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annotate MySQL/Plugins/MySQLIndex.cpp @ 152:063aa53b5917

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 01 Jul 2020 08:54:32 +0200
parents 740d9829f52e
children 275e14f57f1e
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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) 2017-2020 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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29 #include <EmbeddedResources.h> // Auto-generated file
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30
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31 #include <Logging.h>
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32 #include <OrthancException.h>
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33
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34 #include <ctype.h>
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35
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36 namespace OrthancDatabases
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37 {
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38 static void ThrowCannotCreateTrigger()
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39 {
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40 LOG(ERROR) << "The MySQL user is not allowed to create triggers => 2 possible solutions:";
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41 LOG(ERROR) << " 1- Give the SUPER privilege to the MySQL database user, or";
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42 LOG(ERROR) << " 2- Run \"set global log_bin_trust_function_creators=1;\" as MySQL root user.";
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43 LOG(ERROR) << "Once you are done, drop and recreate the MySQL database";
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44 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database,
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45 "Need to fix the MySQL permissions for \"CREATE TRIGGER\"");
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46 }
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47
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48 IDatabase* MySQLIndex::OpenInternal()
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49 {
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50 uint32_t expectedVersion = 6;
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51 if (context_)
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52 {
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53 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(context_);
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54 }
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55 else
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56 {
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57 // This case only occurs during unit testing
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58 expectedVersion = 6;
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59 }
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60
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61 // Check the expected version of the database
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62 if (expectedVersion != 6)
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63 {
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64 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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65 << "expecting the DB schema version " << expectedVersion
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66 << ", but this plugin is only compatible with version 6";
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67 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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68 }
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70 if (!MySQLDatabase::IsValidDatabaseIdentifier(parameters_.GetDatabase()))
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71 {
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72 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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73 }
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74
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75 if (clearAll_)
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76 {
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77 MySQLDatabase::ClearDatabase(parameters_);
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78 }
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79
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80 std::auto_ptr<MySQLDatabase> db(new MySQLDatabase(parameters_));
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81
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82 db->Open();
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83 db->Execute("SET SESSION TRANSACTION ISOLATION LEVEL SERIALIZABLE", false);
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85 {
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86 MySQLDatabase::TransientAdvisoryLock lock(*db, MYSQL_LOCK_DATABASE_SETUP);
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88 /**
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89 * In a first transaction, we create the tables. Such a
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90 * transaction cannot be rollback: "The CREATE TABLE statement
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91 * in InnoDB is processed as a single transaction. This means
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92 * that a ROLLBACK from the user does not undo CREATE TABLE
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93 * statements the user made during that transaction."
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94 * https://dev.mysql.com/doc/refman/8.0/en/implicit-commit.html
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95 *
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96 * As a consequence, we delay the initial population of the
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97 * tables in a sequence of transactions below. This solves the
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98 * error message "MySQL plugin is incompatible with database
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99 * schema version: 0" that was reported in the forum:
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100 * https://groups.google.com/d/msg/orthanc-users/OCFFkm1qm0k/Mbroy8VWAQAJ
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101 **/
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102 {
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103 MySQLTransaction t(*db);
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104
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105 db->Execute("ALTER DATABASE " + parameters_.GetDatabase() +
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106 " CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci", false);
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107
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108 // This is the first table to be created
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109 if (!db->DoesTableExist(t, "GlobalProperties"))
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110 {
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111 std::string query;
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112
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113 Orthanc::EmbeddedResources::GetFileResource
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114 (query, Orthanc::EmbeddedResources::MYSQL_PREPARE_INDEX);
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115 db->Execute(query, true);
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116 }
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117
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118 t.Commit();
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119 }
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120
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121 /**
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122 * This is the sequence of transactions that initially populate
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123 * the database. WARNING - As table creation cannot be rollback,
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124 * don't forget to add "IF NOT EXISTS" if some table must be
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125 * created below this point (in order to recover from failed
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126 * transaction).
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127 **/
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128
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129 int version = 0;
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130
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131 {
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132 MySQLTransaction t(*db);
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133
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134 // This is the last table to be created
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135 if (!db->DoesTableExist(t, "PatientRecyclingOrder"))
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136 {
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137 LOG(ERROR) << "Corrupted MySQL database";
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138 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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139 }
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140
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141 // This is the last item to be created
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142 if (!db->DoesTriggerExist(t, "PatientAdded"))
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143 {
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144 ThrowCannotCreateTrigger();
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145 }
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146
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147 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion))
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148 {
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149 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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150 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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151 version = expectedVersion;
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152 }
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153
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154 if (version != 6)
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155 {
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156 LOG(ERROR) << "MySQL plugin is incompatible with database schema version: " << version;
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157 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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158 }
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159
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160 t.Commit();
0
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161 }
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162
144
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163 int revision = 0;
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164
0
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165 {
144
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166 MySQLTransaction t(*db);
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167
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168 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel))
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169 {
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170 revision = 1;
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171 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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172 }
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173
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174 t.Commit();
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175 }
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176
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177 if (revision == 1)
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178 {
144
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179 MySQLTransaction t(*db);
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180
84
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181 // The serialization of jobs as a global property can lead to
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182 // very long values => switch to the LONGTEXT type that can
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183 // store up to 4GB:
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184 // https://stackoverflow.com/a/13932834/881731
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185 db->Execute("ALTER TABLE GlobalProperties MODIFY value LONGTEXT", false);
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186
84
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187 revision = 2;
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188 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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189
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190 t.Commit();
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191 }
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192
87
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193 if (revision == 2)
144
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194 {
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195 MySQLTransaction t(*db);
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196
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197 // Install the "GetLastChangeIndex" extension
87
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198 std::string query;
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199
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200 Orthanc::EmbeddedResources::GetFileResource
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201 (query, Orthanc::EmbeddedResources::MYSQL_GET_LAST_CHANGE_INDEX);
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202 db->Execute(query, true);
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203
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204 if (!db->DoesTriggerExist(t, "ChangeAdded"))
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205 {
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206 ThrowCannotCreateTrigger();
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207 }
87
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208
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209 revision = 3;
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210 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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211
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212 t.Commit();
87
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213 }
144
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214
109
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215 if (revision == 3)
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216 {
144
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217 MySQLTransaction t(*db);
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218
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219 // Reconfiguration of "Metadata" from TEXT type (up to 64KB)
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220 // to the LONGTEXT type (up to 4GB). This might be important
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221 // for applications such as the Osimis Web viewer that stores
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222 // large amount of metadata.
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223 // http://book.orthanc-server.com/faq/features.html#central-registry-of-metadata-and-attachments
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224 db->Execute("ALTER TABLE Metadata MODIFY value LONGTEXT", false);
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225
109
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226 revision = 4;
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227 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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228
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229 t.Commit();
109
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230 }
144
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231
110
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232 if (revision == 4)
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233 {
144
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234 MySQLTransaction t(*db);
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235
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236 // Install the "CreateInstance" extension
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237 std::string query;
144
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238
110
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239 Orthanc::EmbeddedResources::GetFileResource
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240 (query, Orthanc::EmbeddedResources::MYSQL_CREATE_INSTANCE);
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241 db->Execute(query, true);
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242
110
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243 revision = 5;
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244 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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245
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246 t.Commit();
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247 }
144
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248
110
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249 if (revision != 5)
0
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250 {
53
am@osimis.io
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251 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision;
0
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252 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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253 }
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254 }
137
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255
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256 /**
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257 * WARNING: This lock must be acquired after
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258 * "MYSQL_LOCK_DATABASE_SETUP" is released. Indeed, in MySQL <
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259 * 5.7, it is impossible to acquire more than one lock at a time,
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260 * as calling "SELECT GET_LOCK()" releases all the
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261 * previously-acquired locks.
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262 * https://dev.mysql.com/doc/refman/5.7/en/locking-functions.html
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263 **/
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264 if (parameters_.HasLock())
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265 {
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266 db->AdvisoryLock(MYSQL_LOCK_INDEX);
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267 }
0
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268
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269 return db.release();
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270 }
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271
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272
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273 MySQLIndex::MySQLIndex(const MySQLParameters& parameters) :
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274 IndexBackend(new Factory(*this)),
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275 context_(NULL),
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276 parameters_(parameters),
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277 clearAll_(false)
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278 {
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279 }
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280
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281
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282 int64_t MySQLIndex::CreateResource(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, GetManager(),
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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, GetManager(),
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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(int64_t id)
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313 {
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314 ClearDeletedFiles();
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315
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316 // Recursive exploration of resources to be deleted, from the "id"
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317 // resource to the top of the tree of resources
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318
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319 bool done = false;
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320
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321 while (!done)
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322 {
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323 int64_t parentId;
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324
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325 {
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326 DatabaseManager::CachedStatement lookupSiblings(
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327 STATEMENT_FROM_HERE, GetManager(),
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328 "SELECT parentId FROM Resources "
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329 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});");
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330
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331 lookupSiblings.SetParameterType("id", ValueType_Integer64);
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332
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333 Dictionary args;
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334 args.SetIntegerValue("id", id);
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335
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336 lookupSiblings.Execute(args);
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337
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338 if (lookupSiblings.IsDone())
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339 {
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340 // "id" is a root node
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341 done = true;
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342 }
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343 else
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344 {
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345 parentId = ReadInteger64(lookupSiblings, 0);
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346 lookupSiblings.Next();
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347
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348 if (lookupSiblings.IsDone())
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349 {
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350 // "id" has no sibling node, recursively remove
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351 done = false;
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352 id = parentId;
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353 }
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354 else
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355 {
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356 // "id" has at least one sibling node: the parent node is the remaining ancestor
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357 done = true;
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358
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359 DatabaseManager::CachedStatement parent(
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360 STATEMENT_FROM_HERE, GetManager(),
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361 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};");
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362
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363 parent.SetParameterType("id", ValueType_Integer64);
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364
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365 Dictionary args;
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366 args.SetIntegerValue("id", parentId);
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367
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368 parent.Execute(args);
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369
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370 GetOutput().SignalRemainingAncestor(
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371 ReadString(parent, 0),
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372 static_cast<OrthancPluginResourceType>(ReadInteger32(parent, 1)));
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373 }
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374 }
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375 }
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376 }
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377
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378 {
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379 DatabaseManager::CachedStatement deleteHierarchy(
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380 STATEMENT_FROM_HERE, GetManager(),
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381 "DELETE FROM Resources WHERE internalId IN (SELECT * FROM (SELECT internalId FROM Resources WHERE internalId=${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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382
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383 deleteHierarchy.SetParameterType("id", ValueType_Integer64);
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384
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385 Dictionary args;
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386 args.SetIntegerValue("id", id);
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387
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388 deleteHierarchy.Execute(args);
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389 }
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390
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391 SignalDeletedFiles();
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392 }
87
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393
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394
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395 int64_t MySQLIndex::GetLastChangeIndex()
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396 {
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397 DatabaseManager::CachedStatement statement(
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398 STATEMENT_FROM_HERE, GetManager(),
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399 "SELECT value FROM GlobalIntegers WHERE property = 0");
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400
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401 statement.SetReadOnly(true);
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402 statement.Execute();
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403
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404 return ReadInteger64(statement, 0);
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405 }
110
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406
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407
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408 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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409 void MySQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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410 const char* hashPatient,
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411 const char* hashStudy,
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412 const char* hashSeries,
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413 const char* hashInstance)
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414 {
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415 {
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416 DatabaseManager::CachedStatement statement(
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417 STATEMENT_FROM_HERE, GetManager(),
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418 "CALL CreateInstance(${patient}, ${study}, ${series}, ${instance}, "
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419 "@isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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420 "@patientKey, @studyKey, @seriesKey, @instanceKey)");
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421
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422 statement.SetParameterType("patient", ValueType_Utf8String);
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423 statement.SetParameterType("study", ValueType_Utf8String);
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424 statement.SetParameterType("series", ValueType_Utf8String);
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425 statement.SetParameterType("instance", ValueType_Utf8String);
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426
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427 Dictionary args;
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428 args.SetUtf8Value("patient", hashPatient);
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429 args.SetUtf8Value("study", hashStudy);
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430 args.SetUtf8Value("series", hashSeries);
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431 args.SetUtf8Value("instance", hashInstance);
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432
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433 statement.Execute(args);
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434
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435 if (!statement.IsDone())
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436 {
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437 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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438 }
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439 }
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440
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441 {
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442 DatabaseManager::CachedStatement statement(
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443 STATEMENT_FROM_HERE, GetManager(),
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444 "SELECT @isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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445 "@patientKey, @studyKey, @seriesKey, @instanceKey");
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446
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447 statement.Execute();
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448
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449 for (size_t i = 0; i < 8; i++)
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450 {
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451 statement.SetResultFieldType(i, ValueType_Integer64);
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452 }
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453
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454 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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455 result.instanceId = ReadInteger64(statement, 7);
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456
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457 if (result.isNewInstance)
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458 {
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459 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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460 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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461 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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462 result.patientId = ReadInteger64(statement, 4);
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463 result.studyId = ReadInteger64(statement, 5);
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464 result.seriesId = ReadInteger64(statement, 6);
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465 }
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466 }
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467 }
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468 #endif
0
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469 }