Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 226:8a26a8e85edf
refactoring to read files
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Fri, 30 Nov 2012 09:45:29 +0100 |
| parents | 4eb0c7ce86c9 |
| children | 8098448bd827 |
| 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 | |
| 6 | 35 #ifndef NOMINMAX |
| 2 | 36 #define NOMINMAX |
| 6 | 37 #endif |
| 38 | |
| 8 | 39 #include "EmbeddedResources.h" |
| 0 | 40 #include "../Core/Toolbox.h" |
| 41 #include "../Core/Uuid.h" | |
| 42 #include "../Core/DicomFormat/DicomArray.h" | |
| 43 #include "../Core/SQLite/Transaction.h" | |
| 44 #include "FromDcmtkBridge.h" | |
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45 #include "ServerContext.h" |
| 0 | 46 |
| 47 #include <boost/lexical_cast.hpp> | |
| 48 #include <stdio.h> | |
| 108 | 49 #include <glog/logging.h> |
| 0 | 50 |
| 62 | 51 namespace Orthanc |
| 0 | 52 { |
| 53 namespace Internals | |
| 54 { | |
| 202 | 55 class ServerIndexListener : public IServerIndexListener |
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56 { |
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57 private: |
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58 ServerContext& context_; |
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59 bool hasRemainingLevel_; |
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60 ResourceType remainingType_; |
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61 std::string remainingPublicId_; |
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62 |
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63 public: |
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64 ServerIndexListener(ServerContext& context) : |
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65 context_(context), |
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66 hasRemainingLevel_(false) |
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67 { |
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68 assert(ResourceType_Patient < ResourceType_Study && |
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69 ResourceType_Study < ResourceType_Series && |
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70 ResourceType_Series < ResourceType_Instance); |
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71 } |
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72 |
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73 void Reset() |
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74 { |
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75 hasRemainingLevel_ = false; |
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76 } |
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77 |
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78 virtual void SignalRemainingAncestor(ResourceType parentType, |
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79 const std::string& publicId) |
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80 { |
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81 LOG(INFO) << "Remaining ancestor \"" << publicId << "\" (" << parentType << ")"; |
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82 |
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83 if (hasRemainingLevel_) |
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84 { |
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85 if (parentType < remainingType_) |
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86 { |
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87 remainingType_ = parentType; |
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88 remainingPublicId_ = publicId; |
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89 } |
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90 } |
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91 else |
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92 { |
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93 hasRemainingLevel_ = true; |
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94 remainingType_ = parentType; |
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95 remainingPublicId_ = publicId; |
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96 } |
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97 } |
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98 |
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99 virtual void SignalFileDeleted(const std::string& fileUuid) |
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100 { |
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101 assert(Toolbox::IsUuid(fileUuid)); |
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102 context_.RemoveFile(fileUuid); |
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103 } |
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104 |
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105 bool HasRemainingLevel() const |
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106 { |
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107 return hasRemainingLevel_; |
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108 } |
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109 |
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110 ResourceType GetRemainingType() const |
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111 { |
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112 assert(HasRemainingLevel()); |
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113 return remainingType_; |
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114 } |
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115 |
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116 const std::string& GetRemainingPublicId() const |
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117 { |
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118 assert(HasRemainingLevel()); |
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119 return remainingPublicId_; |
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120 } |
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121 }; |
| 0 | 122 } |
| 123 | |
| 124 | |
| 212 | 125 bool ServerIndex::DeleteResource(Json::Value& target, |
| 0 | 126 const std::string& uuid, |
| 202 | 127 ResourceType expectedType) |
| 0 | 128 { |
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129 boost::mutex::scoped_lock lock(mutex_); |
| 0 | 130 |
| 202 | 131 listener_->Reset(); |
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132 |
| 202 | 133 std::auto_ptr<SQLite::Transaction> t(db_->StartTransaction()); |
| 134 t->Begin(); | |
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135 |
| 202 | 136 int64_t id; |
| 137 ResourceType type; | |
| 138 if (!db_->LookupResource(uuid, id, type) || | |
| 139 expectedType != type) | |
| 0 | 140 { |
| 141 return false; | |
| 142 } | |
| 202 | 143 |
| 144 db_->DeleteResource(id); | |
| 0 | 145 |
| 202 | 146 if (listener_->HasRemainingLevel()) |
| 0 | 147 { |
| 202 | 148 ResourceType type = listener_->GetRemainingType(); |
| 149 const std::string& uuid = listener_->GetRemainingPublicId(); | |
| 0 | 150 |
| 151 target["RemainingAncestor"] = Json::Value(Json::objectValue); | |
| 204 | 152 target["RemainingAncestor"]["Path"] = GetBasePath(type, uuid); |
| 202 | 153 target["RemainingAncestor"]["Type"] = ToString(type); |
| 0 | 154 target["RemainingAncestor"]["ID"] = uuid; |
| 155 } | |
| 156 else | |
| 157 { | |
| 158 target["RemainingAncestor"] = Json::nullValue; | |
| 159 } | |
| 160 | |
| 202 | 161 t->Commit(); |
| 162 | |
| 0 | 163 return true; |
| 164 } | |
| 165 | |
| 166 | |
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167 static void FlushThread(DatabaseWrapper* db, |
| 220 | 168 boost::mutex* mutex, |
| 169 unsigned int sleep) | |
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170 { |
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171 LOG(INFO) << "Starting the database flushing thread (sleep = " << sleep << ")"; |
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172 |
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173 while (1) |
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174 { |
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175 boost::this_thread::sleep(boost::posix_time::seconds(sleep)); |
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176 boost::mutex::scoped_lock lock(*mutex); |
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177 db->FlushToDisk(); |
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178 } |
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179 } |
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180 |
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181 |
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182 ServerIndex::ServerIndex(ServerContext& context, |
| 220 | 183 const std::string& dbPath) : mutex_() |
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184 { |
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185 listener_.reset(new Internals::ServerIndexListener(context)); |
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186 |
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187 if (dbPath == ":memory:") |
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188 { |
| 202 | 189 db_.reset(new DatabaseWrapper(*listener_)); |
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190 } |
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191 else |
| 0 | 192 { |
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193 boost::filesystem::path p = dbPath; |
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194 |
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195 try |
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196 { |
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197 boost::filesystem::create_directories(p); |
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198 } |
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199 catch (boost::filesystem::filesystem_error) |
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200 { |
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201 } |
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202 |
| 202 | 203 db_.reset(new DatabaseWrapper(p.string() + "/index", *listener_)); |
| 0 | 204 } |
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205 |
| 220 | 206 unsigned int sleep; |
| 207 try | |
| 208 { | |
| 209 std::string sleepString = db_->GetGlobalProperty(GlobalProperty_FlushSleep); | |
| 210 sleep = boost::lexical_cast<unsigned int>(sleepString); | |
| 211 } | |
| 212 catch (boost::bad_lexical_cast&) | |
| 213 { | |
| 214 // By default, wait for 10 seconds before flushing | |
| 215 sleep = 10; | |
| 216 } | |
| 217 | |
| 218 flushThread_ = boost::thread(FlushThread, db_.get(), &mutex_, sleep); | |
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219 } |
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220 |
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221 |
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222 ServerIndex::~ServerIndex() |
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223 { |
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224 LOG(INFO) << "Stopping the database flushing thread"; |
| 220 | 225 /*flushThread_.terminate(); |
| 226 flushThread_.join();*/ | |
| 0 | 227 } |
| 228 | |
| 229 | |
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230 StoreStatus ServerIndex::Store(const DicomMap& dicomSummary, |
| 0 | 231 const std::string& fileUuid, |
| 232 uint64_t uncompressedFileSize, | |
| 233 const std::string& jsonUuid, | |
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234 const std::string& remoteAet) |
| 0 | 235 { |
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236 boost::mutex::scoped_lock lock(mutex_); |
| 0 | 237 |
| 178 | 238 DicomInstanceHasher hasher(dicomSummary); |
| 0 | 239 |
| 240 try | |
| 241 { | |
| 202 | 242 std::auto_ptr<SQLite::Transaction> t(db_->StartTransaction()); |
| 243 t->Begin(); | |
| 0 | 244 |
| 202 | 245 int64_t patient, study, series, instance; |
| 246 ResourceType type; | |
| 247 bool isNewSeries = false; | |
| 248 | |
| 249 // Do nothing if the instance already exists | |
| 250 if (db_->LookupResource(hasher.HashInstance(), patient, type)) | |
| 0 | 251 { |
| 202 | 252 assert(type == ResourceType_Instance); |
| 0 | 253 return StoreStatus_AlreadyStored; |
| 254 } | |
| 255 | |
| 202 | 256 // Create the instance |
| 257 instance = db_->CreateResource(hasher.HashInstance(), ResourceType_Instance); | |
| 258 | |
| 259 DicomMap dicom; | |
| 260 dicomSummary.ExtractInstanceInformation(dicom); | |
| 261 db_->SetMainDicomTags(instance, dicom); | |
| 262 | |
| 263 // Create the patient/study/series/instance hierarchy | |
| 264 if (!db_->LookupResource(hasher.HashSeries(), series, type)) | |
| 0 | 265 { |
| 202 | 266 // This is a new series |
| 267 isNewSeries = true; | |
| 268 series = db_->CreateResource(hasher.HashSeries(), ResourceType_Series); | |
| 269 dicomSummary.ExtractSeriesInformation(dicom); | |
| 270 db_->SetMainDicomTags(series, dicom); | |
| 271 db_->AttachChild(series, instance); | |
| 272 | |
| 273 if (!db_->LookupResource(hasher.HashStudy(), study, type)) | |
| 274 { | |
| 275 // This is a new study | |
| 276 study = db_->CreateResource(hasher.HashStudy(), ResourceType_Study); | |
| 277 dicomSummary.ExtractStudyInformation(dicom); | |
| 278 db_->SetMainDicomTags(study, dicom); | |
| 279 db_->AttachChild(study, series); | |
| 280 | |
| 281 if (!db_->LookupResource(hasher.HashPatient(), patient, type)) | |
| 282 { | |
| 283 // This is a new patient | |
| 284 patient = db_->CreateResource(hasher.HashPatient(), ResourceType_Patient); | |
| 285 dicomSummary.ExtractPatientInformation(dicom); | |
| 286 db_->SetMainDicomTags(patient, dicom); | |
| 287 db_->AttachChild(patient, study); | |
| 288 } | |
| 289 else | |
| 290 { | |
| 291 assert(type == ResourceType_Patient); | |
| 292 db_->AttachChild(patient, study); | |
| 293 } | |
| 294 } | |
| 295 else | |
| 296 { | |
| 297 assert(type == ResourceType_Study); | |
| 298 db_->AttachChild(study, series); | |
| 299 } | |
| 0 | 300 } |
| 301 else | |
| 302 { | |
| 202 | 303 assert(type == ResourceType_Series); |
| 304 db_->AttachChild(series, instance); | |
| 0 | 305 } |
| 306 | |
| 202 | 307 // Attach the files to the newly created instance |
| 308 db_->AttachFile(instance, AttachedFileType_Dicom, fileUuid, uncompressedFileSize); | |
| 309 db_->AttachFile(instance, AttachedFileType_Json, jsonUuid, 0); // TODO "0" | |
| 310 | |
| 311 // Attach the metadata | |
| 312 db_->SetMetadata(instance, MetadataType_Instance_ReceptionDate, Toolbox::GetNowIsoString()); | |
| 313 db_->SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); | |
| 314 | |
| 315 const DicomValue* value; | |
| 316 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || | |
| 317 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) | |
| 0 | 318 { |
| 202 | 319 db_->SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->AsString()); |
| 0 | 320 } |
| 321 | |
| 202 | 322 if (isNewSeries) |
| 323 { | |
| 324 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL || | |
| 325 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL || | |
| 326 (value = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL) | |
| 327 { | |
| 328 db_->SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, value->AsString()); | |
| 329 } | |
| 330 } | |
| 331 | |
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332 // Check whether the series of this new instance is now completed |
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333 SeriesStatus seriesStatus = GetSeriesStatus(series); |
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334 if (seriesStatus == SeriesStatus_Complete) |
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335 { |
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336 db_->LogChange(ChangeType_CompletedSeries, series, ResourceType_Series); |
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337 } |
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338 |
| 202 | 339 t->Commit(); |
| 340 | |
| 0 | 341 return StoreStatus_Success; |
| 342 } | |
| 62 | 343 catch (OrthancException& e) |
| 0 | 344 { |
| 202 | 345 LOG(ERROR) << "EXCEPTION2 [" << e.What() << "]" << " " << db_->GetErrorMessage(); |
| 0 | 346 } |
| 347 | |
| 348 return StoreStatus_Failure; | |
| 349 } | |
| 350 | |
| 351 | |
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352 uint64_t ServerIndex::GetTotalCompressedSize() |
| 0 | 353 { |
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354 boost::mutex::scoped_lock lock(mutex_); |
| 202 | 355 return db_->GetTotalCompressedSize(); |
| 0 | 356 } |
| 357 | |
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358 uint64_t ServerIndex::GetTotalUncompressedSize() |
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359 { |
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360 boost::mutex::scoped_lock lock(mutex_); |
| 202 | 361 return db_->GetTotalUncompressedSize(); |
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362 } |
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363 |
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364 |
| 199 | 365 SeriesStatus ServerIndex::GetSeriesStatus(int id) |
| 366 { | |
| 367 // Get the expected number of instances in this series (from the metadata) | |
| 202 | 368 std::string s = db_->GetMetadata(id, MetadataType_Series_ExpectedNumberOfInstances); |
| 199 | 369 |
| 370 size_t expected; | |
| 371 try | |
| 372 { | |
| 373 expected = boost::lexical_cast<size_t>(s); | |
| 374 if (expected < 0) | |
| 375 { | |
| 376 return SeriesStatus_Unknown; | |
| 377 } | |
| 378 } | |
| 379 catch (boost::bad_lexical_cast&) | |
| 380 { | |
| 381 return SeriesStatus_Unknown; | |
| 382 } | |
| 383 | |
| 384 // Loop over the instances of this series | |
| 385 std::list<int64_t> children; | |
| 202 | 386 db_->GetChildrenInternalId(children, id); |
| 199 | 387 |
| 388 std::set<size_t> instances; | |
| 389 for (std::list<int64_t>::const_iterator | |
| 390 it = children.begin(); it != children.end(); it++) | |
| 391 { | |
| 392 // Get the index of this instance in the series | |
| 202 | 393 s = db_->GetMetadata(*it, MetadataType_Instance_IndexInSeries); |
| 199 | 394 size_t index; |
| 395 try | |
| 396 { | |
| 397 index = boost::lexical_cast<size_t>(s); | |
| 398 } | |
| 399 catch (boost::bad_lexical_cast&) | |
| 400 { | |
| 401 return SeriesStatus_Unknown; | |
| 402 } | |
| 403 | |
| 404 if (index <= 0 || index > expected) | |
| 405 { | |
| 406 // Out-of-range instance index | |
| 407 return SeriesStatus_Inconsistent; | |
| 408 } | |
| 409 | |
| 410 if (instances.find(index) != instances.end()) | |
| 411 { | |
| 412 // Twice the same instance index | |
| 413 return SeriesStatus_Inconsistent; | |
| 414 } | |
| 415 | |
| 416 instances.insert(index); | |
| 417 } | |
| 418 | |
| 419 if (instances.size() == expected) | |
| 420 { | |
| 421 return SeriesStatus_Complete; | |
| 422 } | |
| 423 else | |
| 424 { | |
| 425 return SeriesStatus_Missing; | |
| 426 } | |
| 427 } | |
| 428 | |
| 429 | |
| 430 | |
| 202 | 431 void ServerIndex::MainDicomTagsToJson(Json::Value& target, |
| 432 int64_t resourceId) | |
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433 { |
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434 DicomMap tags; |
| 202 | 435 db_->GetMainDicomTags(tags, resourceId); |
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436 target["MainDicomTags"] = Json::objectValue; |
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437 FromDcmtkBridge::ToJson(target["MainDicomTags"], tags); |
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438 } |
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439 |
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440 bool ServerIndex::LookupResource(Json::Value& result, |
| 199 | 441 const std::string& publicId, |
| 442 ResourceType expectedType) | |
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443 { |
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444 result = Json::objectValue; |
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445 |
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446 boost::mutex::scoped_lock lock(mutex_); |
| 199 | 447 |
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448 // Lookup for the requested resource |
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449 int64_t id; |
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450 ResourceType type; |
| 202 | 451 if (!db_->LookupResource(publicId, id, type) || |
| 199 | 452 type != expectedType) |
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453 { |
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454 return false; |
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455 } |
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456 |
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457 // Find the parent resource (if it exists) |
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458 if (type != ResourceType_Patient) |
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459 { |
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460 int64_t parentId; |
| 202 | 461 if (!db_->LookupParent(parentId, id)) |
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462 { |
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463 throw OrthancException(ErrorCode_InternalError); |
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464 } |
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465 |
| 202 | 466 std::string parent = db_->GetPublicId(parentId); |
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467 |
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468 switch (type) |
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469 { |
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470 case ResourceType_Study: |
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471 result["ParentPatient"] = parent; |
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472 break; |
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473 |
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474 case ResourceType_Series: |
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475 result["ParentStudy"] = parent; |
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476 break; |
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477 |
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478 case ResourceType_Instance: |
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479 result["ParentSeries"] = parent; |
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480 break; |
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481 |
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482 default: |
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483 throw OrthancException(ErrorCode_InternalError); |
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484 } |
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485 } |
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486 |
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487 // List the children resources |
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488 std::list<std::string> children; |
| 202 | 489 db_->GetChildrenPublicId(children, id); |
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490 |
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491 if (type != ResourceType_Instance) |
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492 { |
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493 Json::Value c = Json::arrayValue; |
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494 |
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495 for (std::list<std::string>::const_iterator |
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496 it = children.begin(); it != children.end(); it++) |
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497 { |
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498 c.append(*it); |
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499 } |
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500 |
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501 switch (type) |
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502 { |
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503 case ResourceType_Patient: |
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504 result["Studies"] = c; |
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505 break; |
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506 |
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507 case ResourceType_Study: |
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508 result["Series"] = c; |
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509 break; |
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510 |
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511 case ResourceType_Series: |
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512 result["Instances"] = c; |
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513 break; |
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514 |
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515 default: |
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516 throw OrthancException(ErrorCode_InternalError); |
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517 } |
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518 } |
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519 |
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520 // Set the resource type |
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521 switch (type) |
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522 { |
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523 case ResourceType_Patient: |
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524 result["Type"] = "Patient"; |
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525 break; |
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526 |
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527 case ResourceType_Study: |
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528 result["Type"] = "Study"; |
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529 break; |
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530 |
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531 case ResourceType_Series: |
| 199 | 532 { |
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533 result["Type"] = "Series"; |
| 199 | 534 result["Status"] = ToString(GetSeriesStatus(id)); |
| 535 | |
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536 int i; |
| 202 | 537 if (db_->GetMetadataAsInteger(i, id, MetadataType_Series_ExpectedNumberOfInstances)) |
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538 result["ExpectedNumberOfInstances"] = i; |
| 202 | 539 else |
| 199 | 540 result["ExpectedNumberOfInstances"] = Json::nullValue; |
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541 |
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542 break; |
| 199 | 543 } |
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544 |
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545 case ResourceType_Instance: |
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546 { |
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547 result["Type"] = "Instance"; |
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548 |
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549 std::string fileUuid; |
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550 uint64_t uncompressedSize; |
| 202 | 551 if (!db_->LookupFile(id, AttachedFileType_Dicom, fileUuid, uncompressedSize)) |
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552 { |
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553 throw OrthancException(ErrorCode_InternalError); |
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554 } |
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555 |
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556 result["FileSize"] = static_cast<unsigned int>(uncompressedSize); |
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557 result["FileUuid"] = fileUuid; |
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558 |
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559 int i; |
| 202 | 560 if (db_->GetMetadataAsInteger(i, id, MetadataType_Instance_IndexInSeries)) |
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561 result["IndexInSeries"] = i; |
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562 else |
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563 result["IndexInSeries"] = Json::nullValue; |
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564 |
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565 break; |
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566 } |
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567 |
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568 default: |
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569 throw OrthancException(ErrorCode_InternalError); |
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570 } |
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571 |
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572 // Record the remaining information |
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573 result["ID"] = publicId; |
| 202 | 574 MainDicomTagsToJson(result, id); |
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575 |
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576 return true; |
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577 } |
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578 |
| 0 | 579 |
|
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580 bool ServerIndex::GetFile(std::string& fileUuid, |
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581 CompressionType& compressionType, |
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582 const std::string& instanceUuid, |
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583 AttachedFileType contentType) |
| 0 | 584 { |
|
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585 boost::mutex::scoped_lock lock(mutex_); |
| 0 | 586 |
|
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587 int64_t id; |
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588 ResourceType type; |
| 202 | 589 if (!db_->LookupResource(instanceUuid, id, type) || |
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590 type != ResourceType_Instance) |
|
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591 { |
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592 throw OrthancException(ErrorCode_InternalError); |
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593 } |
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594 |
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595 uint64_t compressedSize, uncompressedSize; |
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596 |
| 202 | 597 return db_->LookupFile(id, contentType, fileUuid, compressedSize, uncompressedSize, compressionType); |
|
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598 } |
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599 |
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600 |
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601 |
| 0 | 602 void ServerIndex::GetAllUuids(Json::Value& target, |
| 190 | 603 ResourceType resourceType) |
| 0 | 604 { |
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605 boost::mutex::scoped_lock lock(mutex_); |
| 202 | 606 db_->GetAllPublicIds(target, resourceType); |
| 0 | 607 } |
| 608 | |
| 609 | |
| 610 bool ServerIndex::GetChanges(Json::Value& target, | |
| 204 | 611 int64_t since, |
| 0 | 612 unsigned int maxResults) |
| 613 { | |
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614 boost::mutex::scoped_lock lock(mutex_); |
| 0 | 615 |
| 204 | 616 db_->GetChanges(target, since, maxResults); |
| 0 | 617 |
| 204 | 618 return true; |
| 0 | 619 } |
| 620 } |