Mercurial > hg > orthanc-databases

annotate MySQL/Plugins/MySQLIndex.cpp @ 226:a4918d57435c

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DatabaseManager doesn't IDatabaseFactory anymore
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 02 Apr 2021 19:23:36 +0200
parents 94c9908e6aca
children d1b124d116c1
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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 db.Execute("SET SESSION TRANSACTION ISOLATION LEVEL SERIALIZABLE", false);
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97 {
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98 MySQLDatabase::TransientAdvisoryLock lock(db, MYSQL_LOCK_DATABASE_SETUP);
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100 /**
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101 * In a first transaction, we create the tables. Such a
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102 * transaction cannot be rollback: "The CREATE TABLE statement
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103 * in InnoDB is processed as a single transaction. This means
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104 * that a ROLLBACK from the user does not undo CREATE TABLE
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105 * statements the user made during that transaction."
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106 * https://dev.mysql.com/doc/refman/8.0/en/implicit-commit.html
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107 *
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108 * As a consequence, we delay the initial population of the
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109 * tables in a sequence of transactions below. This solves the
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110 * error message "MySQL plugin is incompatible with database
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111 * schema version: 0" that was reported in the forum:
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112 * https://groups.google.com/d/msg/orthanc-users/OCFFkm1qm0k/Mbroy8VWAQAJ
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113 **/
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114 {
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115 MySQLTransaction t(db, TransactionType_ReadWrite);
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117 db.Execute("ALTER DATABASE " + parameters_.GetDatabase() +
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118 " CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci", false);
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119
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120 // This is the first table to be created
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121 if (!db.DoesTableExist(t, "GlobalProperties"))
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122 {
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123 std::string query;
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124
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125 Orthanc::EmbeddedResources::GetFileResource
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126 (query, Orthanc::EmbeddedResources::MYSQL_PREPARE_INDEX);
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127 db.Execute(query, true);
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128 }
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129
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130 t.Commit();
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131 }
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132
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133 /**
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134 * This is the sequence of transactions that initially populate
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135 * the database. WARNING - As table creation cannot be rollback,
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136 * don't forget to add "IF NOT EXISTS" if some table must be
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137 * created below this point (in order to recover from failed
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138 * transaction).
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139 **/
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140
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141 int version = 0;
144
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142
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143 {
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144 MySQLTransaction t(db, TransactionType_ReadWrite);
144
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145
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146 // This is the last table to be created
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147 if (!db.DoesTableExist(t, "PatientRecyclingOrder"))
144
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148 {
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149 LOG(ERROR) << "Corrupted MySQL database";
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150 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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151 }
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152
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153 // This is the last item to be created
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154 if (!db.DoesTriggerExist(t, "PatientAdded"))
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155 {
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156 ThrowCannotCreateTrigger();
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157 }
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158
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159 if (!LookupGlobalIntegerProperty(version, db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion))
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160 {
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161 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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162 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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163 version = expectedVersion;
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164 }
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165
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166 if (version != 6)
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167 {
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168 LOG(ERROR) << "MySQL plugin is incompatible with database schema version: " << version;
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169 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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170 }
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171
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172 t.Commit();
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173 }
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174
144
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175 int revision = 0;
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176
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177 {
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178 MySQLTransaction t(db, TransactionType_ReadWrite);
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179
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180 if (!LookupGlobalIntegerProperty(revision, db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel))
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181 {
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182 revision = 1;
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183 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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184 }
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185
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186 t.Commit();
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187 }
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188
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189 if (revision == 1)
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190 {
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191 MySQLTransaction t(db, TransactionType_ReadWrite);
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192
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193 // The serialization of jobs as a global property can lead to
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194 // very long values => switch to the LONGTEXT type that can
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195 // store up to 4GB:
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196 // https://stackoverflow.com/a/13932834/881731
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197 db.Execute("ALTER TABLE GlobalProperties MODIFY value LONGTEXT", false);
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198
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199 revision = 2;
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200 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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201
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202 t.Commit();
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203 }
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204
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205 if (revision == 2)
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206 {
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207 MySQLTransaction t(db, TransactionType_ReadWrite);
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208
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209 // Install the "GetLastChangeIndex" extension
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210 std::string query;
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211
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212 Orthanc::EmbeddedResources::GetFileResource
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213 (query, Orthanc::EmbeddedResources::MYSQL_GET_LAST_CHANGE_INDEX);
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214 db.Execute(query, true);
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215
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216 if (!db.DoesTriggerExist(t, "ChangeAdded"))
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217 {
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218 ThrowCannotCreateTrigger();
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219 }
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220
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221 revision = 3;
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222 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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223
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224 t.Commit();
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225 }
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226
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227 if (revision == 3)
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228 {
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229 MySQLTransaction t(db, TransactionType_ReadWrite);
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230
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231 // Reconfiguration of "Metadata" from TEXT type (up to 64KB)
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232 // to the LONGTEXT type (up to 4GB). This might be important
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233 // for applications such as the Osimis Web viewer that stores
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234 // large amount of metadata.
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235 // http://book.orthanc-server.com/faq/features.html#central-registry-of-metadata-and-attachments
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236 db.Execute("ALTER TABLE Metadata MODIFY value LONGTEXT", false);
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237
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238 revision = 4;
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239 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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240
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241 t.Commit();
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242 }
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243
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244 if (revision == 4)
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245 {
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246 MySQLTransaction t(db, TransactionType_ReadWrite);
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247
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248 // Install the "CreateInstance" extension
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249 std::string query;
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250
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251 Orthanc::EmbeddedResources::GetFileResource
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252 (query, Orthanc::EmbeddedResources::MYSQL_CREATE_INSTANCE);
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253 db.Execute(query, true);
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254
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255 revision = 5;
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256 SetGlobalIntegerProperty(db, t, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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257
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258 t.Commit();
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259 }
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260
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261 if (revision != 5)
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262 {
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263 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision;
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264 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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265 }
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266 }
137
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267
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268 /**
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269 * WARNING: This lock must be acquired after
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270 * "MYSQL_LOCK_DATABASE_SETUP" is released. Indeed, in MySQL <
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271 * 5.7, it is impossible to acquire more than one lock at a time,
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272 * as calling "SELECT GET_LOCK()" releases all the
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273 * previously-acquired locks.
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274 * https://dev.mysql.com/doc/refman/5.7/en/locking-functions.html
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275 **/
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276 if (parameters_.HasLock())
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277 {
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278 db.AdvisoryLock(MYSQL_LOCK_INDEX);
137
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279 }
0
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280 }
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281
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282
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283 int64_t MySQLIndex::CreateResource(DatabaseManager& manager,
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284 const char* publicId,
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285 OrthancPluginResourceType type)
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286 {
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287 {
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288 DatabaseManager::CachedStatement statement(
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289 STATEMENT_FROM_HERE, manager,
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290 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL)");
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291
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292 statement.SetParameterType("id", ValueType_Utf8String);
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293 statement.SetParameterType("type", ValueType_Integer64);
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294
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295 Dictionary args;
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296 args.SetUtf8Value("id", publicId);
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297 args.SetIntegerValue("type", static_cast<int>(type));
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298
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299 statement.Execute(args);
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300 }
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301
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302 {
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303 DatabaseManager::CachedStatement statement(
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304 STATEMENT_FROM_HERE, manager,
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305 "SELECT LAST_INSERT_ID()");
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306
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307 statement.Execute();
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308
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309 return ReadInteger64(statement, 0);
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310 }
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311 }
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312
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313
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314 void MySQLIndex::DeleteResource(IDatabaseBackendOutput& output,
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315 DatabaseManager& manager,
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316 int64_t id)
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317 {
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318 ClearDeletedFiles(manager);
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319
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320 // Recursive exploration of resources to be deleted, from the "id"
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321 // resource to the top of the tree of resources
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322
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323 bool done = false;
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324
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325 while (!done)
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326 {
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327 int64_t parentId;
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328
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329 {
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330 DatabaseManager::CachedStatement lookupSiblings(
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331 STATEMENT_FROM_HERE, manager,
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332 "SELECT parentId FROM Resources "
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333 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});");
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334
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335 lookupSiblings.SetParameterType("id", ValueType_Integer64);
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336
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337 Dictionary args;
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338 args.SetIntegerValue("id", id);
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339
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340 lookupSiblings.Execute(args);
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341
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342 if (lookupSiblings.IsDone())
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343 {
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344 // "id" is a root node
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345 done = true;
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346 }
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347 else
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348 {
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349 parentId = ReadInteger64(lookupSiblings, 0);
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350 lookupSiblings.Next();
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351
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352 if (lookupSiblings.IsDone())
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353 {
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354 // "id" has no sibling node, recursively remove
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355 done = false;
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356 id = parentId;
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357 }
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358 else
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359 {
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360 // "id" has at least one sibling node: the parent node is the remaining ancestor
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361 done = true;
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362
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363 DatabaseManager::CachedStatement parent(
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364 STATEMENT_FROM_HERE, manager,
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365 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};");
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366
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367 parent.SetParameterType("id", ValueType_Integer64);
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368
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369 Dictionary args;
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370 args.SetIntegerValue("id", parentId);
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371
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372 parent.Execute(args);
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373
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374 output.SignalRemainingAncestor(
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375 ReadString(parent, 0),
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376 static_cast<OrthancPluginResourceType>(ReadInteger32(parent, 1)));
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377 }
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378 }
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379 }
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380 }
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381
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382 {
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383 DatabaseManager::CachedStatement deleteHierarchy(
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384 STATEMENT_FROM_HERE, manager,
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385 "DELETE FROM Resources WHERE internalId IN (SELECT * FROM (SELECT internalId FROM Resources WHERE internalId=${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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386
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387 deleteHierarchy.SetParameterType("id", ValueType_Integer64);
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388
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389 Dictionary args;
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390 args.SetIntegerValue("id", id);
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391
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392 deleteHierarchy.Execute(args);
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393 }
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394
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395 SignalDeletedFiles(output, manager);
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396 }
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397
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398
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399 int64_t MySQLIndex::GetLastChangeIndex(DatabaseManager& manager)
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400 {
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401 DatabaseManager::CachedStatement statement(
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402 STATEMENT_FROM_HERE, manager,
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403 "SELECT value FROM GlobalIntegers WHERE property = 0");
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404
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405 statement.SetReadOnly(true);
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406 statement.Execute();
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407
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408 return ReadInteger64(statement, 0);
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409 }
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410
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411
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412 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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413 void MySQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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414 DatabaseManager& manager,
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415 const char* hashPatient,
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416 const char* hashStudy,
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417 const char* hashSeries,
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418 const char* hashInstance)
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419 {
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420 {
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421 DatabaseManager::CachedStatement statement(
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422 STATEMENT_FROM_HERE, manager,
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423 "CALL CreateInstance(${patient}, ${study}, ${series}, ${instance}, "
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424 "@isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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425 "@patientKey, @studyKey, @seriesKey, @instanceKey)");
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426
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427 statement.SetParameterType("patient", ValueType_Utf8String);
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428 statement.SetParameterType("study", ValueType_Utf8String);
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429 statement.SetParameterType("series", ValueType_Utf8String);
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430 statement.SetParameterType("instance", ValueType_Utf8String);
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431
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432 Dictionary args;
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433 args.SetUtf8Value("patient", hashPatient);
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434 args.SetUtf8Value("study", hashStudy);
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435 args.SetUtf8Value("series", hashSeries);
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436 args.SetUtf8Value("instance", hashInstance);
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437
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438 statement.Execute(args);
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439
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440 if (!statement.IsDone())
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441 {
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442 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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443 }
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444 }
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445
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446 {
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447 DatabaseManager::CachedStatement statement(
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448 STATEMENT_FROM_HERE, manager,
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449 "SELECT @isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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450 "@patientKey, @studyKey, @seriesKey, @instanceKey");
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451
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452 statement.Execute();
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453
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454 for (size_t i = 0; i < 8; i++)
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455 {
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456 statement.SetResultFieldType(i, ValueType_Integer64);
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457 }
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458
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459 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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460 result.instanceId = ReadInteger64(statement, 7);
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461
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462 if (result.isNewInstance)
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463 {
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464 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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465 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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466 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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467 result.patientId = ReadInteger64(statement, 4);
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468 result.studyId = ReadInteger64(statement, 5);
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469 result.seriesId = ReadInteger64(statement, 6);
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470 }
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471 }
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472 }
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473 #endif
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474 }