Mercurial > hg > orthanc
annotate OrthancServer/DatabaseWrapper.cpp @ 2294:e371519d4ac9
added -U option to gdcmconv to prevent gdcmconv to mess up the files. Without that option, we have seen the SpecificCharSet tag becoming invalid !!! (seen on the VIX samples)
| author | Alain Mazy <am@osimis.io> |
|---|---|
| date | Tue, 04 Jul 2017 15:36:19 +0000 |
| parents | a3a65de1840f |
| children | 878b59270859 |
| rev | line source |
|---|---|
| 183 | 1 /** |
| 2 * Orthanc - A Lightweight, RESTful DICOM Store | |
| 1900 | 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 Osimis, Belgium |
| 183 | 6 * |
| 7 * This program is free software: you can redistribute it and/or | |
| 8 * modify it under the terms of the GNU General Public License as | |
| 9 * published by the Free Software Foundation, either version 3 of the | |
| 10 * License, or (at your option) any later version. | |
| 11 * | |
| 12 * In addition, as a special exception, the copyright holders of this | |
| 13 * program give permission to link the code of its release with the | |
| 14 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 15 * that use the same license as the "OpenSSL" library), and distribute | |
| 16 * the linked executables. You must obey the GNU General Public License | |
| 17 * in all respects for all of the code used other than "OpenSSL". If you | |
| 18 * modify file(s) with this exception, you may extend this exception to | |
| 19 * your version of the file(s), but you are not obligated to do so. If | |
| 20 * you do not wish to do so, delete this exception statement from your | |
| 21 * version. If you delete this exception statement from all source files | |
| 22 * in the program, then also delete it here. | |
| 23 * | |
| 24 * This program is distributed in the hope that it will be useful, but | |
| 25 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 27 * General Public License for more details. | |
| 28 * | |
| 29 * You should have received a copy of the GNU General Public License | |
| 30 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 31 **/ | |
| 32 | |
| 33 | |
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34 #include "PrecompiledHeadersServer.h" |
| 183 | 35 #include "DatabaseWrapper.h" |
| 36 | |
| 37 #include "../Core/DicomFormat/DicomArray.h" | |
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38 #include "../Core/Logging.h" |
| 183 | 39 #include "EmbeddedResources.h" |
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40 #include "ServerToolbox.h" |
| 183 | 41 |
| 42 #include <stdio.h> | |
| 1247 | 43 #include <boost/lexical_cast.hpp> |
| 183 | 44 |
| 45 namespace Orthanc | |
| 46 { | |
| 47 | |
| 48 namespace Internals | |
| 49 { | |
| 50 class SignalFileDeleted : public SQLite::IScalarFunction | |
| 51 { | |
| 52 private: | |
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53 IDatabaseListener& listener_; |
| 183 | 54 |
| 55 public: | |
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56 SignalFileDeleted(IDatabaseListener& listener) : |
| 183 | 57 listener_(listener) |
| 58 { | |
| 59 } | |
| 60 | |
| 61 virtual const char* GetName() const | |
| 62 { | |
| 63 return "SignalFileDeleted"; | |
| 64 } | |
| 65 | |
| 66 virtual unsigned int GetCardinality() const | |
| 67 { | |
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68 return 7; |
| 183 | 69 } |
| 70 | |
| 71 virtual void Compute(SQLite::FunctionContext& context) | |
| 72 { | |
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73 std::string uncompressedMD5, compressedMD5; |
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74 |
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75 if (!context.IsNullValue(5)) |
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76 { |
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77 uncompressedMD5 = context.GetStringValue(5); |
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78 } |
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79 |
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80 if (!context.IsNullValue(6)) |
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81 { |
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82 compressedMD5 = context.GetStringValue(6); |
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83 } |
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84 |
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85 FileInfo info(context.GetStringValue(0), |
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86 static_cast<FileContentType>(context.GetIntValue(1)), |
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87 static_cast<uint64_t>(context.GetInt64Value(2)), |
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88 uncompressedMD5, |
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89 static_cast<CompressionType>(context.GetIntValue(3)), |
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90 static_cast<uint64_t>(context.GetInt64Value(4)), |
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91 compressedMD5); |
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92 |
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93 listener_.SignalFileDeleted(info); |
| 183 | 94 } |
| 95 }; | |
| 96 | |
| 1158 | 97 class SignalResourceDeleted : public SQLite::IScalarFunction |
| 98 { | |
| 99 private: | |
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100 IDatabaseListener& listener_; |
| 1158 | 101 |
| 102 public: | |
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103 SignalResourceDeleted(IDatabaseListener& listener) : |
| 1158 | 104 listener_(listener) |
| 105 { | |
| 106 } | |
| 107 | |
| 108 virtual const char* GetName() const | |
| 109 { | |
| 110 return "SignalResourceDeleted"; | |
| 111 } | |
| 112 | |
| 113 virtual unsigned int GetCardinality() const | |
| 114 { | |
| 115 return 2; | |
| 116 } | |
| 117 | |
| 118 virtual void Compute(SQLite::FunctionContext& context) | |
| 119 { | |
| 120 ResourceType type = static_cast<ResourceType>(context.GetIntValue(1)); | |
| 1198 | 121 ServerIndexChange change(ChangeType_Deleted, type, context.GetStringValue(0)); |
| 122 listener_.SignalChange(change); | |
| 1158 | 123 } |
| 124 }; | |
| 125 | |
| 183 | 126 class SignalRemainingAncestor : public SQLite::IScalarFunction |
| 127 { | |
| 128 private: | |
| 129 bool hasRemainingAncestor_; | |
| 130 std::string remainingPublicId_; | |
| 131 ResourceType remainingType_; | |
| 132 | |
| 133 public: | |
| 660 | 134 SignalRemainingAncestor() : |
| 135 hasRemainingAncestor_(false) | |
| 136 { | |
| 137 } | |
| 138 | |
| 183 | 139 void Reset() |
| 140 { | |
| 141 hasRemainingAncestor_ = false; | |
| 142 } | |
| 143 | |
| 144 virtual const char* GetName() const | |
| 145 { | |
| 146 return "SignalRemainingAncestor"; | |
| 147 } | |
| 148 | |
| 149 virtual unsigned int GetCardinality() const | |
| 150 { | |
| 151 return 2; | |
| 152 } | |
| 153 | |
| 154 virtual void Compute(SQLite::FunctionContext& context) | |
| 155 { | |
| 156 VLOG(1) << "There exists a remaining ancestor with public ID \"" | |
| 157 << context.GetStringValue(0) | |
| 158 << "\" of type " | |
| 159 << context.GetIntValue(1); | |
| 160 | |
| 161 if (!hasRemainingAncestor_ || | |
| 162 remainingType_ >= context.GetIntValue(1)) | |
| 163 { | |
| 164 hasRemainingAncestor_ = true; | |
| 165 remainingPublicId_ = context.GetStringValue(0); | |
| 166 remainingType_ = static_cast<ResourceType>(context.GetIntValue(1)); | |
| 167 } | |
| 168 } | |
| 169 | |
| 170 bool HasRemainingAncestor() const | |
| 171 { | |
| 172 return hasRemainingAncestor_; | |
| 173 } | |
| 174 | |
| 175 const std::string& GetRemainingAncestorId() const | |
| 176 { | |
| 177 assert(hasRemainingAncestor_); | |
| 178 return remainingPublicId_; | |
| 179 } | |
| 180 | |
| 181 ResourceType GetRemainingAncestorType() const | |
| 182 { | |
| 183 assert(hasRemainingAncestor_); | |
| 184 return remainingType_; | |
| 185 } | |
| 186 }; | |
| 187 } | |
| 188 | |
| 189 | |
| 1241 | 190 |
| 191 void DatabaseWrapper::GetChildren(std::list<std::string>& childrenPublicIds, | |
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192 int64_t id) |
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193 { |
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194 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT publicId FROM Resources WHERE parentId=?"); |
| 585 | 195 s.BindInt64(0, id); |
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196 |
| 1241 | 197 childrenPublicIds.clear(); |
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198 while (s.Step()) |
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199 { |
| 1241 | 200 childrenPublicIds.push_back(s.ColumnString(0)); |
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201 } |
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202 } |
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203 |
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204 |
| 183 | 205 void DatabaseWrapper::DeleteResource(int64_t id) |
| 206 { | |
| 207 signalRemainingAncestor_->Reset(); | |
| 208 | |
| 209 SQLite::Statement s(db_, SQLITE_FROM_HERE, "DELETE FROM Resources WHERE internalId=?"); | |
| 585 | 210 s.BindInt64(0, id); |
| 183 | 211 s.Run(); |
| 212 | |
| 1247 | 213 if (signalRemainingAncestor_->HasRemainingAncestor() && |
| 214 listener_ != NULL) | |
| 183 | 215 { |
| 1247 | 216 listener_->SignalRemainingAncestor(signalRemainingAncestor_->GetRemainingAncestorType(), |
| 217 signalRemainingAncestor_->GetRemainingAncestorId()); | |
| 183 | 218 } |
| 219 } | |
| 220 | |
| 221 | |
| 1301 | 222 bool DatabaseWrapper::GetParentPublicId(std::string& target, |
| 183 | 223 int64_t id) |
| 224 { | |
| 225 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT a.publicId FROM Resources AS a, Resources AS b " | |
| 226 "WHERE a.internalId = b.parentId AND b.internalId = ?"); | |
| 585 | 227 s.BindInt64(0, id); |
| 183 | 228 |
| 229 if (s.Step()) | |
| 230 { | |
| 1301 | 231 target = s.ColumnString(0); |
| 183 | 232 return true; |
| 233 } | |
| 234 else | |
| 235 { | |
| 236 return false; | |
| 237 } | |
| 238 } | |
| 239 | |
| 240 | |
| 241 int64_t DatabaseWrapper::GetTableRecordCount(const std::string& table) | |
| 242 { | |
| 243 char buf[128]; | |
| 244 sprintf(buf, "SELECT COUNT(*) FROM %s", table.c_str()); | |
| 245 SQLite::Statement s(db_, buf); | |
| 246 | |
| 218 | 247 if (!s.Step()) |
| 248 { | |
| 249 throw OrthancException(ErrorCode_InternalError); | |
| 250 } | |
| 251 | |
| 183 | 252 int64_t c = s.ColumnInt(0); |
| 253 assert(!s.Step()); | |
| 254 | |
| 255 return c; | |
| 256 } | |
| 257 | |
| 258 | |
| 1847 | 259 DatabaseWrapper::DatabaseWrapper(const std::string& path) : |
| 260 listener_(NULL), | |
| 261 base_(db_), | |
| 262 signalRemainingAncestor_(NULL), | |
| 263 version_(0) | |
| 183 | 264 { |
| 265 db_.Open(path); | |
| 266 } | |
| 267 | |
| 1847 | 268 DatabaseWrapper::DatabaseWrapper() : |
| 269 listener_(NULL), | |
| 270 base_(db_), | |
| 271 signalRemainingAncestor_(NULL), | |
| 272 version_(0) | |
| 183 | 273 { |
| 274 db_.OpenInMemory(); | |
| 275 } | |
| 276 | |
| 277 void DatabaseWrapper::Open() | |
| 278 { | |
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279 db_.Execute("PRAGMA ENCODING=\"UTF-8\";"); |
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280 |
| 374 | 281 // Performance tuning of SQLite with PRAGMAs |
| 282 // http://www.sqlite.org/pragma.html | |
| 283 db_.Execute("PRAGMA SYNCHRONOUS=NORMAL;"); | |
| 284 db_.Execute("PRAGMA JOURNAL_MODE=WAL;"); | |
| 285 db_.Execute("PRAGMA LOCKING_MODE=EXCLUSIVE;"); | |
| 286 db_.Execute("PRAGMA WAL_AUTOCHECKPOINT=1000;"); | |
| 287 //db_.Execute("PRAGMA TEMP_STORE=memory"); | |
| 288 | |
| 183 | 289 if (!db_.DoesTableExist("GlobalProperties")) |
| 290 { | |
| 291 LOG(INFO) << "Creating the database"; | |
| 292 std::string query; | |
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293 EmbeddedResources::GetFileResource(query, EmbeddedResources::PREPARE_DATABASE); |
| 183 | 294 db_.Execute(query); |
| 295 } | |
| 296 | |
| 567 | 297 // Check the version of the database |
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298 std::string tmp; |
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299 if (!LookupGlobalProperty(tmp, GlobalProperty_DatabaseSchemaVersion)) |
| 1239 | 300 { |
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301 tmp = "Unknown"; |
| 1239 | 302 } |
| 303 | |
| 252 | 304 bool ok = false; |
| 305 try | |
| 306 { | |
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307 LOG(INFO) << "Version of the Orthanc database: " << tmp; |
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308 version_ = boost::lexical_cast<unsigned int>(tmp); |
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309 ok = true; |
| 252 | 310 } |
| 311 catch (boost::bad_lexical_cast&) | |
| 312 { | |
| 313 } | |
| 314 | |
| 315 if (!ok) | |
| 316 { | |
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317 LOG(ERROR) << "Incompatible version of the Orthanc database: " << tmp; |
| 252 | 318 throw OrthancException(ErrorCode_IncompatibleDatabaseVersion); |
| 319 } | |
| 320 | |
| 183 | 321 signalRemainingAncestor_ = new Internals::SignalRemainingAncestor; |
| 322 db_.Register(signalRemainingAncestor_); | |
| 1247 | 323 } |
| 324 | |
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325 |
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326 static void ExecuteUpgradeScript(SQLite::Connection& db, |
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327 EmbeddedResources::FileResourceId script) |
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328 { |
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329 std::string upgrade; |
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330 EmbeddedResources::GetFileResource(upgrade, script); |
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331 db.BeginTransaction(); |
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332 db.Execute(upgrade); |
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333 db.CommitTransaction(); |
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334 } |
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335 |
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336 |
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337 void DatabaseWrapper::Upgrade(unsigned int targetVersion, |
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338 IStorageArea& storageArea) |
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339 { |
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340 if (targetVersion != 6) |
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341 { |
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342 throw OrthancException(ErrorCode_IncompatibleDatabaseVersion); |
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343 } |
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344 |
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345 // This version of Orthanc is only compatible with versions 3, 4, |
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346 // 5 and 6 of the DB schema |
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347 if (version_ != 3 && |
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348 version_ != 4 && |
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349 version_ != 5 && |
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350 version_ != 6) |
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351 { |
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352 throw OrthancException(ErrorCode_IncompatibleDatabaseVersion); |
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353 } |
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354 |
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355 if (version_ == 3) |
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356 { |
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357 LOG(WARNING) << "Upgrading database version from 3 to 4"; |
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358 ExecuteUpgradeScript(db_, EmbeddedResources::UPGRADE_DATABASE_3_TO_4); |
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359 version_ = 4; |
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360 } |
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361 |
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362 if (version_ == 4) |
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363 { |
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364 LOG(WARNING) << "Upgrading database version from 4 to 5"; |
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365 ExecuteUpgradeScript(db_, EmbeddedResources::UPGRADE_DATABASE_4_TO_5); |
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366 version_ = 5; |
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367 } |
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368 |
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369 if (version_ == 5) |
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370 { |
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371 LOG(WARNING) << "Upgrading database version from 5 to 6"; |
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372 // No change in the DB schema, the step from version 5 to 6 only |
| 1710 | 373 // consists in reconstructing the main DICOM tags information |
| 374 // (as more tags got included). | |
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375 db_.BeginTransaction(); |
| 2120 | 376 ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Patient); |
| 377 ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Study); | |
| 378 ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Series); | |
| 379 ServerToolbox::ReconstructMainDicomTags(*this, storageArea, ResourceType_Instance); | |
| 1710 | 380 db_.Execute("UPDATE GlobalProperties SET value=\"6\" WHERE property=" + |
| 381 boost::lexical_cast<std::string>(GlobalProperty_DatabaseSchemaVersion) + ";"); | |
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382 db_.CommitTransaction(); |
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383 version_ = 6; |
| 1729 | 384 } |
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385 } |
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386 |
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387 |
|
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388 void DatabaseWrapper::SetListener(IDatabaseListener& listener) |
| 1247 | 389 { |
| 390 listener_ = &listener; | |
| 391 db_.Register(new Internals::SignalFileDeleted(listener)); | |
| 392 db_.Register(new Internals::SignalResourceDeleted(listener)); | |
| 183 | 393 } |
| 238 | 394 |
|
413
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395 |
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396 void DatabaseWrapper::ClearTable(const std::string& tableName) |
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397 { |
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398 db_.Execute("DELETE FROM " + tableName); |
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399 } |
| 513 | 400 |
| 401 | |
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402 bool DatabaseWrapper::LookupParent(int64_t& parentId, |
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403 int64_t resourceId) |
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404 { |
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405 bool found; |
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406 ErrorCode error = base_.LookupParent(found, parentId, resourceId); |
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407 |
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408 if (error != ErrorCode_Success) |
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409 { |
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410 throw OrthancException(error); |
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411 } |
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412 else |
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413 { |
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414 return found; |
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415 } |
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416 } |
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417 |
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418 |
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419 ResourceType DatabaseWrapper::GetResourceType(int64_t resourceId) |
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420 { |
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421 ResourceType result; |
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422 ErrorCode code = base_.GetResourceType(result, resourceId); |
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423 |
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424 if (code == ErrorCode_Success) |
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425 { |
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426 return result; |
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427 } |
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428 else |
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429 { |
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430 throw OrthancException(code); |
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431 } |
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432 } |
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433 |
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434 |
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435 std::string DatabaseWrapper::GetPublicId(int64_t resourceId) |
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436 { |
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437 std::string id; |
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438 |
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439 if (base_.GetPublicId(id, resourceId)) |
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440 { |
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441 return id; |
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442 } |
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443 else |
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444 { |
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445 throw OrthancException(ErrorCode_UnknownResource); |
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446 } |
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447 } |
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448 |
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449 |
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450 void DatabaseWrapper::GetChanges(std::list<ServerIndexChange>& target /*out*/, |
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451 bool& done /*out*/, |
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452 int64_t since, |
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453 uint32_t maxResults) |
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454 { |
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455 ErrorCode code = base_.GetChanges(target, done, since, maxResults); |
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456 |
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457 if (code != ErrorCode_Success) |
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458 { |
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459 throw OrthancException(code); |
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460 } |
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461 } |
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462 |
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463 |
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464 void DatabaseWrapper::GetLastChange(std::list<ServerIndexChange>& target /*out*/) |
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465 { |
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466 ErrorCode code = base_.GetLastChange(target); |
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467 |
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468 if (code != ErrorCode_Success) |
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parents:
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469 { |
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470 throw OrthancException(code); |
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471 } |
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472 } |
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473 |
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474 |
| 1301 | 475 void DatabaseWrapper::GetAllMetadata(std::map<MetadataType, std::string>& target, |
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476 int64_t id) |
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477 { |
| 1301 | 478 target.clear(); |
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479 |
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480 SQLite::Statement s(db_, SQLITE_FROM_HERE, "SELECT type, value FROM Metadata WHERE id=?"); |
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481 s.BindInt64(0, id); |
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482 |
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483 while (s.Step()) |
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proper handling of metadata in Store
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parents:
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484 { |
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parents:
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485 MetadataType key = static_cast<MetadataType>(s.ColumnInt(0)); |
| 1301 | 486 target[key] = s.ColumnString(1); |
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487 } |
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parents:
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488 } |
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489 |
| 183 | 490 } |