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annotate MySQL/Plugins/MySQLIndex.cpp @ 157:275e14f57f1e

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replacing deprecated std::auto_ptr by std::unique_ptr
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 06 Jul 2020 12:45:58 +0200
parents 063aa53b5917
children 3236894320d6
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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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31 #include <Compatibility.h> // For std::unique_ptr<>
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32 #include <Logging.h>
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33 #include <OrthancException.h>
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34
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35 #include <ctype.h>
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36
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37 namespace OrthancDatabases
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38 {
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39 static void ThrowCannotCreateTrigger()
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40 {
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41 LOG(ERROR) << "The MySQL user is not allowed to create triggers => 2 possible solutions:";
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42 LOG(ERROR) << " 1- Give the SUPER privilege to the MySQL database user, or";
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43 LOG(ERROR) << " 2- Run \"set global log_bin_trust_function_creators=1;\" as MySQL root user.";
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44 LOG(ERROR) << "Once you are done, drop and recreate the MySQL database";
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45 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database,
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46 "Need to fix the MySQL permissions for \"CREATE TRIGGER\"");
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47 }
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48
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49 IDatabase* MySQLIndex::OpenInternal()
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50 {
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51 uint32_t expectedVersion = 6;
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52 if (context_)
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53 {
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54 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(context_);
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55 }
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56 else
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57 {
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58 // This case only occurs during unit testing
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59 expectedVersion = 6;
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60 }
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61
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62 // Check the expected version of the database
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63 if (expectedVersion != 6)
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64 {
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65 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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66 << "expecting the DB schema version " << expectedVersion
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67 << ", but this plugin is only compatible with version 6";
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68 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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69 }
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71 if (!MySQLDatabase::IsValidDatabaseIdentifier(parameters_.GetDatabase()))
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72 {
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73 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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74 }
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75
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76 if (clearAll_)
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77 {
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78 MySQLDatabase::ClearDatabase(parameters_);
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79 }
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80
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81 std::unique_ptr<MySQLDatabase> db(new MySQLDatabase(parameters_));
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82
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83 db->Open();
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84 db->Execute("SET SESSION TRANSACTION ISOLATION LEVEL SERIALIZABLE", false);
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86 {
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87 MySQLDatabase::TransientAdvisoryLock lock(*db, MYSQL_LOCK_DATABASE_SETUP);
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88
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89 /**
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90 * In a first transaction, we create the tables. Such a
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91 * transaction cannot be rollback: "The CREATE TABLE statement
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92 * in InnoDB is processed as a single transaction. This means
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93 * that a ROLLBACK from the user does not undo CREATE TABLE
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94 * statements the user made during that transaction."
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95 * https://dev.mysql.com/doc/refman/8.0/en/implicit-commit.html
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96 *
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97 * As a consequence, we delay the initial population of the
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98 * tables in a sequence of transactions below. This solves the
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99 * error message "MySQL plugin is incompatible with database
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100 * schema version: 0" that was reported in the forum:
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101 * https://groups.google.com/d/msg/orthanc-users/OCFFkm1qm0k/Mbroy8VWAQAJ
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102 **/
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103 {
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104 MySQLTransaction t(*db);
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105
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106 db->Execute("ALTER DATABASE " + parameters_.GetDatabase() +
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107 " CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci", false);
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108
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109 // This is the first table to be created
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110 if (!db->DoesTableExist(t, "GlobalProperties"))
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111 {
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112 std::string query;
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113
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114 Orthanc::EmbeddedResources::GetFileResource
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115 (query, Orthanc::EmbeddedResources::MYSQL_PREPARE_INDEX);
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116 db->Execute(query, true);
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117 }
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119 t.Commit();
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120 }
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121
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122 /**
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123 * This is the sequence of transactions that initially populate
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124 * the database. WARNING - As table creation cannot be rollback,
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125 * don't forget to add "IF NOT EXISTS" if some table must be
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126 * created below this point (in order to recover from failed
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127 * transaction).
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128 **/
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129
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130 int version = 0;
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131
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132 {
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133 MySQLTransaction t(*db);
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134
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135 // This is the last table to be created
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136 if (!db->DoesTableExist(t, "PatientRecyclingOrder"))
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137 {
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138 LOG(ERROR) << "Corrupted MySQL database";
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139 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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140 }
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141
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142 // This is the last item to be created
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143 if (!db->DoesTriggerExist(t, "PatientAdded"))
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144 {
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145 ThrowCannotCreateTrigger();
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146 }
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147
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148 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion))
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149 {
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150 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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151 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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152 version = expectedVersion;
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153 }
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154
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155 if (version != 6)
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156 {
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157 LOG(ERROR) << "MySQL plugin is incompatible with database schema version: " << version;
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158 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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159 }
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160
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161 t.Commit();
0
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162 }
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163
144
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164 int revision = 0;
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165
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166 {
144
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167 MySQLTransaction t(*db);
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168
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169 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel))
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170 {
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171 revision = 1;
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172 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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173 }
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174
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175 t.Commit();
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176 }
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177
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178 if (revision == 1)
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179 {
144
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180 MySQLTransaction t(*db);
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181
84
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182 // The serialization of jobs as a global property can lead to
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183 // very long values => switch to the LONGTEXT type that can
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184 // store up to 4GB:
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185 // https://stackoverflow.com/a/13932834/881731
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186 db->Execute("ALTER TABLE GlobalProperties MODIFY value LONGTEXT", false);
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187
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188 revision = 2;
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189 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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190
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191 t.Commit();
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192 }
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193
87
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194 if (revision == 2)
144
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195 {
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196 MySQLTransaction t(*db);
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197
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198 // Install the "GetLastChangeIndex" extension
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199 std::string query;
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200
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201 Orthanc::EmbeddedResources::GetFileResource
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202 (query, Orthanc::EmbeddedResources::MYSQL_GET_LAST_CHANGE_INDEX);
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203 db->Execute(query, true);
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204
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205 if (!db->DoesTriggerExist(t, "ChangeAdded"))
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206 {
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207 ThrowCannotCreateTrigger();
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208 }
87
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209
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210 revision = 3;
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211 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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212
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213 t.Commit();
87
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214 }
144
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215
109
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216 if (revision == 3)
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217 {
144
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218 MySQLTransaction t(*db);
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219
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220 // Reconfiguration of "Metadata" from TEXT type (up to 64KB)
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221 // to the LONGTEXT type (up to 4GB). This might be important
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222 // for applications such as the Osimis Web viewer that stores
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223 // large amount of metadata.
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224 // http://book.orthanc-server.com/faq/features.html#central-registry-of-metadata-and-attachments
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225 db->Execute("ALTER TABLE Metadata MODIFY value LONGTEXT", false);
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226
109
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227 revision = 4;
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228 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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229
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230 t.Commit();
109
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231 }
144
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232
110
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233 if (revision == 4)
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234 {
144
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235 MySQLTransaction t(*db);
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236
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237 // Install the "CreateInstance" extension
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238 std::string query;
144
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239
110
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240 Orthanc::EmbeddedResources::GetFileResource
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241 (query, Orthanc::EmbeddedResources::MYSQL_CREATE_INSTANCE);
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242 db->Execute(query, true);
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243
110
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244 revision = 5;
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245 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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246
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247 t.Commit();
110
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248 }
144
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249
110
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250 if (revision != 5)
0
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251 {
53
am@osimis.io
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252 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision;
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253 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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254 }
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255 }
137
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256
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257 /**
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258 * WARNING: This lock must be acquired after
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259 * "MYSQL_LOCK_DATABASE_SETUP" is released. Indeed, in MySQL <
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260 * 5.7, it is impossible to acquire more than one lock at a time,
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261 * as calling "SELECT GET_LOCK()" releases all the
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262 * previously-acquired locks.
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263 * https://dev.mysql.com/doc/refman/5.7/en/locking-functions.html
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264 **/
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265 if (parameters_.HasLock())
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266 {
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267 db->AdvisoryLock(MYSQL_LOCK_INDEX);
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268 }
0
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269
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270 return db.release();
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271 }
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272
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273
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274 MySQLIndex::MySQLIndex(const MySQLParameters& parameters) :
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275 IndexBackend(new Factory(*this)),
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276 context_(NULL),
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277 parameters_(parameters),
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278 clearAll_(false)
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279 {
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280 }
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281
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282
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283 int64_t MySQLIndex::CreateResource(const char* publicId,
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284 OrthancPluginResourceType type)
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285 {
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286 {
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287 DatabaseManager::CachedStatement statement(
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288 STATEMENT_FROM_HERE, GetManager(),
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289 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL)");
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290
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291 statement.SetParameterType("id", ValueType_Utf8String);
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292 statement.SetParameterType("type", ValueType_Integer64);
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293
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294 Dictionary args;
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295 args.SetUtf8Value("id", publicId);
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296 args.SetIntegerValue("type", static_cast<int>(type));
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297
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298 statement.Execute(args);
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299 }
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300
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301 {
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302 DatabaseManager::CachedStatement statement(
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303 STATEMENT_FROM_HERE, GetManager(),
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304 "SELECT LAST_INSERT_ID()");
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305
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306 statement.Execute();
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307
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308 return ReadInteger64(statement, 0);
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309 }
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310 }
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311
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312
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313 void MySQLIndex::DeleteResource(int64_t id)
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314 {
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315 ClearDeletedFiles();
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316
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317 // Recursive exploration of resources to be deleted, from the "id"
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318 // resource to the top of the tree of resources
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319
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320 bool done = false;
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321
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322 while (!done)
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323 {
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324 int64_t parentId;
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325
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326 {
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327 DatabaseManager::CachedStatement lookupSiblings(
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328 STATEMENT_FROM_HERE, GetManager(),
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329 "SELECT parentId FROM Resources "
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330 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});");
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331
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332 lookupSiblings.SetParameterType("id", ValueType_Integer64);
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333
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334 Dictionary args;
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335 args.SetIntegerValue("id", id);
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336
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337 lookupSiblings.Execute(args);
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338
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339 if (lookupSiblings.IsDone())
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340 {
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341 // "id" is a root node
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342 done = true;
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343 }
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344 else
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345 {
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346 parentId = ReadInteger64(lookupSiblings, 0);
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347 lookupSiblings.Next();
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348
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349 if (lookupSiblings.IsDone())
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350 {
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351 // "id" has no sibling node, recursively remove
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352 done = false;
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353 id = parentId;
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354 }
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355 else
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356 {
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357 // "id" has at least one sibling node: the parent node is the remaining ancestor
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358 done = true;
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359
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360 DatabaseManager::CachedStatement parent(
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361 STATEMENT_FROM_HERE, GetManager(),
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362 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};");
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363
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364 parent.SetParameterType("id", ValueType_Integer64);
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365
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366 Dictionary args;
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367 args.SetIntegerValue("id", parentId);
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368
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369 parent.Execute(args);
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370
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371 GetOutput().SignalRemainingAncestor(
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372 ReadString(parent, 0),
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373 static_cast<OrthancPluginResourceType>(ReadInteger32(parent, 1)));
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374 }
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375 }
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376 }
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377 }
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378
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379 {
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380 DatabaseManager::CachedStatement deleteHierarchy(
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381 STATEMENT_FROM_HERE, GetManager(),
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382 "DELETE FROM Resources WHERE internalId IN (SELECT * FROM (SELECT internalId FROM Resources WHERE internalId=${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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383
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384 deleteHierarchy.SetParameterType("id", ValueType_Integer64);
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385
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386 Dictionary args;
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387 args.SetIntegerValue("id", id);
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388
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389 deleteHierarchy.Execute(args);
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390 }
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391
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392 SignalDeletedFiles();
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393 }
87
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394
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395
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396 int64_t MySQLIndex::GetLastChangeIndex()
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397 {
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398 DatabaseManager::CachedStatement statement(
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399 STATEMENT_FROM_HERE, GetManager(),
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400 "SELECT value FROM GlobalIntegers WHERE property = 0");
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401
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402 statement.SetReadOnly(true);
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403 statement.Execute();
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404
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405 return ReadInteger64(statement, 0);
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406 }
110
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407
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408
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409 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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410 void MySQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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411 const char* hashPatient,
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412 const char* hashStudy,
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413 const char* hashSeries,
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414 const char* hashInstance)
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415 {
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416 {
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417 DatabaseManager::CachedStatement statement(
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418 STATEMENT_FROM_HERE, GetManager(),
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419 "CALL CreateInstance(${patient}, ${study}, ${series}, ${instance}, "
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420 "@isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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421 "@patientKey, @studyKey, @seriesKey, @instanceKey)");
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422
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423 statement.SetParameterType("patient", ValueType_Utf8String);
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424 statement.SetParameterType("study", ValueType_Utf8String);
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425 statement.SetParameterType("series", ValueType_Utf8String);
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426 statement.SetParameterType("instance", ValueType_Utf8String);
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427
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428 Dictionary args;
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429 args.SetUtf8Value("patient", hashPatient);
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430 args.SetUtf8Value("study", hashStudy);
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431 args.SetUtf8Value("series", hashSeries);
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432 args.SetUtf8Value("instance", hashInstance);
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433
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434 statement.Execute(args);
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435
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436 if (!statement.IsDone())
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437 {
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438 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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439 }
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440 }
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441
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442 {
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443 DatabaseManager::CachedStatement statement(
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444 STATEMENT_FROM_HERE, GetManager(),
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445 "SELECT @isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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446 "@patientKey, @studyKey, @seriesKey, @instanceKey");
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447
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448 statement.Execute();
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449
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450 for (size_t i = 0; i < 8; i++)
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451 {
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452 statement.SetResultFieldType(i, ValueType_Integer64);
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453 }
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454
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455 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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456 result.instanceId = ReadInteger64(statement, 7);
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457
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458 if (result.isNewInstance)
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459 {
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460 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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461 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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462 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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463 result.patientId = ReadInteger64(statement, 4);
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464 result.studyId = ReadInteger64(statement, 5);
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465 result.seriesId = ReadInteger64(statement, 6);
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466 }
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467 }
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468 }
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469 #endif
0
7cea966b6829 initial commit
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470 }