Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 224:4eb0c7ce86c9
refactoring for store
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 29 Nov 2012 22:22:00 +0100 |
| parents | bb8c260c0092 |
| children | 8a26a8e85edf |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
| 0 | 3 * Copyright (C) 2012 Medical Physics Department, CHU of Liege, |
| 4 * Belgium | |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 136 | 10 * |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 0 | 22 * |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 32 | |
| 33 #include "ServerIndex.h" | |
| 34 | |
| 62 | 35 using namespace Orthanc; |
| 0 | 36 |
| 6 | 37 #ifndef NOMINMAX |
| 2 | 38 #define NOMINMAX |
| 6 | 39 #endif |
| 40 | |
| 8 | 41 #include "EmbeddedResources.h" |
| 0 | 42 #include "../Core/Toolbox.h" |
| 43 #include "../Core/Uuid.h" | |
| 44 #include "../Core/DicomFormat/DicomArray.h" | |
| 45 #include "../Core/SQLite/Transaction.h" | |
| 46 #include "FromDcmtkBridge.h" | |
| 47 | |
| 48 #include <boost/lexical_cast.hpp> | |
| 49 #include <stdio.h> | |
| 108 | 50 #include <glog/logging.h> |
| 0 | 51 |
| 62 | 52 namespace Orthanc |
| 0 | 53 { |
| 54 namespace Internals | |
| 55 { | |
| 202 | 56 class ServerIndexListener : public IServerIndexListener |
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57 { |
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58 private: |
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59 FileStorage& fileStorage_; |
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60 bool hasRemainingLevel_; |
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61 ResourceType remainingType_; |
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62 std::string remainingPublicId_; |
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63 |
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64 public: |
| 202 | 65 ServerIndexListener(FileStorage& fileStorage) : |
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66 fileStorage_(fileStorage), |
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67 hasRemainingLevel_(false) |
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68 { |
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69 assert(ResourceType_Patient < ResourceType_Study && |
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70 ResourceType_Study < ResourceType_Series && |
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71 ResourceType_Series < ResourceType_Instance); |
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72 } |
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73 |
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74 void Reset() |
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75 { |
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76 hasRemainingLevel_ = false; |
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77 } |
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78 |
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79 virtual void SignalRemainingAncestor(ResourceType parentType, |
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80 const std::string& publicId) |
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81 { |
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82 LOG(INFO) << "Remaining ancestor \"" << publicId << "\" (" << parentType << ")"; |
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83 |
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84 if (hasRemainingLevel_) |
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85 { |
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86 if (parentType < remainingType_) |
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87 { |
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88 remainingType_ = parentType; |
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89 remainingPublicId_ = publicId; |
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90 } |
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91 } |
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92 else |
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93 { |
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94 hasRemainingLevel_ = true; |
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95 remainingType_ = parentType; |
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96 remainingPublicId_ = publicId; |
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97 } |
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98 } |
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99 |
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100 virtual void SignalFileDeleted(const std::string& fileUuid) |
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101 { |
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102 assert(Toolbox::IsUuid(fileUuid)); |
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103 fileStorage_.Remove(fileUuid); |
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104 } |
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105 |
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106 bool HasRemainingLevel() const |
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107 { |
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108 return hasRemainingLevel_; |
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109 } |
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110 |
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111 ResourceType GetRemainingType() const |
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112 { |
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113 assert(HasRemainingLevel()); |
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114 return remainingType_; |
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115 } |
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116 |
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117 const std::string& GetRemainingPublicId() const |
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118 { |
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119 assert(HasRemainingLevel()); |
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120 return remainingPublicId_; |
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121 } |
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122 }; |
| 0 | 123 } |
| 124 | |
| 125 | |
| 212 | 126 bool ServerIndex::DeleteResource(Json::Value& target, |
| 0 | 127 const std::string& uuid, |
| 202 | 128 ResourceType expectedType) |
| 0 | 129 { |
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130 boost::mutex::scoped_lock lock(mutex_); |
| 0 | 131 |
| 202 | 132 listener_->Reset(); |
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133 |
| 202 | 134 std::auto_ptr<SQLite::Transaction> t(db_->StartTransaction()); |
| 135 t->Begin(); | |
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136 |
| 202 | 137 int64_t id; |
| 138 ResourceType type; | |
| 139 if (!db_->LookupResource(uuid, id, type) || | |
| 140 expectedType != type) | |
| 0 | 141 { |
| 142 return false; | |
| 143 } | |
| 202 | 144 |
| 145 db_->DeleteResource(id); | |
| 0 | 146 |
| 202 | 147 if (listener_->HasRemainingLevel()) |
| 0 | 148 { |
| 202 | 149 ResourceType type = listener_->GetRemainingType(); |
| 150 const std::string& uuid = listener_->GetRemainingPublicId(); | |
| 0 | 151 |
| 152 target["RemainingAncestor"] = Json::Value(Json::objectValue); | |
| 204 | 153 target["RemainingAncestor"]["Path"] = GetBasePath(type, uuid); |
| 202 | 154 target["RemainingAncestor"]["Type"] = ToString(type); |
| 0 | 155 target["RemainingAncestor"]["ID"] = uuid; |
| 156 } | |
| 157 else | |
| 158 { | |
| 159 target["RemainingAncestor"] = Json::nullValue; | |
| 160 } | |
| 161 | |
| 202 | 162 t->Commit(); |
| 163 | |
| 0 | 164 return true; |
| 165 } | |
| 166 | |
| 167 | |
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168 static void FlushThread(DatabaseWrapper* db, |
| 220 | 169 boost::mutex* mutex, |
| 170 unsigned int sleep) | |
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171 { |
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172 LOG(INFO) << "Starting the database flushing thread (sleep = " << sleep << ")"; |
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173 |
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174 while (1) |
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175 { |
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176 boost::this_thread::sleep(boost::posix_time::seconds(sleep)); |
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177 boost::mutex::scoped_lock lock(*mutex); |
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178 db->FlushToDisk(); |
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179 } |
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180 } |
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181 |
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182 |
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183 ServerIndex::ServerIndex(FileStorage& fileStorage, |
| 220 | 184 const std::string& dbPath) : mutex_() |
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185 { |
| 202 | 186 listener_.reset(new Internals::ServerIndexListener(fileStorage)); |
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187 |
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188 if (dbPath == ":memory:") |
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189 { |
| 202 | 190 db_.reset(new DatabaseWrapper(*listener_)); |
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191 } |
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192 else |
| 0 | 193 { |
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194 boost::filesystem::path p = dbPath; |
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195 |
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196 try |
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197 { |
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198 boost::filesystem::create_directories(p); |
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199 } |
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200 catch (boost::filesystem::filesystem_error) |
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201 { |
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202 } |
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203 |
| 202 | 204 db_.reset(new DatabaseWrapper(p.string() + "/index", *listener_)); |
| 0 | 205 } |
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206 |
| 220 | 207 unsigned int sleep; |
| 208 try | |
| 209 { | |
| 210 std::string sleepString = db_->GetGlobalProperty(GlobalProperty_FlushSleep); | |
| 211 sleep = boost::lexical_cast<unsigned int>(sleepString); | |
| 212 } | |
| 213 catch (boost::bad_lexical_cast&) | |
| 214 { | |
| 215 // By default, wait for 10 seconds before flushing | |
| 216 sleep = 10; | |
| 217 } | |
| 218 | |
| 219 flushThread_ = boost::thread(FlushThread, db_.get(), &mutex_, sleep); | |
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220 } |
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221 |
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222 |
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223 ServerIndex::~ServerIndex() |
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224 { |
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225 LOG(INFO) << "Stopping the database flushing thread"; |
| 220 | 226 /*flushThread_.terminate(); |
| 227 flushThread_.join();*/ | |
| 0 | 228 } |
| 229 | |
| 230 | |
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231 StoreStatus ServerIndex::Store(const DicomMap& dicomSummary, |
| 0 | 232 const std::string& fileUuid, |
| 233 uint64_t uncompressedFileSize, | |
| 234 const std::string& jsonUuid, | |
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235 const std::string& remoteAet) |
| 0 | 236 { |
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237 boost::mutex::scoped_lock lock(mutex_); |
| 0 | 238 |
| 178 | 239 DicomInstanceHasher hasher(dicomSummary); |
| 0 | 240 |
| 241 try | |
| 242 { | |
| 202 | 243 std::auto_ptr<SQLite::Transaction> t(db_->StartTransaction()); |
| 244 t->Begin(); | |
| 0 | 245 |
| 202 | 246 int64_t patient, study, series, instance; |
| 247 ResourceType type; | |
| 248 bool isNewSeries = false; | |
| 249 | |
| 250 // Do nothing if the instance already exists | |
| 251 if (db_->LookupResource(hasher.HashInstance(), patient, type)) | |
| 0 | 252 { |
| 202 | 253 assert(type == ResourceType_Instance); |
| 0 | 254 return StoreStatus_AlreadyStored; |
| 255 } | |
| 256 | |
| 202 | 257 // Create the instance |
| 258 instance = db_->CreateResource(hasher.HashInstance(), ResourceType_Instance); | |
| 259 | |
| 260 DicomMap dicom; | |
| 261 dicomSummary.ExtractInstanceInformation(dicom); | |
| 262 db_->SetMainDicomTags(instance, dicom); | |
| 263 | |
| 264 // Create the patient/study/series/instance hierarchy | |
| 265 if (!db_->LookupResource(hasher.HashSeries(), series, type)) | |
| 0 | 266 { |
| 202 | 267 // This is a new series |
| 268 isNewSeries = true; | |
| 269 series = db_->CreateResource(hasher.HashSeries(), ResourceType_Series); | |
| 270 dicomSummary.ExtractSeriesInformation(dicom); | |
| 271 db_->SetMainDicomTags(series, dicom); | |
| 272 db_->AttachChild(series, instance); | |
| 273 | |
| 274 if (!db_->LookupResource(hasher.HashStudy(), study, type)) | |
| 275 { | |
| 276 // This is a new study | |
| 277 study = db_->CreateResource(hasher.HashStudy(), ResourceType_Study); | |
| 278 dicomSummary.ExtractStudyInformation(dicom); | |
| 279 db_->SetMainDicomTags(study, dicom); | |
| 280 db_->AttachChild(study, series); | |
| 281 | |
| 282 if (!db_->LookupResource(hasher.HashPatient(), patient, type)) | |
| 283 { | |
| 284 // This is a new patient | |
| 285 patient = db_->CreateResource(hasher.HashPatient(), ResourceType_Patient); | |
| 286 dicomSummary.ExtractPatientInformation(dicom); | |
| 287 db_->SetMainDicomTags(patient, dicom); | |
| 288 db_->AttachChild(patient, study); | |
| 289 } | |
| 290 else | |
| 291 { | |
| 292 assert(type == ResourceType_Patient); | |
| 293 db_->AttachChild(patient, study); | |
| 294 } | |
| 295 } | |
| 296 else | |
| 297 { | |
| 298 assert(type == ResourceType_Study); | |
| 299 db_->AttachChild(study, series); | |
| 300 } | |
| 0 | 301 } |
| 302 else | |
| 303 { | |
| 202 | 304 assert(type == ResourceType_Series); |
| 305 db_->AttachChild(series, instance); | |
| 0 | 306 } |
| 307 | |
| 202 | 308 // Attach the files to the newly created instance |
| 309 db_->AttachFile(instance, AttachedFileType_Dicom, fileUuid, uncompressedFileSize); | |
| 310 db_->AttachFile(instance, AttachedFileType_Json, jsonUuid, 0); // TODO "0" | |
| 311 | |
| 312 // Attach the metadata | |
| 313 db_->SetMetadata(instance, MetadataType_Instance_ReceptionDate, Toolbox::GetNowIsoString()); | |
| 314 db_->SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); | |
| 315 | |
| 316 const DicomValue* value; | |
| 317 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || | |
| 318 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) | |
| 0 | 319 { |
| 202 | 320 db_->SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->AsString()); |
| 0 | 321 } |
| 322 | |
| 202 | 323 if (isNewSeries) |
| 324 { | |
| 325 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL || | |
| 326 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL || | |
| 327 (value = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL) | |
| 328 { | |
| 329 db_->SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, value->AsString()); | |
| 330 } | |
| 331 } | |
| 332 | |
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333 // Check whether the series of this new instance is now completed |
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334 SeriesStatus seriesStatus = GetSeriesStatus(series); |
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335 if (seriesStatus == SeriesStatus_Complete) |
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336 { |
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337 db_->LogChange(ChangeType_CompletedSeries, series, ResourceType_Series); |
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338 } |
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339 |
| 202 | 340 t->Commit(); |
| 341 | |
| 0 | 342 return StoreStatus_Success; |
| 343 } | |
| 62 | 344 catch (OrthancException& e) |
| 0 | 345 { |
| 202 | 346 LOG(ERROR) << "EXCEPTION2 [" << e.What() << "]" << " " << db_->GetErrorMessage(); |
| 0 | 347 } |
| 348 | |
| 349 return StoreStatus_Failure; | |
| 350 } | |
| 351 | |
| 352 | |
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353 uint64_t ServerIndex::GetTotalCompressedSize() |
| 0 | 354 { |
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355 boost::mutex::scoped_lock lock(mutex_); |
| 202 | 356 return db_->GetTotalCompressedSize(); |
| 0 | 357 } |
| 358 | |
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359 uint64_t ServerIndex::GetTotalUncompressedSize() |
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360 { |
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361 boost::mutex::scoped_lock lock(mutex_); |
| 202 | 362 return db_->GetTotalUncompressedSize(); |
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363 } |
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364 |
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365 |
| 199 | 366 SeriesStatus ServerIndex::GetSeriesStatus(int id) |
| 367 { | |
| 368 // Get the expected number of instances in this series (from the metadata) | |
| 202 | 369 std::string s = db_->GetMetadata(id, MetadataType_Series_ExpectedNumberOfInstances); |
| 199 | 370 |
| 371 size_t expected; | |
| 372 try | |
| 373 { | |
| 374 expected = boost::lexical_cast<size_t>(s); | |
| 375 if (expected < 0) | |
| 376 { | |
| 377 return SeriesStatus_Unknown; | |
| 378 } | |
| 379 } | |
| 380 catch (boost::bad_lexical_cast&) | |
| 381 { | |
| 382 return SeriesStatus_Unknown; | |
| 383 } | |
| 384 | |
| 385 // Loop over the instances of this series | |
| 386 std::list<int64_t> children; | |
| 202 | 387 db_->GetChildrenInternalId(children, id); |
| 199 | 388 |
| 389 std::set<size_t> instances; | |
| 390 for (std::list<int64_t>::const_iterator | |
| 391 it = children.begin(); it != children.end(); it++) | |
| 392 { | |
| 393 // Get the index of this instance in the series | |
| 202 | 394 s = db_->GetMetadata(*it, MetadataType_Instance_IndexInSeries); |
| 199 | 395 size_t index; |
| 396 try | |
| 397 { | |
| 398 index = boost::lexical_cast<size_t>(s); | |
| 399 } | |
| 400 catch (boost::bad_lexical_cast&) | |
| 401 { | |
| 402 return SeriesStatus_Unknown; | |
| 403 } | |
| 404 | |
| 405 if (index <= 0 || index > expected) | |
| 406 { | |
| 407 // Out-of-range instance index | |
| 408 return SeriesStatus_Inconsistent; | |
| 409 } | |
| 410 | |
| 411 if (instances.find(index) != instances.end()) | |
| 412 { | |
| 413 // Twice the same instance index | |
| 414 return SeriesStatus_Inconsistent; | |
| 415 } | |
| 416 | |
| 417 instances.insert(index); | |
| 418 } | |
| 419 | |
| 420 if (instances.size() == expected) | |
| 421 { | |
| 422 return SeriesStatus_Complete; | |
| 423 } | |
| 424 else | |
| 425 { | |
| 426 return SeriesStatus_Missing; | |
| 427 } | |
| 428 } | |
| 429 | |
| 430 | |
| 431 | |
| 202 | 432 void ServerIndex::MainDicomTagsToJson(Json::Value& target, |
| 433 int64_t resourceId) | |
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434 { |
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435 DicomMap tags; |
| 202 | 436 db_->GetMainDicomTags(tags, resourceId); |
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437 target["MainDicomTags"] = Json::objectValue; |
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438 FromDcmtkBridge::ToJson(target["MainDicomTags"], tags); |
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439 } |
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440 |
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441 bool ServerIndex::LookupResource(Json::Value& result, |
| 199 | 442 const std::string& publicId, |
| 443 ResourceType expectedType) | |
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444 { |
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445 result = Json::objectValue; |
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446 |
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447 boost::mutex::scoped_lock lock(mutex_); |
| 199 | 448 |
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449 // Lookup for the requested resource |
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450 int64_t id; |
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451 ResourceType type; |
| 202 | 452 if (!db_->LookupResource(publicId, id, type) || |
| 199 | 453 type != expectedType) |
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454 { |
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455 return false; |
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456 } |
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457 |
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458 // Find the parent resource (if it exists) |
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459 if (type != ResourceType_Patient) |
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460 { |
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461 int64_t parentId; |
| 202 | 462 if (!db_->LookupParent(parentId, id)) |
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463 { |
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464 throw OrthancException(ErrorCode_InternalError); |
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465 } |
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466 |
| 202 | 467 std::string parent = db_->GetPublicId(parentId); |
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468 |
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469 switch (type) |
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470 { |
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471 case ResourceType_Study: |
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472 result["ParentPatient"] = parent; |
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473 break; |
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474 |
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475 case ResourceType_Series: |
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476 result["ParentStudy"] = parent; |
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477 break; |
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478 |
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479 case ResourceType_Instance: |
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480 result["ParentSeries"] = parent; |
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481 break; |
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482 |
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483 default: |
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484 throw OrthancException(ErrorCode_InternalError); |
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485 } |
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486 } |
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487 |
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488 // List the children resources |
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489 std::list<std::string> children; |
| 202 | 490 db_->GetChildrenPublicId(children, id); |
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491 |
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492 if (type != ResourceType_Instance) |
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493 { |
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494 Json::Value c = Json::arrayValue; |
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495 |
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496 for (std::list<std::string>::const_iterator |
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497 it = children.begin(); it != children.end(); it++) |
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498 { |
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499 c.append(*it); |
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500 } |
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501 |
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502 switch (type) |
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503 { |
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504 case ResourceType_Patient: |
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505 result["Studies"] = c; |
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506 break; |
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507 |
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508 case ResourceType_Study: |
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509 result["Series"] = c; |
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510 break; |
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511 |
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512 case ResourceType_Series: |
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513 result["Instances"] = c; |
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514 break; |
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515 |
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516 default: |
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517 throw OrthancException(ErrorCode_InternalError); |
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518 } |
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519 } |
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520 |
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521 // Set the resource type |
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522 switch (type) |
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523 { |
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524 case ResourceType_Patient: |
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525 result["Type"] = "Patient"; |
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526 break; |
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527 |
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528 case ResourceType_Study: |
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529 result["Type"] = "Study"; |
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530 break; |
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531 |
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532 case ResourceType_Series: |
| 199 | 533 { |
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534 result["Type"] = "Series"; |
| 199 | 535 result["Status"] = ToString(GetSeriesStatus(id)); |
| 536 | |
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537 int i; |
| 202 | 538 if (db_->GetMetadataAsInteger(i, id, MetadataType_Series_ExpectedNumberOfInstances)) |
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539 result["ExpectedNumberOfInstances"] = i; |
| 202 | 540 else |
| 199 | 541 result["ExpectedNumberOfInstances"] = Json::nullValue; |
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542 |
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543 break; |
| 199 | 544 } |
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545 |
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546 case ResourceType_Instance: |
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547 { |
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548 result["Type"] = "Instance"; |
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549 |
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550 std::string fileUuid; |
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551 uint64_t uncompressedSize; |
| 202 | 552 if (!db_->LookupFile(id, AttachedFileType_Dicom, fileUuid, uncompressedSize)) |
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553 { |
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554 throw OrthancException(ErrorCode_InternalError); |
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555 } |
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556 |
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557 result["FileSize"] = static_cast<unsigned int>(uncompressedSize); |
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558 result["FileUuid"] = fileUuid; |
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559 |
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560 int i; |
| 202 | 561 if (db_->GetMetadataAsInteger(i, id, MetadataType_Instance_IndexInSeries)) |
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562 result["IndexInSeries"] = i; |
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563 else |
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564 result["IndexInSeries"] = Json::nullValue; |
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565 |
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566 break; |
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567 } |
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568 |
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569 default: |
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570 throw OrthancException(ErrorCode_InternalError); |
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571 } |
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572 |
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573 // Record the remaining information |
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574 result["ID"] = publicId; |
| 202 | 575 MainDicomTagsToJson(result, id); |
|
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576 |
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577 return true; |
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578 } |
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579 |
| 0 | 580 |
|
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581 bool ServerIndex::GetFile(std::string& fileUuid, |
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582 CompressionType& compressionType, |
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583 const std::string& instanceUuid, |
|
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584 AttachedFileType contentType) |
| 0 | 585 { |
|
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586 boost::mutex::scoped_lock lock(mutex_); |
| 0 | 587 |
|
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588 int64_t id; |
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589 ResourceType type; |
| 202 | 590 if (!db_->LookupResource(instanceUuid, id, type) || |
|
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591 type != ResourceType_Instance) |
|
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592 { |
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593 throw OrthancException(ErrorCode_InternalError); |
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594 } |
|
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595 |
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596 uint64_t compressedSize, uncompressedSize; |
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597 |
| 202 | 598 return db_->LookupFile(id, contentType, fileUuid, compressedSize, uncompressedSize, compressionType); |
|
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599 } |
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600 |
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601 |
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602 |
| 0 | 603 void ServerIndex::GetAllUuids(Json::Value& target, |
| 190 | 604 ResourceType resourceType) |
| 0 | 605 { |
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606 boost::mutex::scoped_lock lock(mutex_); |
| 202 | 607 db_->GetAllPublicIds(target, resourceType); |
| 0 | 608 } |
| 609 | |
| 610 | |
| 611 bool ServerIndex::GetChanges(Json::Value& target, | |
| 204 | 612 int64_t since, |
| 0 | 613 unsigned int maxResults) |
| 614 { | |
|
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615 boost::mutex::scoped_lock lock(mutex_); |
| 0 | 616 |
| 204 | 617 db_->GetChanges(target, since, maxResults); |
| 0 | 618 |
| 204 | 619 return true; |
| 0 | 620 } |
| 621 } |