Mercurial > hg > orthanc-databases
annotate MySQL/Plugins/MySQLIndex.cpp @ 272:c7dc70a0a477
upgrade to Orthanc SDK 1.9.2
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 22 Apr 2021 14:09:46 +0200 |
parents | 29d2b76516f6 |
children | 0868500060f3 |
rev | line source |
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0 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics | |
4 * Department, University Hospital of Liege, Belgium | |
193
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium |
0 | 6 * |
7 * This program is free software: you can redistribute it and/or | |
8 * modify it under the terms of the GNU Affero General Public License | |
9 * as published by the Free Software Foundation, either version 3 of | |
10 * the License, or (at your option) any later version. | |
11 * | |
12 * This program is distributed in the hope that it will be useful, but | |
13 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
15 * Affero General Public License for more details. | |
16 * | |
17 * You should have received a copy of the GNU Affero General Public License | |
18 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
19 **/ | |
20 | |
21 | |
22 #include "MySQLIndex.h" | |
23 | |
24 #include "../../Framework/Plugins/GlobalProperties.h" | |
25 #include "../../Framework/MySQL/MySQLDatabase.h" | |
26 #include "../../Framework/MySQL/MySQLTransaction.h" | |
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27 #include "MySQLDefinitions.h" |
0 | 28 |
29 #include <EmbeddedResources.h> // Auto-generated file | |
30 | |
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31 #include <Compatibility.h> // For std::unique_ptr<> |
152 | 32 #include <Logging.h> |
33 #include <OrthancException.h> | |
0 | 34 |
35 #include <ctype.h> | |
36 | |
37 namespace OrthancDatabases | |
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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46 |
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47 |
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48 IDatabaseFactory* MySQLIndex::CreateDatabaseFactory() |
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49 { |
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50 return MySQLDatabase::CreateDatabaseFactory(parameters_); |
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51 } |
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52 |
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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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63 |
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64 |
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65 void MySQLIndex::ConfigureDatabase(DatabaseManager& manager) |
0 | 66 { |
67 uint32_t expectedVersion = 6; | |
199 | 68 |
69 if (GetContext()) // "GetContext()" can possibly be NULL in the unit tests | |
0 | 70 { |
199 | 71 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(GetContext()); |
0 | 72 } |
73 | |
74 // Check the expected version of the database | |
75 if (expectedVersion != 6) | |
76 { | |
77 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc " | |
78 << "expecting the DB schema version " << expectedVersion | |
79 << ", but this plugin is only compatible with version 6"; | |
80 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin); | |
81 } | |
82 | |
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83 if (!MySQLDatabase::IsValidDatabaseIdentifier(parameters_.GetDatabase())) |
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84 { |
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85 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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86 } |
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87 |
0 | 88 if (clearAll_) |
89 { | |
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90 MySQLDatabase::ClearDatabase(parameters_); |
0 | 91 } |
92 | |
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93 MySQLDatabase& db = dynamic_cast<MySQLDatabase&>(manager.GetDatabase()); |
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94 |
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95 { |
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96 MySQLDatabase::TransientAdvisoryLock lock(db, MYSQL_LOCK_DATABASE_SETUP); |
0 | 97 |
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98 /** |
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99 * In a first transaction, we create the tables. Such a |
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100 * transaction cannot be rollback: "The CREATE TABLE statement |
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101 * in InnoDB is processed as a single transaction. This means |
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102 * that a ROLLBACK from the user does not undo CREATE TABLE |
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103 * statements the user made during that transaction." |
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104 * https://dev.mysql.com/doc/refman/8.0/en/implicit-commit.html |
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105 * |
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106 * As a consequence, we delay the initial population of the |
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107 * tables in a sequence of transactions below. This solves the |
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108 * error message "MySQL plugin is incompatible with database |
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109 * schema version: 0" that was reported in the forum: |
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110 * https://groups.google.com/d/msg/orthanc-users/OCFFkm1qm0k/Mbroy8VWAQAJ |
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111 **/ |
0 | 112 { |
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113 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite); |
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114 |
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115 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER DATABASE " + parameters_.GetDatabase() + |
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116 " CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci"); |
0 | 117 |
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118 // This is the first table to be created |
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119 if (!t.GetDatabaseTransaction().DoesTableExist("GlobalProperties")) |
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120 { |
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121 std::string query; |
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122 |
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123 Orthanc::EmbeddedResources::GetFileResource |
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124 (query, Orthanc::EmbeddedResources::MYSQL_PREPARE_INDEX); |
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125 |
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126 // Need to escape arobases: Don't use "t.GetDatabaseTransaction().ExecuteMultiLines()" here |
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127 db.ExecuteMultiLines(query, true); |
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128 } |
0 | 129 |
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130 t.Commit(); |
0 | 131 } |
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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141 int version = 0; | |
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142 |
0 | 143 { |
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144 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite); |
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145 |
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146 // This is the last table to be created |
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147 if (!t.GetDatabaseTransaction().DoesTableExist("PatientRecyclingOrder")) |
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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 (!t.GetDatabaseTransaction().DoesTriggerExist("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, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion)) |
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160 { |
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161 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion); |
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162 SetGlobalIntegerProperty(manager, 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(); |
0 | 173 } |
174 | |
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175 int revision = 0; |
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176 |
0 | 177 { |
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178 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite); |
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179 |
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180 if (!LookupGlobalIntegerProperty(revision, manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel)) |
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181 { |
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182 revision = 1; |
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183 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision); |
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184 } |
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185 |
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186 t.Commit(); |
0 | 187 } |
188 | |
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189 if (revision == 1) |
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190 { |
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191 DatabaseManager::Transaction t(manager, 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 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE GlobalProperties MODIFY value LONGTEXT"); |
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198 |
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199 revision = 2; |
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200 SetGlobalIntegerProperty(manager, 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 DatabaseManager::Transaction t(manager, 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 |
241
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215 // Need to escape arobases: Don't use "t.GetDatabaseTransaction().ExecuteMultiLines()" here |
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216 db.ExecuteMultiLines(query, true); |
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217 |
241
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218 if (!t.GetDatabaseTransaction().DoesTriggerExist("ChangeAdded")) |
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219 { |
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220 ThrowCannotCreateTrigger(); |
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221 } |
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222 |
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223 revision = 3; |
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224 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision); |
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225 |
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226 t.Commit(); |
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227 } |
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228 |
109
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229 if (revision == 3) |
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230 { |
237
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231 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite); |
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232 |
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233 // Reconfiguration of "Metadata" from TEXT type (up to 64KB) |
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234 // to the LONGTEXT type (up to 4GB). This might be important |
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235 // for applications such as the Osimis Web viewer that stores |
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236 // large amount of metadata. |
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237 // http://book.orthanc-server.com/faq/features.html#central-registry-of-metadata-and-attachments |
241
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238 t.GetDatabaseTransaction().ExecuteMultiLines("ALTER TABLE Metadata MODIFY value LONGTEXT"); |
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239 |
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240 revision = 4; |
237
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241 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision); |
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242 |
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243 t.Commit(); |
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244 } |
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245 |
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246 if (revision == 4) |
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247 { |
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248 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite); |
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249 |
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250 // Install the "CreateInstance" extension |
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251 std::string query; |
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252 |
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253 Orthanc::EmbeddedResources::GetFileResource |
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254 (query, Orthanc::EmbeddedResources::MYSQL_CREATE_INSTANCE); |
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255 |
241
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256 // Need to escape arobases: Don't use "t.GetDatabaseTransaction().ExecuteMultiLines()" here |
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257 db.ExecuteMultiLines(query, true); |
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258 |
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259 revision = 5; |
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260 SetGlobalIntegerProperty(manager, MISSING_SERVER_IDENTIFIER, Orthanc::GlobalProperty_DatabasePatchLevel, revision); |
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261 |
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262 t.Commit(); |
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263 } |
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264 |
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265 if (revision != 5) |
0 | 266 { |
53 | 267 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision; |
0 | 268 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); |
269 } | |
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270 |
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271 |
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272 { |
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273 // New in release 4.0 to deal with multiple writers |
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274 DatabaseManager::Transaction t(manager, TransactionType_ReadWrite); |
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275 |
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276 if (!t.GetDatabaseTransaction().DoesTableExist("ServerProperties")) |
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277 { |
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278 t.GetDatabaseTransaction().ExecuteMultiLines("CREATE TABLE ServerProperties(server VARCHAR(64) NOT NULL, " |
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279 "property INTEGER, value TEXT, PRIMARY KEY(server, property))"); |
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280 } |
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281 |
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282 t.Commit(); |
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283 } |
0 | 284 } |
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285 |
238
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286 |
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287 /** |
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288 * WARNING: This lock must be acquired after |
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289 * "MYSQL_LOCK_DATABASE_SETUP" is released. Indeed, in MySQL < |
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290 * 5.7, it is impossible to acquire more than one lock at a time, |
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291 * as calling "SELECT GET_LOCK()" releases all the |
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292 * previously-acquired locks. |
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293 * https://dev.mysql.com/doc/refman/5.7/en/locking-functions.html |
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294 **/ |
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295 if (parameters_.HasLock()) |
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296 { |
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297 db.AdvisoryLock(MYSQL_LOCK_INDEX); |
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298 } |
0 | 299 } |
300 | |
301 | |
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302 int64_t MySQLIndex::CreateResource(DatabaseManager& manager, |
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303 const char* publicId, |
0 | 304 OrthancPluginResourceType type) |
305 { | |
306 { | |
307 DatabaseManager::CachedStatement statement( | |
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308 STATEMENT_FROM_HERE, manager, |
0 | 309 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL)"); |
310 | |
311 statement.SetParameterType("id", ValueType_Utf8String); | |
312 statement.SetParameterType("type", ValueType_Integer64); | |
313 | |
314 Dictionary args; | |
315 args.SetUtf8Value("id", publicId); | |
316 args.SetIntegerValue("type", static_cast<int>(type)); | |
317 | |
318 statement.Execute(args); | |
319 } | |
320 | |
321 { | |
322 DatabaseManager::CachedStatement statement( | |
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323 STATEMENT_FROM_HERE, manager, |
0 | 324 "SELECT LAST_INSERT_ID()"); |
325 | |
326 statement.Execute(); | |
327 | |
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328 return statement.ReadInteger64(0); |
0 | 329 } |
330 } | |
331 | |
332 | |
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333 void MySQLIndex::DeleteResource(IDatabaseBackendOutput& output, |
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334 DatabaseManager& manager, |
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335 int64_t id) |
0 | 336 { |
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337 ClearDeletedFiles(manager); |
0 | 338 |
339 // Recursive exploration of resources to be deleted, from the "id" | |
340 // resource to the top of the tree of resources | |
341 | |
342 bool done = false; | |
343 | |
344 while (!done) | |
345 { | |
346 { | |
347 DatabaseManager::CachedStatement lookupSiblings( | |
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348 STATEMENT_FROM_HERE, manager, |
0 | 349 "SELECT parentId FROM Resources " |
350 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});"); | |
351 | |
352 lookupSiblings.SetParameterType("id", ValueType_Integer64); | |
353 | |
354 Dictionary args; | |
355 args.SetIntegerValue("id", id); | |
356 | |
357 lookupSiblings.Execute(args); | |
358 | |
359 if (lookupSiblings.IsDone()) | |
360 { | |
361 // "id" is a root node | |
362 done = true; | |
363 } | |
364 else | |
365 { | |
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366 int64_t parentId = lookupSiblings.ReadInteger64(0); |
0 | 367 lookupSiblings.Next(); |
368 | |
369 if (lookupSiblings.IsDone()) | |
370 { | |
371 // "id" has no sibling node, recursively remove | |
372 done = false; | |
373 id = parentId; | |
374 } | |
375 else | |
376 { | |
377 // "id" has at least one sibling node: the parent node is the remaining ancestor | |
378 done = true; | |
379 | |
380 DatabaseManager::CachedStatement parent( | |
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381 STATEMENT_FROM_HERE, manager, |
0 | 382 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};"); |
383 | |
384 parent.SetParameterType("id", ValueType_Integer64); | |
385 | |
252 | 386 Dictionary args2; |
387 args2.SetIntegerValue("id", parentId); | |
0 | 388 |
252 | 389 parent.Execute(args2); |
0 | 390 |
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391 output.SignalRemainingAncestor( |
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392 parent.ReadString(0), |
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393 static_cast<OrthancPluginResourceType>(parent.ReadInteger32(1))); |
0 | 394 } |
395 } | |
396 } | |
397 } | |
398 | |
399 { | |
400 DatabaseManager::CachedStatement deleteHierarchy( | |
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401 STATEMENT_FROM_HERE, manager, |
0 | 402 "DELETE FROM Resources WHERE internalId IN (SELECT * FROM (SELECT internalId FROM Resources WHERE internalId=${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);"); |
403 | |
404 deleteHierarchy.SetParameterType("id", ValueType_Integer64); | |
405 | |
406 Dictionary args; | |
407 args.SetIntegerValue("id", id); | |
408 | |
409 deleteHierarchy.Execute(args); | |
410 } | |
411 | |
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412 SignalDeletedFiles(output, manager); |
0 | 413 } |
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414 |
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415 |
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416 int64_t MySQLIndex::GetLastChangeIndex(DatabaseManager& manager) |
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417 { |
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418 DatabaseManager::CachedStatement statement( |
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419 STATEMENT_FROM_HERE, manager, |
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420 "SELECT value FROM GlobalIntegers WHERE property = 0"); |
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421 |
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422 statement.SetReadOnly(true); |
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423 statement.Execute(); |
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424 |
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425 return statement.ReadInteger64(0); |
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426 } |
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427 |
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428 |
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429 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1 |
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430 void MySQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result, |
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431 DatabaseManager& manager, |
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432 const char* hashPatient, |
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433 const char* hashStudy, |
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434 const char* hashSeries, |
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435 const char* hashInstance) |
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436 { |
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437 { |
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438 DatabaseManager::CachedStatement statement( |
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439 STATEMENT_FROM_HERE, manager, |
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440 "CALL CreateInstance(${patient}, ${study}, ${series}, ${instance}, " |
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441 "@isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, " |
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442 "@patientKey, @studyKey, @seriesKey, @instanceKey)"); |
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443 |
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444 statement.SetParameterType("patient", ValueType_Utf8String); |
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445 statement.SetParameterType("study", ValueType_Utf8String); |
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446 statement.SetParameterType("series", ValueType_Utf8String); |
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447 statement.SetParameterType("instance", ValueType_Utf8String); |
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448 |
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449 Dictionary args; |
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450 args.SetUtf8Value("patient", hashPatient); |
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451 args.SetUtf8Value("study", hashStudy); |
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452 args.SetUtf8Value("series", hashSeries); |
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453 args.SetUtf8Value("instance", hashInstance); |
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454 |
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455 statement.Execute(args); |
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456 |
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457 if (!statement.IsDone()) |
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458 { |
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459 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); |
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460 } |
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461 } |
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462 |
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463 { |
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464 DatabaseManager::CachedStatement statement( |
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465 STATEMENT_FROM_HERE, manager, |
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466 "SELECT @isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, " |
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467 "@patientKey, @studyKey, @seriesKey, @instanceKey"); |
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468 |
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469 statement.Execute(); |
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470 |
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471 for (size_t i = 0; i < 8; i++) |
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472 { |
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473 statement.SetResultFieldType(i, ValueType_Integer64); |
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474 } |
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475 |
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476 result.isNewInstance = (statement.ReadInteger64(3) == 1); |
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477 result.instanceId = statement.ReadInteger64(7); |
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478 |
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479 if (result.isNewInstance) |
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480 { |
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481 result.isNewPatient = (statement.ReadInteger64(0) == 1); |
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482 result.isNewStudy = (statement.ReadInteger64(1) == 1); |
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483 result.isNewSeries = (statement.ReadInteger64(2) == 1); |
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484 result.patientId = statement.ReadInteger64(4); |
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485 result.studyId = statement.ReadInteger64(5); |
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486 result.seriesId = statement.ReadInteger64(6); |
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487 } |
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488 } |
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489 } |
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490 #endif |
0 | 491 } |