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annotate MySQL/Plugins/MySQLIndex.cpp @ 137:52b3859ee0b7

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MySQL: acquiring named locks instead of numbers
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 09 May 2019 11:29:17 +0200
parents e26690365c25
children 4cd7e45b671e
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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) 2017-2019 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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31 #include <Core/Logging.h>
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32 #include <Core/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 IDatabase* MySQLIndex::OpenInternal()
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39 {
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40 uint32_t expectedVersion = 6;
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41 if (context_)
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42 {
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43 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(context_);
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44 }
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45 else
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46 {
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47 // This case only occurs during unit testing
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48 expectedVersion = 6;
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49 }
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50
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51 // Check the expected version of the database
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52 if (expectedVersion != 6)
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53 {
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54 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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55 << "expecting the DB schema version " << expectedVersion
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56 << ", but this plugin is only compatible with version 6";
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57 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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58 }
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59
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60 if (!MySQLDatabase::IsValidDatabaseIdentifier(parameters_.GetDatabase()))
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61 {
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62 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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63 }
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64
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65 if (clearAll_)
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66 {
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67 MySQLDatabase::ClearDatabase(parameters_);
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68 }
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69
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70 std::auto_ptr<MySQLDatabase> db(new MySQLDatabase(parameters_));
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72 db->Open();
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73 db->Execute("SET SESSION TRANSACTION ISOLATION LEVEL SERIALIZABLE", false);
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75 {
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76 MySQLDatabase::TransientAdvisoryLock lock(*db, MYSQL_LOCK_DATABASE_SETUP);
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77 MySQLTransaction t(*db);
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78
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79 db->Execute("ALTER DATABASE " + parameters_.GetDatabase() +
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80 " CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci", false);
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81
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82 if (!db->DoesTableExist(t, "Resources"))
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83 {
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84 std::string query;
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85
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86 Orthanc::EmbeddedResources::GetFileResource
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87 (query, Orthanc::EmbeddedResources::MYSQL_PREPARE_INDEX);
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88 db->Execute(query, true);
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89
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90 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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91 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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92 }
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93
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94 if (!db->DoesTableExist(t, "Resources"))
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95 {
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96 LOG(ERROR) << "Corrupted MySQL database";
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97 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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98 }
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99
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100 int version = 0;
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101 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion) ||
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102 version != 6)
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103 {
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104 LOG(ERROR) << "MySQL plugin is incompatible with database schema version: " << version;
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105 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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106 }
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107
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108 int revision;
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109 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel))
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110 {
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111 revision = 1;
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112 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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113 }
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114
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115 if (revision == 1)
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116 {
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117 // The serialization of jobs as a global property can lead to
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118 // very long values => switch to the LONGTEXT type that can
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119 // store up to 4GB:
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120 // https://stackoverflow.com/a/13932834/881731
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121 db->Execute("ALTER TABLE GlobalProperties MODIFY value LONGTEXT", false);
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122
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123 revision = 2;
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124 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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125 }
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126
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127 if (revision == 2)
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128 {
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129 // Install the "GetLastChangeIndex" extension
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130 std::string query;
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131
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132 Orthanc::EmbeddedResources::GetFileResource
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133 (query, Orthanc::EmbeddedResources::MYSQL_GET_LAST_CHANGE_INDEX);
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134 db->Execute(query, true);
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135
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136 revision = 3;
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137 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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138 }
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139
109
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140 if (revision == 3)
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141 {
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142 // Reconfiguration of "Metadata" from TEXT type (up to 64KB)
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143 // to the LONGTEXT type (up to 4GB). This might be important
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144 // for applications such as the Osimis Web viewer that stores
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145 // large amount of metadata.
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146 // http://book.orthanc-server.com/faq/features.html#central-registry-of-metadata-and-attachments
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147 db->Execute("ALTER TABLE Metadata MODIFY value LONGTEXT", false);
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148
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149 revision = 4;
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150 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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151 }
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152
110
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153 if (revision == 4)
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154 {
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155 // Install the "CreateInstance" extension
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156 std::string query;
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157
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158 Orthanc::EmbeddedResources::GetFileResource
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159 (query, Orthanc::EmbeddedResources::MYSQL_CREATE_INSTANCE);
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160 db->Execute(query, true);
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161
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162 revision = 5;
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163 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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164 }
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165
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166 if (revision != 5)
0
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167 {
53
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168 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision;
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169 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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170 }
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171
16
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172 t.Commit();
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173 }
137
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174
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175 /**
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176 * WARNING: This lock must be acquired after
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177 * "MYSQL_LOCK_DATABASE_SETUP" is released. Indeed, in MySQL <
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178 * 5.7, it is impossible to acquire more than one lock at a time,
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179 * as calling "SELECT GET_LOCK()" releases all the
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180 * previously-acquired locks.
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181 * https://dev.mysql.com/doc/refman/5.7/en/locking-functions.html
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182 **/
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183 if (parameters_.HasLock())
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184 {
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185 db->AdvisoryLock(MYSQL_LOCK_INDEX);
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186 }
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187
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188 return db.release();
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189 }
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190
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191
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192 MySQLIndex::MySQLIndex(const MySQLParameters& parameters) :
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193 IndexBackend(new Factory(*this)),
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194 context_(NULL),
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195 parameters_(parameters),
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196 clearAll_(false)
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197 {
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198 }
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199
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200
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201 int64_t MySQLIndex::CreateResource(const char* publicId,
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202 OrthancPluginResourceType type)
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203 {
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204 {
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205 DatabaseManager::CachedStatement statement(
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206 STATEMENT_FROM_HERE, GetManager(),
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207 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL)");
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208
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209 statement.SetParameterType("id", ValueType_Utf8String);
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210 statement.SetParameterType("type", ValueType_Integer64);
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211
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212 Dictionary args;
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213 args.SetUtf8Value("id", publicId);
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214 args.SetIntegerValue("type", static_cast<int>(type));
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215
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216 statement.Execute(args);
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217 }
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218
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219 {
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220 DatabaseManager::CachedStatement statement(
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221 STATEMENT_FROM_HERE, GetManager(),
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222 "SELECT LAST_INSERT_ID()");
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223
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224 statement.Execute();
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225
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226 return ReadInteger64(statement, 0);
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227 }
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228 }
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229
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230
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231 void MySQLIndex::DeleteResource(int64_t id)
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232 {
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233 ClearDeletedFiles();
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234
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235 // Recursive exploration of resources to be deleted, from the "id"
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236 // resource to the top of the tree of resources
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237
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238 bool done = false;
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239
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240 while (!done)
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241 {
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242 int64_t parentId;
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243
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244 {
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245 DatabaseManager::CachedStatement lookupSiblings(
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246 STATEMENT_FROM_HERE, GetManager(),
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247 "SELECT parentId FROM Resources "
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248 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});");
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249
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250 lookupSiblings.SetParameterType("id", ValueType_Integer64);
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251
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252 Dictionary args;
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253 args.SetIntegerValue("id", id);
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254
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255 lookupSiblings.Execute(args);
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256
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257 if (lookupSiblings.IsDone())
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258 {
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259 // "id" is a root node
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260 done = true;
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261 }
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262 else
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263 {
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264 parentId = ReadInteger64(lookupSiblings, 0);
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265 lookupSiblings.Next();
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266
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267 if (lookupSiblings.IsDone())
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268 {
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269 // "id" has no sibling node, recursively remove
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270 done = false;
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271 id = parentId;
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272 }
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273 else
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274 {
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275 // "id" has at least one sibling node: the parent node is the remaining ancestor
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276 done = true;
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277
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278 DatabaseManager::CachedStatement parent(
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279 STATEMENT_FROM_HERE, GetManager(),
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280 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};");
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281
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282 parent.SetParameterType("id", ValueType_Integer64);
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283
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284 Dictionary args;
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285 args.SetIntegerValue("id", parentId);
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286
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287 parent.Execute(args);
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288
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289 GetOutput().SignalRemainingAncestor(
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290 ReadString(parent, 0),
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291 static_cast<OrthancPluginResourceType>(ReadInteger32(parent, 1)));
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292 }
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293 }
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294 }
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295 }
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297 {
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298 DatabaseManager::CachedStatement deleteHierarchy(
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299 STATEMENT_FROM_HERE, GetManager(),
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300 "DELETE FROM Resources WHERE internalId IN (SELECT * FROM (SELECT internalId FROM Resources WHERE internalId=${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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301
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302 deleteHierarchy.SetParameterType("id", ValueType_Integer64);
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303
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304 Dictionary args;
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305 args.SetIntegerValue("id", id);
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306
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307 deleteHierarchy.Execute(args);
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308 }
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309
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310 SignalDeletedFiles();
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311 }
87
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312
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313
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314 int64_t MySQLIndex::GetLastChangeIndex()
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315 {
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316 DatabaseManager::CachedStatement statement(
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317 STATEMENT_FROM_HERE, GetManager(),
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318 "SELECT value FROM GlobalIntegers WHERE property = 0");
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319
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320 statement.SetReadOnly(true);
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321 statement.Execute();
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322
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323 return ReadInteger64(statement, 0);
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324 }
110
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325
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326
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327 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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328 void MySQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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329 const char* hashPatient,
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330 const char* hashStudy,
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331 const char* hashSeries,
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332 const char* hashInstance)
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333 {
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334 {
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335 DatabaseManager::CachedStatement statement(
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336 STATEMENT_FROM_HERE, GetManager(),
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337 "CALL CreateInstance(${patient}, ${study}, ${series}, ${instance}, "
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338 "@isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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339 "@patientKey, @studyKey, @seriesKey, @instanceKey)");
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340
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341 statement.SetParameterType("patient", ValueType_Utf8String);
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342 statement.SetParameterType("study", ValueType_Utf8String);
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343 statement.SetParameterType("series", ValueType_Utf8String);
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344 statement.SetParameterType("instance", ValueType_Utf8String);
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345
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346 Dictionary args;
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347 args.SetUtf8Value("patient", hashPatient);
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348 args.SetUtf8Value("study", hashStudy);
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349 args.SetUtf8Value("series", hashSeries);
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350 args.SetUtf8Value("instance", hashInstance);
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351
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352 statement.Execute(args);
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353
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354 if (!statement.IsDone())
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355 {
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356 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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357 }
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358 }
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359
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360 {
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361 DatabaseManager::CachedStatement statement(
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362 STATEMENT_FROM_HERE, GetManager(),
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363 "SELECT @isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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364 "@patientKey, @studyKey, @seriesKey, @instanceKey");
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365
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366 statement.Execute();
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367
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368 for (size_t i = 0; i < 8; i++)
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369 {
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370 statement.SetResultFieldType(i, ValueType_Integer64);
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371 }
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372
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373 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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374 result.instanceId = ReadInteger64(statement, 7);
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375
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376 if (result.isNewInstance)
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377 {
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378 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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379 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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380 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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381 result.patientId = ReadInteger64(statement, 4);
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382 result.studyId = ReadInteger64(statement, 5);
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383 result.seriesId = ReadInteger64(statement, 6);
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384 }
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385 }
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386 }
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387 #endif
0
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388 }