Mercurial > hg > orthanc-databases
annotate MySQL/Plugins/MySQLIndex.cpp @ 185:7c46155b5bb4
fix mingw build
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 16 Dec 2020 13:59:17 +0100 |
parents | 275e14f57f1e |
children | 3236894320d6 |
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 | |
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5 * Copyright (C) 2017-2020 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 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 |
0 | 49 IDatabase* MySQLIndex::OpenInternal() |
50 { | |
51 uint32_t expectedVersion = 6; | |
52 if (context_) | |
53 { | |
54 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(context_); | |
55 } | |
56 else | |
57 { | |
58 // This case only occurs during unit testing | |
59 expectedVersion = 6; | |
60 } | |
61 | |
62 // Check the expected version of the database | |
63 if (expectedVersion != 6) | |
64 { | |
65 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc " | |
66 << "expecting the DB schema version " << expectedVersion | |
67 << ", but this plugin is only compatible with version 6"; | |
68 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin); | |
69 } | |
70 | |
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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 |
0 | 76 if (clearAll_) |
77 { | |
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78 MySQLDatabase::ClearDatabase(parameters_); |
0 | 79 } |
80 | |
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81 std::unique_ptr<MySQLDatabase> db(new MySQLDatabase(parameters_)); |
0 | 82 |
83 db->Open(); | |
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84 db->Execute("SET SESSION TRANSACTION ISOLATION LEVEL SERIALIZABLE", false); |
0 | 85 |
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86 { |
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87 MySQLDatabase::TransientAdvisoryLock lock(*db, MYSQL_LOCK_DATABASE_SETUP); |
0 | 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 **/ |
0 | 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); |
0 | 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 } |
0 | 118 |
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119 t.Commit(); |
0 | 120 } |
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 **/ |
0 | 129 |
130 int version = 0; | |
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131 |
0 | 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 | 162 } |
163 | |
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164 int revision = 0; |
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165 |
0 | 166 { |
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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(); |
0 | 176 } |
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 |
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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); |
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190 |
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191 t.Commit(); |
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192 } |
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193 |
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194 if (revision == 2) |
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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 } |
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209 |
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210 revision = 3; |
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211 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision); |
144
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212 |
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213 t.Commit(); |
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214 } |
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215 |
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216 if (revision == 3) |
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217 { |
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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 |
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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(); |
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231 } |
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232 |
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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; |
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239 |
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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 |
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244 revision = 5; |
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245 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision); |
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246 |
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247 t.Commit(); |
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248 } |
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249 |
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250 if (revision != 5) |
0 | 251 { |
53 | 252 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision; |
0 | 253 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); |
254 } | |
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 | 269 |
270 return db.release(); | |
271 } | |
272 | |
273 | |
274 MySQLIndex::MySQLIndex(const MySQLParameters& parameters) : | |
275 IndexBackend(new Factory(*this)), | |
276 context_(NULL), | |
277 parameters_(parameters), | |
278 clearAll_(false) | |
279 { | |
280 } | |
281 | |
282 | |
283 int64_t MySQLIndex::CreateResource(const char* publicId, | |
284 OrthancPluginResourceType type) | |
285 { | |
286 { | |
287 DatabaseManager::CachedStatement statement( | |
288 STATEMENT_FROM_HERE, GetManager(), | |
289 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL)"); | |
290 | |
291 statement.SetParameterType("id", ValueType_Utf8String); | |
292 statement.SetParameterType("type", ValueType_Integer64); | |
293 | |
294 Dictionary args; | |
295 args.SetUtf8Value("id", publicId); | |
296 args.SetIntegerValue("type", static_cast<int>(type)); | |
297 | |
298 statement.Execute(args); | |
299 } | |
300 | |
301 { | |
302 DatabaseManager::CachedStatement statement( | |
303 STATEMENT_FROM_HERE, GetManager(), | |
304 "SELECT LAST_INSERT_ID()"); | |
305 | |
306 statement.Execute(); | |
307 | |
308 return ReadInteger64(statement, 0); | |
309 } | |
310 } | |
311 | |
312 | |
313 void MySQLIndex::DeleteResource(int64_t id) | |
314 { | |
315 ClearDeletedFiles(); | |
316 | |
317 // Recursive exploration of resources to be deleted, from the "id" | |
318 // resource to the top of the tree of resources | |
319 | |
320 bool done = false; | |
321 | |
322 while (!done) | |
323 { | |
324 int64_t parentId; | |
325 | |
326 { | |
327 DatabaseManager::CachedStatement lookupSiblings( | |
328 STATEMENT_FROM_HERE, GetManager(), | |
329 "SELECT parentId FROM Resources " | |
330 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});"); | |
331 | |
332 lookupSiblings.SetParameterType("id", ValueType_Integer64); | |
333 | |
334 Dictionary args; | |
335 args.SetIntegerValue("id", id); | |
336 | |
337 lookupSiblings.Execute(args); | |
338 | |
339 if (lookupSiblings.IsDone()) | |
340 { | |
341 // "id" is a root node | |
342 done = true; | |
343 } | |
344 else | |
345 { | |
346 parentId = ReadInteger64(lookupSiblings, 0); | |
347 lookupSiblings.Next(); | |
348 | |
349 if (lookupSiblings.IsDone()) | |
350 { | |
351 // "id" has no sibling node, recursively remove | |
352 done = false; | |
353 id = parentId; | |
354 } | |
355 else | |
356 { | |
357 // "id" has at least one sibling node: the parent node is the remaining ancestor | |
358 done = true; | |
359 | |
360 DatabaseManager::CachedStatement parent( | |
361 STATEMENT_FROM_HERE, GetManager(), | |
362 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};"); | |
363 | |
364 parent.SetParameterType("id", ValueType_Integer64); | |
365 | |
366 Dictionary args; | |
367 args.SetIntegerValue("id", parentId); | |
368 | |
369 parent.Execute(args); | |
370 | |
371 GetOutput().SignalRemainingAncestor( | |
372 ReadString(parent, 0), | |
373 static_cast<OrthancPluginResourceType>(ReadInteger32(parent, 1))); | |
374 } | |
375 } | |
376 } | |
377 } | |
378 | |
379 { | |
380 DatabaseManager::CachedStatement deleteHierarchy( | |
381 STATEMENT_FROM_HERE, GetManager(), | |
382 "DELETE FROM Resources WHERE internalId IN (SELECT * FROM (SELECT internalId FROM Resources WHERE internalId=${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);"); | |
383 | |
384 deleteHierarchy.SetParameterType("id", ValueType_Integer64); | |
385 | |
386 Dictionary args; | |
387 args.SetIntegerValue("id", id); | |
388 | |
389 deleteHierarchy.Execute(args); | |
390 } | |
391 | |
392 SignalDeletedFiles(); | |
393 } | |
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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 } |
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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 | 470 } |