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446
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447 Dictionary args;
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448 args.SetIntegerValue("id", id);
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449 lookupResourcesToDelete.Execute(args);
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450 }
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451
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452 {
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453 DatabaseManager::CachedStatement deleteHierarchy(
225
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454 STATEMENT_FROM_HERE, manager,
307
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455 "DELETE FROM Resources WHERE internalId IN (SELECT internalId FROM DeletedResources)");
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456 deleteHierarchy.Execute();
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457 }
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458
307
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459 SignalDeletedResources(output, manager);
225
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460 SignalDeletedFiles(output, manager);
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461 }
87
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462
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463
225
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464 int64_t MySQLIndex::GetLastChangeIndex(DatabaseManager& manager)
87
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465 {
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466 DatabaseManager::CachedStatement statement(
225
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467 STATEMENT_FROM_HERE, manager,
87
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468 "SELECT value FROM GlobalIntegers WHERE property = 0");
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469
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470 statement.SetReadOnly(true);
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471 statement.Execute();
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472
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473 return statement.ReadInteger64(0);
87
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474 }
110
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475
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476
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477 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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478 void MySQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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479 DatabaseManager& manager,
110
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480 const char* hashPatient,
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481 const char* hashStudy,
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482 const char* hashSeries,
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483 const char* hashInstance)
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484 {
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485 {
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486 DatabaseManager::CachedStatement statement(
225
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487 STATEMENT_FROM_HERE, manager,
110
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diff changeset
488 "CALL CreateInstance(${patient}, ${study}, ${series}, ${instance}, "
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489 "@isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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diff changeset
490 "@patientKey, @studyKey, @seriesKey, @instanceKey)");
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diff changeset
491
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492 statement.SetParameterType("patient", ValueType_Utf8String);
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493 statement.SetParameterType("study", ValueType_Utf8String);
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494 statement.SetParameterType("series", ValueType_Utf8String);
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495 statement.SetParameterType("instance", ValueType_Utf8String);
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diff changeset
496
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diff changeset
497 Dictionary args;
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498 args.SetUtf8Value("patient", hashPatient);
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499 args.SetUtf8Value("study", hashStudy);
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500 args.SetUtf8Value("series", hashSeries);
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501 args.SetUtf8Value("instance", hashInstance);
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diff changeset
502
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diff changeset
503 statement.Execute(args);
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diff changeset
504
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diff changeset
505 if (!statement.IsDone())
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506 {
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507 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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508 }
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diff changeset
509 }
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diff changeset
510
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diff changeset
511 {
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512 DatabaseManager::CachedStatement statement(
225
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513 STATEMENT_FROM_HERE, manager,
110
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514 "SELECT @isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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diff changeset
515 "@patientKey, @studyKey, @seriesKey, @instanceKey");
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diff changeset
516
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diff changeset
517 statement.Execute();
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diff changeset
518
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diff changeset
519 for (size_t i = 0; i < 8; i++)
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diff changeset
520 {
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diff changeset
521 statement.SetResultFieldType(i, ValueType_Integer64);
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diff changeset
522 }
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diff changeset
523
263
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524 result.isNewInstance = (statement.ReadInteger64(3) == 1);
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525 result.instanceId = statement.ReadInteger64(7);
110
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diff changeset
526
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diff changeset
527 if (result.isNewInstance)
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528 {
263
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529 result.isNewPatient = (statement.ReadInteger64(0) == 1);
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530 result.isNewStudy = (statement.ReadInteger64(1) == 1);
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531 result.isNewSeries = (statement.ReadInteger64(2) == 1);
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532 result.patientId = statement.ReadInteger64(4);
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533 result.studyId = statement.ReadInteger64(5);
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534 result.seriesId = statement.ReadInteger64(6);
110
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535 }
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536 }
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537 }
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538 #endif
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539 }