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annotate MySQL/Plugins/MySQLIndex.cpp @ 217:ee5858d438dc

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TransactionType given to MySQLTransaction constructor
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 26 Mar 2021 18:02:34 +0100
parents 2089d4071408
children 73cc85f3d9c1
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU Affero General Public License
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9 * as published by the Free Software Foundation, either version 3 of
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10 * the License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * Affero General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU Affero General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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20
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21
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22 #include "MySQLIndex.h"
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23
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24 #include "../../Framework/Plugins/GlobalProperties.h"
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25 #include "../../Framework/MySQL/MySQLDatabase.h"
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26 #include "../../Framework/MySQL/MySQLTransaction.h"
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27 #include "MySQLDefinitions.h"
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29 #include <EmbeddedResources.h> // Auto-generated file
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30
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31 #include <Compatibility.h> // For std::unique_ptr<>
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32 #include <Logging.h>
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33 #include <OrthancException.h>
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34
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35 #include <ctype.h>
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36
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37 namespace OrthancDatabases
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38 {
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39 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
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53 if (GetContext()) // "GetContext()" can possibly be NULL in the unit tests
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54 {
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55 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(GetContext());
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56 }
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57
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58 // Check the expected version of the database
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59 if (expectedVersion != 6)
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60 {
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61 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc "
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62 << "expecting the DB schema version " << expectedVersion
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63 << ", but this plugin is only compatible with version 6";
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64 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin);
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65 }
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66
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67 if (!MySQLDatabase::IsValidDatabaseIdentifier(parameters_.GetDatabase()))
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68 {
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69 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange);
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70 }
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71
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72 if (clearAll_)
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73 {
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74 MySQLDatabase::ClearDatabase(parameters_);
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75 }
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76
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77 std::unique_ptr<MySQLDatabase> db(new MySQLDatabase(parameters_));
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78
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79 db->Open();
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80 db->Execute("SET SESSION TRANSACTION ISOLATION LEVEL SERIALIZABLE", false);
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81
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82 {
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83 MySQLDatabase::TransientAdvisoryLock lock(*db, MYSQL_LOCK_DATABASE_SETUP);
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85 /**
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86 * In a first transaction, we create the tables. Such a
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87 * transaction cannot be rollback: "The CREATE TABLE statement
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88 * in InnoDB is processed as a single transaction. This means
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89 * that a ROLLBACK from the user does not undo CREATE TABLE
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90 * statements the user made during that transaction."
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91 * https://dev.mysql.com/doc/refman/8.0/en/implicit-commit.html
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92 *
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93 * As a consequence, we delay the initial population of the
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94 * tables in a sequence of transactions below. This solves the
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95 * error message "MySQL plugin is incompatible with database
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96 * schema version: 0" that was reported in the forum:
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97 * https://groups.google.com/d/msg/orthanc-users/OCFFkm1qm0k/Mbroy8VWAQAJ
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98 **/
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99 {
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100 MySQLTransaction t(*db, TransactionType_ReadWrite);
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101
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102 db->Execute("ALTER DATABASE " + parameters_.GetDatabase() +
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103 " CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci", false);
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104
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105 // This is the first table to be created
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106 if (!db->DoesTableExist(t, "GlobalProperties"))
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107 {
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108 std::string query;
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109
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110 Orthanc::EmbeddedResources::GetFileResource
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111 (query, Orthanc::EmbeddedResources::MYSQL_PREPARE_INDEX);
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112 db->Execute(query, true);
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113 }
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114
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115 t.Commit();
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116 }
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117
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118 /**
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119 * This is the sequence of transactions that initially populate
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120 * the database. WARNING - As table creation cannot be rollback,
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121 * don't forget to add "IF NOT EXISTS" if some table must be
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122 * created below this point (in order to recover from failed
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123 * transaction).
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124 **/
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125
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126 int version = 0;
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127
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128 {
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129 MySQLTransaction t(*db, TransactionType_ReadWrite);
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130
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131 // This is the last table to be created
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132 if (!db->DoesTableExist(t, "PatientRecyclingOrder"))
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133 {
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134 LOG(ERROR) << "Corrupted MySQL database";
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135 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError);
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136 }
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137
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138 // This is the last item to be created
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139 if (!db->DoesTriggerExist(t, "PatientAdded"))
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140 {
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141 ThrowCannotCreateTrigger();
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142 }
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143
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144 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion))
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145 {
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146 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion);
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147 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1);
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148 version = expectedVersion;
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149 }
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150
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151 if (version != 6)
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152 {
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153 LOG(ERROR) << "MySQL plugin is incompatible with database schema version: " << version;
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154 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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155 }
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156
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157 t.Commit();
0
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158 }
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159
144
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160 int revision = 0;
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161
0
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162 {
217
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163 MySQLTransaction t(*db, TransactionType_ReadWrite);
144
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164
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165 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel))
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166 {
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167 revision = 1;
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168 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
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169 }
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170
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171 t.Commit();
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172 }
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173
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174 if (revision == 1)
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175 {
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176 MySQLTransaction t(*db, TransactionType_ReadWrite);
144
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177
84
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178 // The serialization of jobs as a global property can lead to
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179 // very long values => switch to the LONGTEXT type that can
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180 // store up to 4GB:
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181 // https://stackoverflow.com/a/13932834/881731
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182 db->Execute("ALTER TABLE GlobalProperties MODIFY value LONGTEXT", false);
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183
84
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184 revision = 2;
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185 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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186
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187 t.Commit();
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188 }
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189
87
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190 if (revision == 2)
144
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191 {
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192 MySQLTransaction t(*db, TransactionType_ReadWrite);
144
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193
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194 // Install the "GetLastChangeIndex" extension
87
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195 std::string query;
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196
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197 Orthanc::EmbeddedResources::GetFileResource
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198 (query, Orthanc::EmbeddedResources::MYSQL_GET_LAST_CHANGE_INDEX);
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199 db->Execute(query, true);
144
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200
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201 if (!db->DoesTriggerExist(t, "ChangeAdded"))
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202 {
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203 ThrowCannotCreateTrigger();
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204 }
87
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205
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206 revision = 3;
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207 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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208
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209 t.Commit();
87
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210 }
144
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211
109
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212 if (revision == 3)
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213 {
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214 MySQLTransaction t(*db, TransactionType_ReadWrite);
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215
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216 // Reconfiguration of "Metadata" from TEXT type (up to 64KB)
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217 // to the LONGTEXT type (up to 4GB). This might be important
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218 // for applications such as the Osimis Web viewer that stores
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219 // large amount of metadata.
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220 // http://book.orthanc-server.com/faq/features.html#central-registry-of-metadata-and-attachments
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221 db->Execute("ALTER TABLE Metadata MODIFY value LONGTEXT", false);
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222
109
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223 revision = 4;
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224 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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225
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226 t.Commit();
109
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227 }
144
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228
110
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229 if (revision == 4)
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230 {
217
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231 MySQLTransaction t(*db, TransactionType_ReadWrite);
144
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232
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233 // Install the "CreateInstance" extension
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234 std::string query;
144
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235
110
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236 Orthanc::EmbeddedResources::GetFileResource
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237 (query, Orthanc::EmbeddedResources::MYSQL_CREATE_INSTANCE);
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238 db->Execute(query, true);
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239
110
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240 revision = 5;
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241 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision);
144
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242
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243 t.Commit();
110
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244 }
144
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245
110
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246 if (revision != 5)
0
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247 {
53
am@osimis.io
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248 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision;
0
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249 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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250 }
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251 }
137
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252
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253 /**
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254 * WARNING: This lock must be acquired after
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255 * "MYSQL_LOCK_DATABASE_SETUP" is released. Indeed, in MySQL <
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256 * 5.7, it is impossible to acquire more than one lock at a time,
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257 * as calling "SELECT GET_LOCK()" releases all the
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258 * previously-acquired locks.
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259 * https://dev.mysql.com/doc/refman/5.7/en/locking-functions.html
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260 **/
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261 if (parameters_.HasLock())
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262 {
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263 db->AdvisoryLock(MYSQL_LOCK_INDEX);
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264 }
0
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265
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266 return db.release();
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267 }
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268
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269
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270 MySQLIndex::MySQLIndex(OrthancPluginContext* context,
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271 const MySQLParameters& parameters) :
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272 IndexBackend(context, new Factory(*this)),
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273 parameters_(parameters),
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274 clearAll_(false)
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275 {
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276 }
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277
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278
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279 int64_t MySQLIndex::CreateResource(const char* publicId,
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280 OrthancPluginResourceType type)
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281 {
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282 {
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283 DatabaseManager::CachedStatement statement(
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284 STATEMENT_FROM_HERE, GetManager(),
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285 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL)");
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286
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287 statement.SetParameterType("id", ValueType_Utf8String);
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288 statement.SetParameterType("type", ValueType_Integer64);
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289
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290 Dictionary args;
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291 args.SetUtf8Value("id", publicId);
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292 args.SetIntegerValue("type", static_cast<int>(type));
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293
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294 statement.Execute(args);
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295 }
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296
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297 {
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298 DatabaseManager::CachedStatement statement(
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299 STATEMENT_FROM_HERE, GetManager(),
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300 "SELECT LAST_INSERT_ID()");
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301
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302 statement.Execute();
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303
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304 return ReadInteger64(statement, 0);
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305 }
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306 }
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307
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308
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309 void MySQLIndex::DeleteResource(IDatabaseBackendOutput& output,
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310 int64_t id)
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311 {
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312 ClearDeletedFiles();
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313
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314 // Recursive exploration of resources to be deleted, from the "id"
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315 // resource to the top of the tree of resources
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316
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317 bool done = false;
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318
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319 while (!done)
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320 {
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321 int64_t parentId;
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322
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323 {
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324 DatabaseManager::CachedStatement lookupSiblings(
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325 STATEMENT_FROM_HERE, GetManager(),
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326 "SELECT parentId FROM Resources "
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327 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});");
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328
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329 lookupSiblings.SetParameterType("id", ValueType_Integer64);
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330
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331 Dictionary args;
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332 args.SetIntegerValue("id", id);
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333
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334 lookupSiblings.Execute(args);
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335
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336 if (lookupSiblings.IsDone())
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337 {
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338 // "id" is a root node
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339 done = true;
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340 }
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341 else
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342 {
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343 parentId = ReadInteger64(lookupSiblings, 0);
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344 lookupSiblings.Next();
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345
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346 if (lookupSiblings.IsDone())
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347 {
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348 // "id" has no sibling node, recursively remove
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349 done = false;
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350 id = parentId;
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351 }
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352 else
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353 {
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354 // "id" has at least one sibling node: the parent node is the remaining ancestor
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355 done = true;
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356
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357 DatabaseManager::CachedStatement parent(
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358 STATEMENT_FROM_HERE, GetManager(),
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359 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};");
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360
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361 parent.SetParameterType("id", ValueType_Integer64);
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362
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363 Dictionary args;
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364 args.SetIntegerValue("id", parentId);
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365
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366 parent.Execute(args);
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367
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368 output.SignalRemainingAncestor(
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369 ReadString(parent, 0),
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370 static_cast<OrthancPluginResourceType>(ReadInteger32(parent, 1)));
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371 }
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372 }
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373 }
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374 }
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375
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376 {
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377 DatabaseManager::CachedStatement deleteHierarchy(
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378 STATEMENT_FROM_HERE, GetManager(),
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379 "DELETE FROM Resources WHERE internalId IN (SELECT * FROM (SELECT internalId FROM Resources WHERE internalId=${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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380
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381 deleteHierarchy.SetParameterType("id", ValueType_Integer64);
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382
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383 Dictionary args;
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384 args.SetIntegerValue("id", id);
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385
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386 deleteHierarchy.Execute(args);
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387 }
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388
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389 SignalDeletedFiles(output);
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390 }
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391
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392
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393 int64_t MySQLIndex::GetLastChangeIndex()
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394 {
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395 DatabaseManager::CachedStatement statement(
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396 STATEMENT_FROM_HERE, GetManager(),
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397 "SELECT value FROM GlobalIntegers WHERE property = 0");
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398
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399 statement.SetReadOnly(true);
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400 statement.Execute();
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401
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402 return ReadInteger64(statement, 0);
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403 }
110
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404
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405
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406 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1
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407 void MySQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result,
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408 const char* hashPatient,
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409 const char* hashStudy,
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410 const char* hashSeries,
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411 const char* hashInstance)
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412 {
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413 {
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414 DatabaseManager::CachedStatement statement(
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415 STATEMENT_FROM_HERE, GetManager(),
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416 "CALL CreateInstance(${patient}, ${study}, ${series}, ${instance}, "
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417 "@isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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418 "@patientKey, @studyKey, @seriesKey, @instanceKey)");
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419
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420 statement.SetParameterType("patient", ValueType_Utf8String);
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421 statement.SetParameterType("study", ValueType_Utf8String);
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422 statement.SetParameterType("series", ValueType_Utf8String);
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423 statement.SetParameterType("instance", ValueType_Utf8String);
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424
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425 Dictionary args;
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426 args.SetUtf8Value("patient", hashPatient);
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427 args.SetUtf8Value("study", hashStudy);
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428 args.SetUtf8Value("series", hashSeries);
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429 args.SetUtf8Value("instance", hashInstance);
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430
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431 statement.Execute(args);
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432
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433 if (!statement.IsDone())
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434 {
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435 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database);
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436 }
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437 }
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438
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439 {
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440 DatabaseManager::CachedStatement statement(
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441 STATEMENT_FROM_HERE, GetManager(),
441a472bfd93 new extension implemented for MySQL: CreateInstance
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442 "SELECT @isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, "
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443 "@patientKey, @studyKey, @seriesKey, @instanceKey");
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444
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445 statement.Execute();
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446
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447 for (size_t i = 0; i < 8; i++)
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448 {
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449 statement.SetResultFieldType(i, ValueType_Integer64);
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450 }
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451
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452 result.isNewInstance = (ReadInteger64(statement, 3) == 1);
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453 result.instanceId = ReadInteger64(statement, 7);
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454
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455 if (result.isNewInstance)
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456 {
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457 result.isNewPatient = (ReadInteger64(statement, 0) == 1);
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458 result.isNewStudy = (ReadInteger64(statement, 1) == 1);
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459 result.isNewSeries = (ReadInteger64(statement, 2) == 1);
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460 result.patientId = ReadInteger64(statement, 4);
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461 result.studyId = ReadInteger64(statement, 5);
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462 result.seriesId = ReadInteger64(statement, 6);
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463 }
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464 }
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465 }
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466 #endif
0
7cea966b6829 initial commit
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467 }