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annotate MySQL/Plugins/MySQLIndex.cpp @ 234:d1b124d116c1

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PostgreSQL index plugin handles retries for collisions between multiple writers
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 08 Apr 2021 10:50:01 +0200
parents a4918d57435c
children 35598014f140
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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) 2017-2021 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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20
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21
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22 #include "MySQLIndex.h"
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23
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24 #include "../../Framework/Plugins/GlobalProperties.h"
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25 #include "../../Framework/MySQL/MySQLDatabase.h"
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26 #include "../../Framework/MySQL/MySQLTransaction.h"
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27 #include "MySQLDefinitions.h"
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28
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29 #include <EmbeddedResources.h> // Auto-generated file
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30
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31 #include <Compatibility.h> // For std::unique_ptr<>
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32 #include <Logging.h>
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33 #include <OrthancException.h>
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34
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35 #include <ctype.h>
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36
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37 namespace OrthancDatabases
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38 {
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39 MySQLIndex::MySQLIndex(OrthancPluginContext* context,
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40 const MySQLParameters& parameters) :
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41 IndexBackend(context),
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42 parameters_(parameters),
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43 clearAll_(false)
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44 {
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45 }
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47
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48 IDatabase* MySQLIndex::OpenDatabaseConnection()
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49 {
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50 return MySQLDatabase::OpenDatabaseConnection(parameters_);
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51 }
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53
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54 static void ThrowCannotCreateTrigger()
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55 {
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56 LOG(ERROR) << "The MySQL user is not allowed to create triggers => 2 possible solutions:";
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57 LOG(ERROR) << " 1- Give the SUPER privilege to the MySQL database user, or";
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58 LOG(ERROR) << " 2- Run \"set global log_bin_trust_function_creators=1;\" as MySQL root user.";
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59 LOG(ERROR) << "Once you are done, drop and recreate the MySQL database";
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60 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database,
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61 "Need to fix the MySQL permissions for \"CREATE TRIGGER\"");
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62 }
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64
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65 void MySQLIndex::ConfigureDatabase(IDatabase& database)
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66 {
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67 MySQLDatabase& db = dynamic_cast<MySQLDatabase&>(database);
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68
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69 uint32_t expectedVersion = 6;
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70
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71 if (GetContext()) // "GetContext()" can possibly be NULL in the unit tests
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72 {
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73 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(GetContext());
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74 }
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75
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76 // Check the expected version of the database
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77 if (expectedVersion != 6)
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78 {
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79 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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80 << "expecting the DB schema version " << expectedVersion
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81 << ", but this plugin is only compatible with version 6";
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82 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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83 }
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84
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85 if (!MySQLDatabase::IsValidDatabaseIdentifier(parameters_.GetDatabase()))
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86 {
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87 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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88 }
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89
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90 if (clearAll_)
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91 {
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92 MySQLDatabase::ClearDatabase(parameters_);
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93 }
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94
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95 {
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96 MySQLDatabase::TransientAdvisoryLock lock(db, MYSQL_LOCK_DATABASE_SETUP);
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98 /**
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99 * In a first transaction, we create the tables. Such a
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100 * transaction cannot be rollback: "The CREATE TABLE statement
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101 * in InnoDB is processed as a single transaction. This means
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102 * that a ROLLBACK from the user does not undo CREATE TABLE
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103 * statements the user made during that transaction."
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104 * https://dev.mysql.com/doc/refman/8.0/en/implicit-commit.html
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105 *
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106 * As a consequence, we delay the initial population of the
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107 * tables in a sequence of transactions below. This solves the
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108 * error message "MySQL plugin is incompatible with database
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109 * schema version: 0" that was reported in the forum:
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110 * https://groups.google.com/d/msg/orthanc-users/OCFFkm1qm0k/Mbroy8VWAQAJ
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111 **/
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112 {
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113 MySQLTransaction t(db, TransactionType_ReadWrite);
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114
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115 db.Execute("ALTER DATABASE " + parameters_.GetDatabase() +
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116 " CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci", false);
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118 // This is the first table to be created
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119 if (!db.DoesTableExist(t, "GlobalProperties"))
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120 {
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121 std::string query;
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122
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123 Orthanc::EmbeddedResources::GetFileResource
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124 (query, Orthanc::EmbeddedResources::MYSQL_PREPARE_INDEX);
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125 db.Execute(query, true);
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126 }
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127
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128 t.Commit();
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129 }
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130
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131 /**
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132 * This is the sequence of transactions that initially populate
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133 * the database. WARNING - As table creation cannot be rollback,
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134 * don't forget to add "IF NOT EXISTS" if some table must be
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135 * created below this point (in order to recover from failed
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136 * transaction).
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137 **/
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138
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139 int version = 0;
144
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140
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141 {
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142 MySQLTransaction t(db, TransactionType_ReadWrite);
144
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143
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144 // This is the last table to be created
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145 if (!db.DoesTableExist(t, "PatientRecyclingOrder"))
144
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146 {
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147 LOG(ERROR) << "Corrupted MySQL database";
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148 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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149 }
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150
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151 // This is the last item to be created
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152 if (!db.DoesTriggerExist(t, "PatientAdded"))
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153 {
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154 ThrowCannotCreateTrigger();
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155 }
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156
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157 if (!LookupGlobalIntegerProperty(version, db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion))
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158 {
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159 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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160 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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161 version = expectedVersion;
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162 }
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163
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164 if (version != 6)
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165 {
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166 LOG(ERROR) << "MySQL plugin is incompatible with database schema version: " << version;
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167 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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168 }
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169
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170 t.Commit();
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171 }
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172
144
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173 int revision = 0;
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174
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175 {
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176 MySQLTransaction t(db, TransactionType_ReadWrite);
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177
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178 if (!LookupGlobalIntegerProperty(revision, db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel))
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179 {
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180 revision = 1;
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181 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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182 }
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183
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184 t.Commit();
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185 }
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186
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187 if (revision == 1)
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188 {
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189 MySQLTransaction t(db, TransactionType_ReadWrite);
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190
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191 // The serialization of jobs as a global property can lead to
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192 // very long values => switch to the LONGTEXT type that can
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193 // store up to 4GB:
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194 // https://stackoverflow.com/a/13932834/881731
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195 db.Execute("ALTER TABLE GlobalProperties MODIFY value LONGTEXT", false);
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196
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197 revision = 2;
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198 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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199
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200 t.Commit();
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201 }
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202
87
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203 if (revision == 2)
144
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204 {
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205 MySQLTransaction t(db, TransactionType_ReadWrite);
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206
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207 // Install the "GetLastChangeIndex" extension
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208 std::string query;
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209
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210 Orthanc::EmbeddedResources::GetFileResource
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211 (query, Orthanc::EmbeddedResources::MYSQL_GET_LAST_CHANGE_INDEX);
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212 db.Execute(query, true);
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213
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214 if (!db.DoesTriggerExist(t, "ChangeAdded"))
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215 {
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216 ThrowCannotCreateTrigger();
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217 }
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218
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219 revision = 3;
226
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220 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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221
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222 t.Commit();
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223 }
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224
109
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225 if (revision == 3)
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226 {
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227 MySQLTransaction t(db, TransactionType_ReadWrite);
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228
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229 // Reconfiguration of "Metadata" from TEXT type (up to 64KB)
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230 // to the LONGTEXT type (up to 4GB). This might be important
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231 // for applications such as the Osimis Web viewer that stores
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232 // large amount of metadata.
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233 // http://book.orthanc-server.com/faq/features.html#central-registry-of-metadata-and-attachments
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234 db.Execute("ALTER TABLE Metadata MODIFY value LONGTEXT", false);
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235
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236 revision = 4;
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237 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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238
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239 t.Commit();
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240 }
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241
110
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242 if (revision == 4)
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243 {
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244 MySQLTransaction t(db, TransactionType_ReadWrite);
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245
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246 // Install the "CreateInstance" extension
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247 std::string query;
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248
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249 Orthanc::EmbeddedResources::GetFileResource
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250 (query, Orthanc::EmbeddedResources::MYSQL_CREATE_INSTANCE);
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251 db.Execute(query, true);
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252
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253 revision = 5;
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254 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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255
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256 t.Commit();
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257 }
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258
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259 if (revision != 5)
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260 {
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261 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision;
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262 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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263 }
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264 }
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265
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266 /**
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267 * WARNING: This lock must be acquired after
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268 * "MYSQL_LOCK_DATABASE_SETUP" is released. Indeed, in MySQL <
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269 * 5.7, it is impossible to acquire more than one lock at a time,
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270 * as calling "SELECT GET_LOCK()" releases all the
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271 * previously-acquired locks.
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272 * https://dev.mysql.com/doc/refman/5.7/en/locking-functions.html
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273 **/
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274 if (parameters_.HasLock())
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275 {
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276 db.AdvisoryLock(MYSQL_LOCK_INDEX);
137
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277 }
0
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278 }
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279
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280
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281 int64_t MySQLIndex::CreateResource(DatabaseManager& manager,
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282 const char* publicId,
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283 OrthancPluginResourceType type)
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284 {
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285 {
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286 DatabaseManager::CachedStatement statement(
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287 STATEMENT_FROM_HERE, manager,
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288 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL)");
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289
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290 statement.SetParameterType("id", ValueType_Utf8String);
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291 statement.SetParameterType("type", ValueType_Integer64);
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292
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293 Dictionary args;
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294 args.SetUtf8Value("id", publicId);
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295 args.SetIntegerValue("type", static_cast<int>(type));
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296
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297 statement.Execute(args);
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298 }
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299
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300 {
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301 DatabaseManager::CachedStatement statement(
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302 STATEMENT_FROM_HERE, manager,
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303 "SELECT LAST_INSERT_ID()");
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304
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305 statement.Execute();
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306
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307 return ReadInteger64(statement, 0);
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308 }
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309 }
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310
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311
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312 void MySQLIndex::DeleteResource(IDatabaseBackendOutput& output,
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313 DatabaseManager& manager,
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314 int64_t id)
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315 {
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316 ClearDeletedFiles(manager);
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317
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318 // Recursive exploration of resources to be deleted, from the "id"
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319 // resource to the top of the tree of resources
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320
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321 bool done = false;
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322
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323 while (!done)
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324 {
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325 int64_t parentId;
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326
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327 {
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328 DatabaseManager::CachedStatement lookupSiblings(
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329 STATEMENT_FROM_HERE, manager,
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330 "SELECT parentId FROM Resources "
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331 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});");
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332
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333 lookupSiblings.SetParameterType("id", ValueType_Integer64);
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334
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335 Dictionary args;
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336 args.SetIntegerValue("id", id);
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337
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338 lookupSiblings.Execute(args);
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339
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340 if (lookupSiblings.IsDone())
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341 {
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342 // "id" is a root node
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343 done = true;
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344 }
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345 else
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346 {
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347 parentId = ReadInteger64(lookupSiblings, 0);
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348 lookupSiblings.Next();
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349
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350 if (lookupSiblings.IsDone())
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351 {
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352 // "id" has no sibling node, recursively remove
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353 done = false;
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354 id = parentId;
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355 }
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356 else
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357 {
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358 // "id" has at least one sibling node: the parent node is the remaining ancestor
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359 done = true;
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360
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361 DatabaseManager::CachedStatement parent(
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362 STATEMENT_FROM_HERE, manager,
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363 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};");
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364
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365 parent.SetParameterType("id", ValueType_Integer64);
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366
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367 Dictionary args;
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368 args.SetIntegerValue("id", parentId);
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369
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370 parent.Execute(args);
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371
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372 output.SignalRemainingAncestor(
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373 ReadString(parent, 0),
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374 static_cast<OrthancPluginResourceType>(ReadInteger32(parent, 1)));
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375 }
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376 }
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377 }
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378 }
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379
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380 {
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381 DatabaseManager::CachedStatement deleteHierarchy(
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382 STATEMENT_FROM_HERE, manager,
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383 "DELETE FROM Resources WHERE internalId IN (SELECT * FROM (SELECT internalId FROM Resources WHERE internalId=${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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384
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385 deleteHierarchy.SetParameterType("id", ValueType_Integer64);
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386
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387 Dictionary args;
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388 args.SetIntegerValue("id", id);
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389
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390 deleteHierarchy.Execute(args);
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391 }
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392
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393 SignalDeletedFiles(output, manager);
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394 }
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395
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396
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397 int64_t MySQLIndex::GetLastChangeIndex(DatabaseManager& manager)
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398 {
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399 DatabaseManager::CachedStatement statement(
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400 STATEMENT_FROM_HERE, manager,
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401 "SELECT value FROM GlobalIntegers WHERE property = 0");
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402
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403 statement.SetReadOnly(true);
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404 statement.Execute();
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405
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406 return ReadInteger64(statement, 0);
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407 }
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408
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409
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410 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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411 void MySQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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412 DatabaseManager& manager,
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413 const char* hashPatient,
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414 const char* hashStudy,
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415 const char* hashSeries,
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416 const char* hashInstance)
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417 {
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418 {
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419 DatabaseManager::CachedStatement statement(
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420 STATEMENT_FROM_HERE, manager,
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421 "CALL CreateInstance(${patient}, ${study}, ${series}, ${instance}, "
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422 "@isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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423 "@patientKey, @studyKey, @seriesKey, @instanceKey)");
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424
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425 statement.SetParameterType("patient", ValueType_Utf8String);
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426 statement.SetParameterType("study", ValueType_Utf8String);
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427 statement.SetParameterType("series", ValueType_Utf8String);
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428 statement.SetParameterType("instance", ValueType_Utf8String);
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429
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430 Dictionary args;
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431 args.SetUtf8Value("patient", hashPatient);
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432 args.SetUtf8Value("study", hashStudy);
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433 args.SetUtf8Value("series", hashSeries);
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434 args.SetUtf8Value("instance", hashInstance);
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435
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436 statement.Execute(args);
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437
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438 if (!statement.IsDone())
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439 {
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440 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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441 }
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442 }
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443
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444 {
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445 DatabaseManager::CachedStatement statement(
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446 STATEMENT_FROM_HERE, manager,
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447 "SELECT @isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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448 "@patientKey, @studyKey, @seriesKey, @instanceKey");
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449
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450 statement.Execute();
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451
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452 for (size_t i = 0; i < 8; i++)
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453 {
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454 statement.SetResultFieldType(i, ValueType_Integer64);
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455 }
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456
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457 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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458 result.instanceId = ReadInteger64(statement, 7);
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459
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460 if (result.isNewInstance)
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461 {
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462 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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463 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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464 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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465 result.patientId = ReadInteger64(statement, 4);
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466 result.studyId = ReadInteger64(statement, 5);
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467 result.seriesId = ReadInteger64(statement, 6);
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468 }
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469 }
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470 }
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471 #endif
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472 }