Mercurial > hg > orthanc-databases
annotate MySQL/Plugins/MySQLIndex.cpp @ 135:e26690365c25
MySQL: Added an advisory lock to avoid race conditions during database setup
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Wed, 08 May 2019 21:09:18 +0200 |
| parents | 441a472bfd93 |
| children | 52b3859ee0b7 |
| rev | line source |
|---|---|
| 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 | |
| 67 | 5 * Copyright (C) 2017-2019 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" | |
| 27 | |
| 28 #include <EmbeddedResources.h> // Auto-generated file | |
| 29 | |
| 30 #include <Core/Logging.h> | |
| 31 #include <Core/OrthancException.h> | |
| 32 | |
| 33 #include <ctype.h> | |
| 34 | |
| 35 namespace OrthancDatabases | |
| 36 { | |
| 37 IDatabase* MySQLIndex::OpenInternal() | |
| 38 { | |
| 39 uint32_t expectedVersion = 6; | |
| 40 if (context_) | |
| 41 { | |
| 42 expectedVersion = OrthancPluginGetExpectedDatabaseVersion(context_); | |
| 43 } | |
| 44 else | |
| 45 { | |
| 46 // This case only occurs during unit testing | |
| 47 expectedVersion = 6; | |
| 48 } | |
| 49 | |
| 50 // Check the expected version of the database | |
| 51 if (expectedVersion != 6) | |
| 52 { | |
| 53 LOG(ERROR) << "This database plugin is incompatible with your version of Orthanc " | |
| 54 << "expecting the DB schema version " << expectedVersion | |
| 55 << ", but this plugin is only compatible with version 6"; | |
| 56 throw Orthanc::OrthancException(Orthanc::ErrorCode_Plugin); | |
| 57 } | |
| 58 | |
|
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59 if (!MySQLDatabase::IsValidDatabaseIdentifier(parameters_.GetDatabase())) |
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60 { |
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61 throw Orthanc::OrthancException(Orthanc::ErrorCode_ParameterOutOfRange); |
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62 } |
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63 |
| 0 | 64 if (clearAll_) |
| 65 { | |
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66 MySQLDatabase::ClearDatabase(parameters_); |
| 0 | 67 } |
| 68 | |
| 69 std::auto_ptr<MySQLDatabase> db(new MySQLDatabase(parameters_)); | |
| 70 | |
| 71 db->Open(); | |
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72 |
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73 db->Execute("SET SESSION TRANSACTION ISOLATION LEVEL SERIALIZABLE", false); |
| 0 | 74 |
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75 if (parameters_.HasLock()) |
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76 { |
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77 db->AdvisoryLock(42 /* some arbitrary constant */); |
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78 } |
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79 |
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80 /** |
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81 * Try and acquire a transient advisory lock to protect the setup |
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82 * of the database, because concurrent statements like "CREATE |
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83 * TABLE" are not protected by transactions. |
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84 * https://groups.google.com/d/msg/orthanc-users/yV3LSTh_TjI/h3PRApJFBAAJ |
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85 **/ |
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86 MySQLDatabase::TransientAdvisoryLock lock(*db, 44 /* some arbitrary constant */); |
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87 |
| 0 | 88 { |
| 89 MySQLTransaction t(*db); | |
| 90 | |
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91 db->Execute("ALTER DATABASE " + parameters_.GetDatabase() + |
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92 " CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci", false); |
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93 |
| 0 | 94 if (!db->DoesTableExist(t, "Resources")) |
| 95 { | |
| 96 std::string query; | |
| 97 | |
| 98 Orthanc::EmbeddedResources::GetFileResource | |
| 99 (query, Orthanc::EmbeddedResources::MYSQL_PREPARE_INDEX); | |
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100 db->Execute(query, true); |
| 0 | 101 |
| 102 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion, expectedVersion); | |
| 103 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, 1); | |
| 104 } | |
| 105 | |
| 106 if (!db->DoesTableExist(t, "Resources")) | |
| 107 { | |
| 108 LOG(ERROR) << "Corrupted MySQL database"; | |
| 109 throw Orthanc::OrthancException(Orthanc::ErrorCode_InternalError); | |
| 110 } | |
| 111 | |
| 112 int version = 0; | |
| 113 if (!LookupGlobalIntegerProperty(version, *db, t, Orthanc::GlobalProperty_DatabaseSchemaVersion) || | |
| 114 version != 6) | |
| 115 { | |
| 53 | 116 LOG(ERROR) << "MySQL plugin is incompatible with database schema version: " << version; |
| 0 | 117 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); |
| 118 } | |
| 119 | |
| 120 int revision; | |
| 121 if (!LookupGlobalIntegerProperty(revision, *db, t, Orthanc::GlobalProperty_DatabasePatchLevel)) | |
| 122 { | |
| 123 revision = 1; | |
| 124 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision); | |
| 125 } | |
| 126 | |
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127 if (revision == 1) |
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128 { |
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129 // The serialization of jobs as a global property can lead to |
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130 // very long values => switch to the LONGTEXT type that can |
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131 // store up to 4GB: |
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132 // https://stackoverflow.com/a/13932834/881731 |
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133 db->Execute("ALTER TABLE GlobalProperties MODIFY value LONGTEXT", false); |
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134 |
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135 revision = 2; |
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136 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision); |
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137 } |
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138 |
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139 if (revision == 2) |
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140 { |
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141 // Install the "GetLastChangeIndex" extension |
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142 std::string query; |
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143 |
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144 Orthanc::EmbeddedResources::GetFileResource |
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145 (query, Orthanc::EmbeddedResources::MYSQL_GET_LAST_CHANGE_INDEX); |
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146 db->Execute(query, true); |
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147 |
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148 revision = 3; |
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149 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision); |
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150 } |
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151 |
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152 if (revision == 3) |
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153 { |
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154 // Reconfiguration of "Metadata" from TEXT type (up to 64KB) |
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155 // to the LONGTEXT type (up to 4GB). This might be important |
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156 // for applications such as the Osimis Web viewer that stores |
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157 // large amount of metadata. |
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158 // http://book.orthanc-server.com/faq/features.html#central-registry-of-metadata-and-attachments |
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159 db->Execute("ALTER TABLE Metadata MODIFY value LONGTEXT", false); |
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160 |
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161 revision = 4; |
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162 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision); |
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163 } |
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164 |
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165 if (revision == 4) |
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166 { |
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167 // Install the "CreateInstance" extension |
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168 std::string query; |
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169 |
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170 Orthanc::EmbeddedResources::GetFileResource |
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171 (query, Orthanc::EmbeddedResources::MYSQL_CREATE_INSTANCE); |
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172 db->Execute(query, true); |
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173 |
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174 revision = 5; |
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175 SetGlobalIntegerProperty(*db, t, Orthanc::GlobalProperty_DatabasePatchLevel, revision); |
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176 } |
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177 |
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178 if (revision != 5) |
| 0 | 179 { |
| 53 | 180 LOG(ERROR) << "MySQL plugin is incompatible with database schema revision: " << revision; |
| 0 | 181 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); |
| 182 } | |
| 183 | |
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184 t.Commit(); |
| 0 | 185 } |
| 186 | |
| 187 return db.release(); | |
| 188 } | |
| 189 | |
| 190 | |
| 191 MySQLIndex::MySQLIndex(const MySQLParameters& parameters) : | |
| 192 IndexBackend(new Factory(*this)), | |
| 193 context_(NULL), | |
| 194 parameters_(parameters), | |
| 195 clearAll_(false) | |
| 196 { | |
| 197 } | |
| 198 | |
| 199 | |
| 200 int64_t MySQLIndex::CreateResource(const char* publicId, | |
| 201 OrthancPluginResourceType type) | |
| 202 { | |
| 203 { | |
| 204 DatabaseManager::CachedStatement statement( | |
| 205 STATEMENT_FROM_HERE, GetManager(), | |
| 206 "INSERT INTO Resources VALUES(${}, ${type}, ${id}, NULL)"); | |
| 207 | |
| 208 statement.SetParameterType("id", ValueType_Utf8String); | |
| 209 statement.SetParameterType("type", ValueType_Integer64); | |
| 210 | |
| 211 Dictionary args; | |
| 212 args.SetUtf8Value("id", publicId); | |
| 213 args.SetIntegerValue("type", static_cast<int>(type)); | |
| 214 | |
| 215 statement.Execute(args); | |
| 216 } | |
| 217 | |
| 218 { | |
| 219 DatabaseManager::CachedStatement statement( | |
| 220 STATEMENT_FROM_HERE, GetManager(), | |
| 221 "SELECT LAST_INSERT_ID()"); | |
| 222 | |
| 223 statement.Execute(); | |
| 224 | |
| 225 return ReadInteger64(statement, 0); | |
| 226 } | |
| 227 } | |
| 228 | |
| 229 | |
| 230 void MySQLIndex::DeleteResource(int64_t id) | |
| 231 { | |
| 232 ClearDeletedFiles(); | |
| 233 | |
| 234 // Recursive exploration of resources to be deleted, from the "id" | |
| 235 // resource to the top of the tree of resources | |
| 236 | |
| 237 bool done = false; | |
| 238 | |
| 239 while (!done) | |
| 240 { | |
| 241 int64_t parentId; | |
| 242 | |
| 243 { | |
| 244 DatabaseManager::CachedStatement lookupSiblings( | |
| 245 STATEMENT_FROM_HERE, GetManager(), | |
| 246 "SELECT parentId FROM Resources " | |
| 247 "WHERE parentId = (SELECT parentId FROM Resources WHERE internalId=${id});"); | |
| 248 | |
| 249 lookupSiblings.SetParameterType("id", ValueType_Integer64); | |
| 250 | |
| 251 Dictionary args; | |
| 252 args.SetIntegerValue("id", id); | |
| 253 | |
| 254 lookupSiblings.Execute(args); | |
| 255 | |
| 256 if (lookupSiblings.IsDone()) | |
| 257 { | |
| 258 // "id" is a root node | |
| 259 done = true; | |
| 260 } | |
| 261 else | |
| 262 { | |
| 263 parentId = ReadInteger64(lookupSiblings, 0); | |
| 264 lookupSiblings.Next(); | |
| 265 | |
| 266 if (lookupSiblings.IsDone()) | |
| 267 { | |
| 268 // "id" has no sibling node, recursively remove | |
| 269 done = false; | |
| 270 id = parentId; | |
| 271 } | |
| 272 else | |
| 273 { | |
| 274 // "id" has at least one sibling node: the parent node is the remaining ancestor | |
| 275 done = true; | |
| 276 | |
| 277 DatabaseManager::CachedStatement parent( | |
| 278 STATEMENT_FROM_HERE, GetManager(), | |
| 279 "SELECT publicId, resourceType FROM Resources WHERE internalId=${id};"); | |
| 280 | |
| 281 parent.SetParameterType("id", ValueType_Integer64); | |
| 282 | |
| 283 Dictionary args; | |
| 284 args.SetIntegerValue("id", parentId); | |
| 285 | |
| 286 parent.Execute(args); | |
| 287 | |
| 288 GetOutput().SignalRemainingAncestor( | |
| 289 ReadString(parent, 0), | |
| 290 static_cast<OrthancPluginResourceType>(ReadInteger32(parent, 1))); | |
| 291 } | |
| 292 } | |
| 293 } | |
| 294 } | |
| 295 | |
| 296 { | |
| 297 DatabaseManager::CachedStatement deleteHierarchy( | |
| 298 STATEMENT_FROM_HERE, GetManager(), | |
| 299 "DELETE FROM Resources WHERE internalId IN (SELECT * FROM (SELECT internalId FROM Resources WHERE internalId=${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);"); | |
| 300 | |
| 301 deleteHierarchy.SetParameterType("id", ValueType_Integer64); | |
| 302 | |
| 303 Dictionary args; | |
| 304 args.SetIntegerValue("id", id); | |
| 305 | |
| 306 deleteHierarchy.Execute(args); | |
| 307 } | |
| 308 | |
| 309 SignalDeletedFiles(); | |
| 310 } | |
|
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311 |
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312 |
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313 int64_t MySQLIndex::GetLastChangeIndex() |
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314 { |
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315 DatabaseManager::CachedStatement statement( |
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316 STATEMENT_FROM_HERE, GetManager(), |
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317 "SELECT value FROM GlobalIntegers WHERE property = 0"); |
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318 |
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319 statement.SetReadOnly(true); |
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320 statement.Execute(); |
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321 |
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322 return ReadInteger64(statement, 0); |
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323 } |
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324 |
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325 |
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326 #if ORTHANC_PLUGINS_HAS_DATABASE_CONSTRAINT == 1 |
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327 void MySQLIndex::CreateInstance(OrthancPluginCreateInstanceResult& result, |
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328 const char* hashPatient, |
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329 const char* hashStudy, |
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330 const char* hashSeries, |
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331 const char* hashInstance) |
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332 { |
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333 { |
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334 DatabaseManager::CachedStatement statement( |
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335 STATEMENT_FROM_HERE, GetManager(), |
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336 "CALL CreateInstance(${patient}, ${study}, ${series}, ${instance}, " |
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337 "@isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, " |
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338 "@patientKey, @studyKey, @seriesKey, @instanceKey)"); |
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339 |
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340 statement.SetParameterType("patient", ValueType_Utf8String); |
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341 statement.SetParameterType("study", ValueType_Utf8String); |
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342 statement.SetParameterType("series", ValueType_Utf8String); |
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343 statement.SetParameterType("instance", ValueType_Utf8String); |
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344 |
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345 Dictionary args; |
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346 args.SetUtf8Value("patient", hashPatient); |
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347 args.SetUtf8Value("study", hashStudy); |
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348 args.SetUtf8Value("series", hashSeries); |
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349 args.SetUtf8Value("instance", hashInstance); |
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350 |
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351 statement.Execute(args); |
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352 |
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353 if (!statement.IsDone()) |
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354 { |
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355 throw Orthanc::OrthancException(Orthanc::ErrorCode_Database); |
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356 } |
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357 } |
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358 |
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359 { |
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360 DatabaseManager::CachedStatement statement( |
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361 STATEMENT_FROM_HERE, GetManager(), |
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362 "SELECT @isNewPatient, @isNewStudy, @isNewSeries, @isNewInstance, " |
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363 "@patientKey, @studyKey, @seriesKey, @instanceKey"); |
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364 |
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365 statement.Execute(); |
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366 |
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367 for (size_t i = 0; i < 8; i++) |
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368 { |
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369 statement.SetResultFieldType(i, ValueType_Integer64); |
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370 } |
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371 |
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372 result.isNewInstance = (ReadInteger64(statement, 3) == 1); |
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373 result.instanceId = ReadInteger64(statement, 7); |
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374 |
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375 if (result.isNewInstance) |
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376 { |
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377 result.isNewPatient = (ReadInteger64(statement, 0) == 1); |
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378 result.isNewStudy = (ReadInteger64(statement, 1) == 1); |
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379 result.isNewSeries = (ReadInteger64(statement, 2) == 1); |
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380 result.patientId = ReadInteger64(statement, 4); |
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381 result.studyId = ReadInteger64(statement, 5); |
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382 result.seriesId = ReadInteger64(statement, 6); |
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383 } |
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384 } |
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385 } |
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386 #endif |
| 0 | 387 } |