Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 1004:a226e0959d8b lua-scripting
DicomInstanceToStore
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Tue, 08 Jul 2014 14:06:05 +0200 |
| parents | b067017a8a5b |
| children | 649d47854314 |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
| 689 | 3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege, |
| 0 | 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 | |
|
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33 #include "PrecompiledHeadersServer.h" |
| 0 | 34 #include "ServerIndex.h" |
| 35 | |
| 6 | 36 #ifndef NOMINMAX |
| 2 | 37 #define NOMINMAX |
| 6 | 38 #endif |
| 39 | |
| 8 | 40 #include "EmbeddedResources.h" |
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41 #include "OrthancInitialization.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" | |
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47 #include "ServerContext.h" |
| 0 | 48 |
| 49 #include <boost/lexical_cast.hpp> | |
| 50 #include <stdio.h> | |
| 108 | 51 #include <glog/logging.h> |
| 0 | 52 |
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53 static const uint64_t MEGA_BYTES = 1024 * 1024; |
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54 |
| 62 | 55 namespace Orthanc |
| 0 | 56 { |
| 57 namespace Internals | |
| 58 { | |
| 202 | 59 class ServerIndexListener : public IServerIndexListener |
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60 { |
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61 private: |
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62 ServerContext& context_; |
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63 bool hasRemainingLevel_; |
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64 ResourceType remainingType_; |
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65 std::string remainingPublicId_; |
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66 std::list<std::string> pendingFilesToRemove_; |
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67 uint64_t sizeOfFilesToRemove_; |
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68 |
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69 public: |
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70 ServerIndexListener(ServerContext& context) : |
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71 context_(context) |
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72 { |
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73 Reset(); |
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74 assert(ResourceType_Patient < ResourceType_Study && |
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75 ResourceType_Study < ResourceType_Series && |
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76 ResourceType_Series < ResourceType_Instance); |
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77 } |
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78 |
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79 void Reset() |
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80 { |
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81 sizeOfFilesToRemove_ = 0; |
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82 hasRemainingLevel_ = false; |
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83 pendingFilesToRemove_.clear(); |
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84 } |
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85 |
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86 uint64_t GetSizeOfFilesToRemove() |
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87 { |
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88 return sizeOfFilesToRemove_; |
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89 } |
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90 |
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91 void CommitFilesToRemove() |
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92 { |
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93 for (std::list<std::string>::iterator |
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94 it = pendingFilesToRemove_.begin(); |
| 656 | 95 it != pendingFilesToRemove_.end(); ++it) |
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96 { |
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97 context_.RemoveFile(*it); |
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98 } |
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99 } |
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100 |
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101 virtual void SignalRemainingAncestor(ResourceType parentType, |
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102 const std::string& publicId) |
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103 { |
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104 LOG(INFO) << "Remaining ancestor \"" << publicId << "\" (" << parentType << ")"; |
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105 |
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106 if (hasRemainingLevel_) |
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107 { |
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108 if (parentType < remainingType_) |
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109 { |
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110 remainingType_ = parentType; |
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111 remainingPublicId_ = publicId; |
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112 } |
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113 } |
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114 else |
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115 { |
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116 hasRemainingLevel_ = true; |
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117 remainingType_ = parentType; |
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118 remainingPublicId_ = publicId; |
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119 } |
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120 } |
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121 |
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122 virtual void SignalFileDeleted(const FileInfo& info) |
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123 { |
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124 assert(Toolbox::IsUuid(info.GetUuid())); |
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125 pendingFilesToRemove_.push_back(info.GetUuid()); |
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126 sizeOfFilesToRemove_ += info.GetCompressedSize(); |
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127 } |
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128 |
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129 bool HasRemainingLevel() const |
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130 { |
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131 return hasRemainingLevel_; |
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132 } |
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133 |
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134 ResourceType GetRemainingType() const |
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135 { |
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136 assert(HasRemainingLevel()); |
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137 return remainingType_; |
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138 } |
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139 |
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140 const std::string& GetRemainingPublicId() const |
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141 { |
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142 assert(HasRemainingLevel()); |
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143 return remainingPublicId_; |
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144 } |
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145 }; |
| 0 | 146 } |
| 147 | |
| 148 | |
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149 class ServerIndex::Transaction |
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150 { |
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151 private: |
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152 ServerIndex& index_; |
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153 std::auto_ptr<SQLite::Transaction> transaction_; |
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154 bool isCommitted_; |
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155 |
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156 public: |
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157 Transaction(ServerIndex& index) : |
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158 index_(index), |
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159 isCommitted_(false) |
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160 { |
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161 assert(index_.currentStorageSize_ == index_.db_->GetTotalCompressedSize()); |
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162 |
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163 index_.listener_->Reset(); |
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164 transaction_.reset(index_.db_->StartTransaction()); |
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165 transaction_->Begin(); |
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166 } |
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167 |
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168 void Commit(uint64_t sizeOfAddedFiles) |
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169 { |
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170 if (!isCommitted_) |
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171 { |
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172 transaction_->Commit(); |
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173 |
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174 // We can remove the files once the SQLite transaction has |
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175 // been successfully committed. Some files might have to be |
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176 // deleted because of recycling. |
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177 index_.listener_->CommitFilesToRemove(); |
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178 |
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179 index_.currentStorageSize_ += sizeOfAddedFiles; |
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180 |
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181 assert(index_.currentStorageSize_ >= index_.listener_->GetSizeOfFilesToRemove()); |
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182 index_.currentStorageSize_ -= index_.listener_->GetSizeOfFilesToRemove(); |
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183 |
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184 assert(index_.currentStorageSize_ == index_.db_->GetTotalCompressedSize()); |
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185 |
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186 isCommitted_ = true; |
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187 } |
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188 } |
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189 }; |
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190 |
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191 |
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192 struct ServerIndex::UnstableResourcePayload |
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193 { |
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194 Orthanc::ResourceType type_; |
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195 boost::posix_time::ptime time_; |
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196 |
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197 UnstableResourcePayload() : type_(Orthanc::ResourceType_Instance) |
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198 { |
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199 } |
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200 |
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201 UnstableResourcePayload(Orthanc::ResourceType type) : type_(type) |
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202 { |
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203 time_ = boost::posix_time::second_clock::local_time(); |
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204 } |
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205 |
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206 unsigned int GetAge() const |
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207 { |
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208 return (boost::posix_time::second_clock::local_time() - time_).total_seconds(); |
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209 } |
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210 }; |
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211 |
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212 |
| 212 | 213 bool ServerIndex::DeleteResource(Json::Value& target, |
| 0 | 214 const std::string& uuid, |
| 202 | 215 ResourceType expectedType) |
| 0 | 216 { |
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217 boost::mutex::scoped_lock lock(mutex_); |
| 202 | 218 listener_->Reset(); |
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201
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219 |
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220 Transaction t(*this); |
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221 |
| 202 | 222 int64_t id; |
| 223 ResourceType type; | |
| 224 if (!db_->LookupResource(uuid, id, type) || | |
| 225 expectedType != type) | |
| 0 | 226 { |
| 227 return false; | |
| 228 } | |
| 202 | 229 |
| 230 db_->DeleteResource(id); | |
| 0 | 231 |
| 202 | 232 if (listener_->HasRemainingLevel()) |
| 0 | 233 { |
| 202 | 234 ResourceType type = listener_->GetRemainingType(); |
| 235 const std::string& uuid = listener_->GetRemainingPublicId(); | |
| 0 | 236 |
| 237 target["RemainingAncestor"] = Json::Value(Json::objectValue); | |
| 204 | 238 target["RemainingAncestor"]["Path"] = GetBasePath(type, uuid); |
|
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239 target["RemainingAncestor"]["Type"] = EnumerationToString(type); |
| 0 | 240 target["RemainingAncestor"]["ID"] = uuid; |
| 241 } | |
| 242 else | |
| 243 { | |
| 244 target["RemainingAncestor"] = Json::nullValue; | |
| 245 } | |
| 246 | |
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247 t.Commit(0); |
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248 |
| 0 | 249 return true; |
| 250 } | |
| 251 | |
| 252 | |
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253 void ServerIndex::FlushThread(ServerIndex* that) |
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254 { |
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255 unsigned int sleep; |
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256 |
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257 try |
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258 { |
| 744 | 259 boost::mutex::scoped_lock lock(that->mutex_); |
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260 std::string sleepString = that->db_->GetGlobalProperty(GlobalProperty_FlushSleep); |
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261 sleep = boost::lexical_cast<unsigned int>(sleepString); |
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262 } |
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263 catch (boost::bad_lexical_cast&) |
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264 { |
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265 // By default, wait for 10 seconds before flushing |
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266 sleep = 10; |
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267 } |
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268 |
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269 LOG(INFO) << "Starting the database flushing thread (sleep = " << sleep << ")"; |
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270 |
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271 unsigned int count = 0; |
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272 |
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273 while (!that->done_) |
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274 { |
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275 boost::this_thread::sleep(boost::posix_time::seconds(1)); |
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276 count++; |
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277 if (count < sleep) |
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278 { |
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279 continue; |
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280 } |
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281 |
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282 boost::mutex::scoped_lock lock(that->mutex_); |
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283 that->db_->FlushToDisk(); |
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284 count = 0; |
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285 } |
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286 |
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287 LOG(INFO) << "Stopping the database flushing thread"; |
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288 } |
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289 |
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290 |
| 433 | 291 static void ComputeExpectedNumberOfInstances(DatabaseWrapper& db, |
| 292 int64_t series, | |
| 293 const DicomMap& dicomSummary) | |
| 294 { | |
| 295 try | |
| 296 { | |
| 656 | 297 const DicomValue* value; |
| 298 const DicomValue* value2; | |
| 299 | |
| 433 | 300 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL && |
| 301 (value2 = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS)) != NULL) | |
| 302 { | |
| 303 // Patch for series with temporal positions thanks to Will Ryder | |
| 304 int64_t imagesInAcquisition = boost::lexical_cast<int64_t>(value->AsString()); | |
| 305 int64_t countTemporalPositions = boost::lexical_cast<int64_t>(value2->AsString()); | |
| 306 std::string expected = boost::lexical_cast<std::string>(imagesInAcquisition * countTemporalPositions); | |
| 307 db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, expected); | |
| 308 } | |
| 309 | |
| 310 else if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL && | |
| 311 (value2 = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_TIME_SLICES)) != NULL) | |
| 312 { | |
| 313 // Support of Cardio-PET images | |
| 314 int64_t numberOfSlices = boost::lexical_cast<int64_t>(value->AsString()); | |
| 315 int64_t numberOfTimeSlices = boost::lexical_cast<int64_t>(value2->AsString()); | |
| 316 std::string expected = boost::lexical_cast<std::string>(numberOfSlices * numberOfTimeSlices); | |
| 317 db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, expected); | |
| 318 } | |
| 319 | |
| 320 else if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL) | |
| 321 { | |
| 322 db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, value->AsString()); | |
| 323 } | |
| 324 } | |
| 325 catch (boost::bad_lexical_cast) | |
| 326 { | |
| 327 } | |
| 328 } | |
| 329 | |
| 330 | |
|
226
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331 ServerIndex::ServerIndex(ServerContext& context, |
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332 const std::string& dbPath) : |
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333 done_(false), |
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334 maximumStorageSize_(0), |
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335 maximumPatients_(0) |
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336 { |
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337 listener_.reset(new Internals::ServerIndexListener(context)); |
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338 |
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339 if (dbPath == ":memory:") |
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340 { |
| 202 | 341 db_.reset(new DatabaseWrapper(*listener_)); |
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342 } |
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343 else |
| 0 | 344 { |
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345 boost::filesystem::path p = dbPath; |
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346 |
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347 try |
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348 { |
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349 boost::filesystem::create_directories(p); |
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350 } |
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351 catch (boost::filesystem::filesystem_error) |
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352 { |
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353 } |
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354 |
| 202 | 355 db_.reset(new DatabaseWrapper(p.string() + "/index", *listener_)); |
| 0 | 356 } |
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357 |
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358 currentStorageSize_ = db_->GetTotalCompressedSize(); |
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359 |
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360 // Initial recycling if the parameters have changed since the last |
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361 // execution of Orthanc |
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362 StandaloneRecycling(); |
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363 |
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364 flushThread_ = boost::thread(FlushThread, this); |
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365 unstableResourcesMonitorThread_ = boost::thread(UnstableResourcesMonitorThread, this); |
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366 } |
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367 |
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368 |
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369 ServerIndex::~ServerIndex() |
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370 { |
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371 done_ = true; |
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372 |
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373 if (flushThread_.joinable()) |
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374 { |
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375 flushThread_.join(); |
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376 } |
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377 |
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378 if (unstableResourcesMonitorThread_.joinable()) |
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379 { |
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380 unstableResourcesMonitorThread_.join(); |
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381 } |
| 0 | 382 } |
| 383 | |
| 384 | |
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385 StoreStatus ServerIndex::Store(const DicomMap& dicomSummary, |
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386 const Attachments& attachments, |
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387 const std::string& remoteAet, |
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388 MetadataMap* metadata) |
| 0 | 389 { |
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390 boost::mutex::scoped_lock lock(mutex_); |
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391 listener_->Reset(); |
| 0 | 392 |
| 178 | 393 DicomInstanceHasher hasher(dicomSummary); |
| 0 | 394 |
| 395 try | |
| 396 { | |
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397 Transaction t(*this); |
| 0 | 398 |
| 202 | 399 // Do nothing if the instance already exists |
| 0 | 400 { |
| 432 | 401 ResourceType type; |
| 402 int64_t tmp; | |
| 403 if (db_->LookupResource(hasher.HashInstance(), tmp, type)) | |
| 404 { | |
| 405 assert(type == ResourceType_Instance); | |
| 406 return StoreStatus_AlreadyStored; | |
| 407 } | |
| 0 | 408 } |
| 409 | |
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410 // Ensure there is enough room in the storage for the new instance |
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411 uint64_t instanceSize = 0; |
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412 for (Attachments::const_iterator it = attachments.begin(); |
| 656 | 413 it != attachments.end(); ++it) |
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414 { |
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415 instanceSize += it->GetCompressedSize(); |
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416 } |
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417 |
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418 Recycle(instanceSize, hasher.HashPatient()); |
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419 |
| 202 | 420 // Create the instance |
| 432 | 421 int64_t instance = db_->CreateResource(hasher.HashInstance(), ResourceType_Instance); |
| 202 | 422 |
| 423 DicomMap dicom; | |
| 424 dicomSummary.ExtractInstanceInformation(dicom); | |
| 425 db_->SetMainDicomTags(instance, dicom); | |
| 426 | |
| 432 | 427 // Detect up to which level the patient/study/series/instance |
| 428 // hierarchy must be created | |
| 429 int64_t patient = -1, study = -1, series = -1; | |
| 430 bool isNewPatient = false; | |
| 431 bool isNewStudy = false; | |
| 432 bool isNewSeries = false; | |
| 433 | |
| 0 | 434 { |
| 432 | 435 ResourceType dummy; |
| 436 | |
| 437 if (db_->LookupResource(hasher.HashSeries(), series, dummy)) | |
| 438 { | |
| 439 assert(dummy == ResourceType_Series); | |
| 440 // The patient, the study and the series already exist | |
| 441 | |
| 442 bool ok = (db_->LookupResource(hasher.HashPatient(), patient, dummy) && | |
| 443 db_->LookupResource(hasher.HashStudy(), study, dummy)); | |
| 444 assert(ok); | |
| 445 } | |
| 446 else if (db_->LookupResource(hasher.HashStudy(), study, dummy)) | |
| 447 { | |
| 448 assert(dummy == ResourceType_Study); | |
| 449 | |
| 450 // New series: The patient and the study already exist | |
| 451 isNewSeries = true; | |
| 452 | |
| 453 bool ok = db_->LookupResource(hasher.HashPatient(), patient, dummy); | |
| 454 assert(ok); | |
| 455 } | |
| 456 else if (db_->LookupResource(hasher.HashPatient(), patient, dummy)) | |
| 457 { | |
| 458 assert(dummy == ResourceType_Patient); | |
| 459 | |
| 460 // New study and series: The patient already exist | |
| 461 isNewStudy = true; | |
| 462 isNewSeries = true; | |
| 463 } | |
| 464 else | |
| 465 { | |
| 466 // New patient, study and series: Nothing exists | |
| 467 isNewPatient = true; | |
| 468 isNewStudy = true; | |
| 469 isNewSeries = true; | |
| 470 } | |
| 471 } | |
| 472 | |
| 473 // Create the series if needed | |
| 474 if (isNewSeries) | |
| 475 { | |
| 202 | 476 series = db_->CreateResource(hasher.HashSeries(), ResourceType_Series); |
| 477 dicomSummary.ExtractSeriesInformation(dicom); | |
| 478 db_->SetMainDicomTags(series, dicom); | |
| 432 | 479 } |
| 202 | 480 |
| 432 | 481 // Create the study if needed |
| 482 if (isNewStudy) | |
| 483 { | |
| 484 study = db_->CreateResource(hasher.HashStudy(), ResourceType_Study); | |
| 485 dicomSummary.ExtractStudyInformation(dicom); | |
| 486 db_->SetMainDicomTags(study, dicom); | |
| 487 } | |
| 488 | |
| 489 // Create the patient if needed | |
| 490 if (isNewPatient) | |
| 491 { | |
| 492 patient = db_->CreateResource(hasher.HashPatient(), ResourceType_Patient); | |
| 493 dicomSummary.ExtractPatientInformation(dicom); | |
| 494 db_->SetMainDicomTags(patient, dicom); | |
| 495 } | |
| 202 | 496 |
| 432 | 497 // Create the parent-to-child links |
| 498 db_->AttachChild(series, instance); | |
| 499 | |
| 500 if (isNewSeries) | |
| 501 { | |
| 502 db_->AttachChild(study, series); | |
| 0 | 503 } |
| 432 | 504 |
| 505 if (isNewStudy) | |
| 0 | 506 { |
| 432 | 507 db_->AttachChild(patient, study); |
| 0 | 508 } |
| 509 | |
| 432 | 510 // Sanity checks |
| 511 assert(patient != -1); | |
| 512 assert(study != -1); | |
| 513 assert(series != -1); | |
| 514 assert(instance != -1); | |
| 515 | |
| 202 | 516 // Attach the files to the newly created instance |
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517 for (Attachments::const_iterator it = attachments.begin(); |
| 656 | 518 it != attachments.end(); ++it) |
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519 { |
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520 db_->AddAttachment(instance, *it); |
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521 } |
| 202 | 522 |
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523 // Attach the user-specified metadata |
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524 if (metadata) |
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525 { |
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526 for (MetadataMap::const_iterator |
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527 it = metadata->begin(); it != metadata->end(); ++it) |
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528 { |
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529 switch (it->first.first) |
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530 { |
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531 case ResourceType_Patient: |
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532 db_->SetMetadata(patient, it->first.second, it->second); |
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533 break; |
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534 |
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535 case ResourceType_Study: |
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536 db_->SetMetadata(study, it->first.second, it->second); |
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537 break; |
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538 |
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539 case ResourceType_Series: |
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540 db_->SetMetadata(series, it->first.second, it->second); |
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541 break; |
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542 |
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543 case ResourceType_Instance: |
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544 db_->SetMetadata(instance, it->first.second, it->second); |
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545 break; |
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546 |
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547 default: |
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548 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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549 } |
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550 } |
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551 } |
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552 |
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553 // Attach the auto-computed metadata for the patient/study/series levels |
| 432 | 554 std::string now = Toolbox::GetNowIsoString(); |
| 555 db_->SetMetadata(series, MetadataType_LastUpdate, now); | |
| 556 db_->SetMetadata(study, MetadataType_LastUpdate, now); | |
| 557 db_->SetMetadata(patient, MetadataType_LastUpdate, now); | |
|
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558 |
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559 // Attach the auto-computed metadata for the instance level, |
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560 // reflecting these additions into the input metadata map |
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561 db_->SetMetadata(instance, MetadataType_Instance_ReceptionDate, now); |
| 202 | 562 db_->SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); |
| 563 | |
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564 if (metadata) |
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565 { |
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566 (*metadata) [std::make_pair(ResourceType_Instance, MetadataType_Instance_ReceptionDate)] = now; |
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567 (*metadata) [std::make_pair(ResourceType_Instance, MetadataType_Instance_RemoteAet)] = remoteAet; |
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568 } |
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569 |
| 202 | 570 const DicomValue* value; |
| 571 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || | |
| 572 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) | |
| 0 | 573 { |
| 202 | 574 db_->SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->AsString()); |
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575 |
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576 if (metadata) |
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577 { |
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578 (*metadata) [std::make_pair(ResourceType_Instance, MetadataType_Instance_IndexInSeries)] = value->AsString(); |
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579 } |
| 0 | 580 } |
| 581 | |
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582 // Check whether the series of this new instance is now completed |
| 202 | 583 if (isNewSeries) |
| 584 { | |
| 433 | 585 ComputeExpectedNumberOfInstances(*db_, series, dicomSummary); |
| 202 | 586 } |
| 587 | |
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588 SeriesStatus seriesStatus = GetSeriesStatus(series); |
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589 if (seriesStatus == SeriesStatus_Complete) |
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590 { |
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591 db_->LogChange(ChangeType_CompletedSeries, series, ResourceType_Series); |
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592 } |
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593 |
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511
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594 // Mark the parent resources of this instance as unstable |
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595 MarkAsUnstable(patient, ResourceType_Patient); |
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596 MarkAsUnstable(study, ResourceType_Study); |
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597 MarkAsUnstable(series, ResourceType_Series); |
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598 |
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599 t.Commit(instanceSize); |
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600 |
| 0 | 601 return StoreStatus_Success; |
| 602 } | |
| 62 | 603 catch (OrthancException& e) |
| 0 | 604 { |
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605 LOG(ERROR) << "EXCEPTION [" << e.What() << "]" |
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606 << " (SQLite status: " << db_->GetErrorMessage() << ")"; |
| 0 | 607 } |
| 608 | |
| 609 return StoreStatus_Failure; | |
| 610 } | |
| 611 | |
| 612 | |
| 238 | 613 void ServerIndex::ComputeStatistics(Json::Value& target) |
| 0 | 614 { |
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615 boost::mutex::scoped_lock lock(mutex_); |
| 238 | 616 target = Json::objectValue; |
| 0 | 617 |
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618 uint64_t cs = currentStorageSize_; |
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619 assert(cs == db_->GetTotalCompressedSize()); |
| 238 | 620 uint64_t us = db_->GetTotalUncompressedSize(); |
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621 target["TotalDiskSize"] = boost::lexical_cast<std::string>(cs); |
| 238 | 622 target["TotalUncompressedSize"] = boost::lexical_cast<std::string>(us); |
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623 target["TotalDiskSizeMB"] = boost::lexical_cast<unsigned int>(cs / MEGA_BYTES); |
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624 target["TotalUncompressedSizeMB"] = boost::lexical_cast<unsigned int>(us / MEGA_BYTES); |
| 238 | 625 |
| 626 target["CountPatients"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Patient)); | |
| 627 target["CountStudies"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Study)); | |
| 628 target["CountSeries"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Series)); | |
| 629 target["CountInstances"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Instance)); | |
| 630 } | |
| 631 | |
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632 |
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633 |
| 585 | 634 SeriesStatus ServerIndex::GetSeriesStatus(int64_t id) |
| 199 | 635 { |
| 636 // Get the expected number of instances in this series (from the metadata) | |
| 202 | 637 std::string s = db_->GetMetadata(id, MetadataType_Series_ExpectedNumberOfInstances); |
| 199 | 638 |
| 639 size_t expected; | |
| 640 try | |
| 641 { | |
| 642 expected = boost::lexical_cast<size_t>(s); | |
| 643 } | |
| 644 catch (boost::bad_lexical_cast&) | |
| 645 { | |
| 646 return SeriesStatus_Unknown; | |
| 647 } | |
| 648 | |
| 649 // Loop over the instances of this series | |
| 650 std::list<int64_t> children; | |
| 202 | 651 db_->GetChildrenInternalId(children, id); |
| 199 | 652 |
| 653 std::set<size_t> instances; | |
| 654 for (std::list<int64_t>::const_iterator | |
| 656 | 655 it = children.begin(); it != children.end(); ++it) |
| 199 | 656 { |
| 657 // Get the index of this instance in the series | |
| 202 | 658 s = db_->GetMetadata(*it, MetadataType_Instance_IndexInSeries); |
| 199 | 659 size_t index; |
| 660 try | |
| 661 { | |
| 662 index = boost::lexical_cast<size_t>(s); | |
| 663 } | |
| 664 catch (boost::bad_lexical_cast&) | |
| 665 { | |
| 666 return SeriesStatus_Unknown; | |
| 667 } | |
| 668 | |
| 656 | 669 if (!(index > 0 && index <= expected)) |
| 199 | 670 { |
| 671 // Out-of-range instance index | |
| 672 return SeriesStatus_Inconsistent; | |
| 673 } | |
| 674 | |
| 675 if (instances.find(index) != instances.end()) | |
| 676 { | |
| 677 // Twice the same instance index | |
| 678 return SeriesStatus_Inconsistent; | |
| 679 } | |
| 680 | |
| 681 instances.insert(index); | |
| 682 } | |
| 683 | |
| 684 if (instances.size() == expected) | |
| 685 { | |
| 686 return SeriesStatus_Complete; | |
| 687 } | |
| 688 else | |
| 689 { | |
| 690 return SeriesStatus_Missing; | |
| 691 } | |
| 692 } | |
| 693 | |
| 694 | |
| 695 | |
| 202 | 696 void ServerIndex::MainDicomTagsToJson(Json::Value& target, |
| 697 int64_t resourceId) | |
|
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698 { |
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699 DicomMap tags; |
| 202 | 700 db_->GetMainDicomTags(tags, resourceId); |
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701 target["MainDicomTags"] = Json::objectValue; |
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702 FromDcmtkBridge::ToJson(target["MainDicomTags"], tags); |
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703 } |
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704 |
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705 bool ServerIndex::LookupResource(Json::Value& result, |
| 199 | 706 const std::string& publicId, |
| 707 ResourceType expectedType) | |
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708 { |
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709 result = Json::objectValue; |
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710 |
|
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711 boost::mutex::scoped_lock lock(mutex_); |
| 199 | 712 |
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713 // Lookup for the requested resource |
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714 int64_t id; |
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715 ResourceType type; |
| 202 | 716 if (!db_->LookupResource(publicId, id, type) || |
| 199 | 717 type != expectedType) |
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718 { |
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719 return false; |
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720 } |
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721 |
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722 // Find the parent resource (if it exists) |
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723 if (type != ResourceType_Patient) |
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724 { |
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725 int64_t parentId; |
| 202 | 726 if (!db_->LookupParent(parentId, id)) |
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727 { |
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728 throw OrthancException(ErrorCode_InternalError); |
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729 } |
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730 |
| 202 | 731 std::string parent = db_->GetPublicId(parentId); |
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732 |
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733 switch (type) |
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734 { |
|
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735 case ResourceType_Study: |
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736 result["ParentPatient"] = parent; |
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737 break; |
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738 |
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739 case ResourceType_Series: |
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740 result["ParentStudy"] = parent; |
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741 break; |
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742 |
|
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743 case ResourceType_Instance: |
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744 result["ParentSeries"] = parent; |
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745 break; |
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746 |
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747 default: |
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748 throw OrthancException(ErrorCode_InternalError); |
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749 } |
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750 } |
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751 |
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752 // List the children resources |
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753 std::list<std::string> children; |
| 202 | 754 db_->GetChildrenPublicId(children, id); |
|
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755 |
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|
756 if (type != ResourceType_Instance) |
|
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|
757 { |
|
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|
758 Json::Value c = Json::arrayValue; |
|
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|
759 |
|
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|
760 for (std::list<std::string>::const_iterator |
| 656 | 761 it = children.begin(); it != children.end(); ++it) |
|
198
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|
762 { |
|
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|
763 c.append(*it); |
|
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|
764 } |
|
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|
765 |
|
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|
766 switch (type) |
|
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|
767 { |
|
269
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|
768 case ResourceType_Patient: |
|
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|
769 result["Studies"] = c; |
|
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|
770 break; |
|
198
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|
771 |
|
269
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|
772 case ResourceType_Study: |
|
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|
773 result["Series"] = c; |
|
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|
774 break; |
|
198
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changeset
|
775 |
|
269
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|
776 case ResourceType_Series: |
|
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|
777 result["Instances"] = c; |
|
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diff
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|
778 break; |
|
198
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|
779 |
|
269
f6fdf5abe751
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|
780 default: |
|
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|
781 throw OrthancException(ErrorCode_InternalError); |
|
198
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|
782 } |
|
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|
783 } |
|
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|
784 |
|
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|
785 // Set the resource type |
|
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|
786 switch (type) |
|
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|
787 { |
|
269
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|
788 case ResourceType_Patient: |
|
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|
789 result["Type"] = "Patient"; |
|
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|
790 break; |
|
198
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diff
changeset
|
791 |
|
269
f6fdf5abe751
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|
792 case ResourceType_Study: |
|
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|
793 result["Type"] = "Study"; |
|
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|
794 break; |
| 199 | 795 |
|
269
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|
796 case ResourceType_Series: |
|
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|
797 { |
|
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|
798 result["Type"] = "Series"; |
|
434
ccf3a0a43dac
EnumerationDictionary
Sebastien Jodogne <s.jodogne@gmail.com>
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433
diff
changeset
|
799 result["Status"] = EnumerationToString(GetSeriesStatus(id)); |
|
198
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|
800 |
|
269
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|
801 int i; |
|
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|
802 if (db_->GetMetadataAsInteger(i, id, MetadataType_Series_ExpectedNumberOfInstances)) |
|
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|
803 result["ExpectedNumberOfInstances"] = i; |
|
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|
804 else |
|
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|
805 result["ExpectedNumberOfInstances"] = Json::nullValue; |
|
200
9c58b2b03cf0
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diff
changeset
|
806 |
|
269
f6fdf5abe751
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diff
changeset
|
807 break; |
|
200
9c58b2b03cf0
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diff
changeset
|
808 } |
|
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diff
changeset
|
809 |
|
269
f6fdf5abe751
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diff
changeset
|
810 case ResourceType_Instance: |
|
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diff
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|
811 { |
|
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|
812 result["Type"] = "Instance"; |
|
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diff
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|
813 |
|
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diff
changeset
|
814 FileInfo attachment; |
|
f6fdf5abe751
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diff
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|
815 if (!db_->LookupAttachment(attachment, id, FileContentType_Dicom)) |
|
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diff
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|
816 { |
|
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changeset
|
817 throw OrthancException(ErrorCode_InternalError); |
|
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diff
changeset
|
818 } |
|
200
9c58b2b03cf0
refactoring of read operations
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199
diff
changeset
|
819 |
|
269
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|
820 result["FileSize"] = static_cast<unsigned int>(attachment.GetUncompressedSize()); |
|
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diff
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|
821 result["FileUuid"] = attachment.GetUuid(); |
|
200
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diff
changeset
|
822 |
|
269
f6fdf5abe751
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diff
changeset
|
823 int i; |
|
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diff
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|
824 if (db_->GetMetadataAsInteger(i, id, MetadataType_Instance_IndexInSeries)) |
|
f6fdf5abe751
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diff
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|
825 result["IndexInSeries"] = i; |
|
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diff
changeset
|
826 else |
|
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diff
changeset
|
827 result["IndexInSeries"] = Json::nullValue; |
|
198
663cc6c46d0a
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changeset
|
828 |
|
269
f6fdf5abe751
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diff
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|
829 break; |
|
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diff
changeset
|
830 } |
|
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|
831 |
|
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diff
changeset
|
832 default: |
|
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diff
changeset
|
833 throw OrthancException(ErrorCode_InternalError); |
|
198
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|
834 } |
|
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|
835 |
|
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|
836 // Record the remaining information |
|
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diff
changeset
|
837 result["ID"] = publicId; |
| 202 | 838 MainDicomTagsToJson(result, id); |
|
198
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|
839 |
| 315 | 840 std::string tmp; |
| 841 | |
| 842 tmp = db_->GetMetadata(id, MetadataType_AnonymizedFrom); | |
| 843 if (tmp.size() != 0) | |
| 844 result["AnonymizedFrom"] = tmp; | |
| 845 | |
| 846 tmp = db_->GetMetadata(id, MetadataType_ModifiedFrom); | |
| 847 if (tmp.size() != 0) | |
| 848 result["ModifiedFrom"] = tmp; | |
| 849 | |
|
511
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
850 if (type == ResourceType_Patient || |
|
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
851 type == ResourceType_Study || |
|
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
852 type == ResourceType_Series) |
|
3b735fdf320b
monitoring of stable patients/studies/series
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parents:
440
diff
changeset
|
853 { |
|
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
854 result["IsStable"] = !unstableResources_.Contains(id); |
|
3b735fdf320b
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
855 } |
|
3b735fdf320b
monitoring of stable patients/studies/series
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440
diff
changeset
|
856 |
|
198
663cc6c46d0a
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diff
changeset
|
857 return true; |
|
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changeset
|
858 } |
|
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changeset
|
859 |
| 0 | 860 |
|
232
5368bbe813cf
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diff
changeset
|
861 bool ServerIndex::LookupAttachment(FileInfo& attachment, |
|
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diff
changeset
|
862 const std::string& instanceUuid, |
| 233 | 863 FileContentType contentType) |
| 0 | 864 { |
|
206
4453a010d0db
flush to disk thread
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205
diff
changeset
|
865 boost::mutex::scoped_lock lock(mutex_); |
| 0 | 866 |
|
193
a1b9d1e1497b
failed attempt to compile with linux standard base
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parents:
192
diff
changeset
|
867 int64_t id; |
|
a1b9d1e1497b
failed attempt to compile with linux standard base
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192
diff
changeset
|
868 ResourceType type; |
| 701 | 869 if (!db_->LookupResource(instanceUuid, id, type)) |
|
192
c56dc32266e0
refactoring getfile
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191
diff
changeset
|
870 { |
|
c56dc32266e0
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191
diff
changeset
|
871 throw OrthancException(ErrorCode_InternalError); |
|
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191
diff
changeset
|
872 } |
|
193
a1b9d1e1497b
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192
diff
changeset
|
873 |
|
232
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refactoring of attachments
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231
diff
changeset
|
874 if (db_->LookupAttachment(attachment, id, contentType)) |
|
5368bbe813cf
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231
diff
changeset
|
875 { |
| 233 | 876 assert(attachment.GetContentType() == contentType); |
|
232
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diff
changeset
|
877 return true; |
|
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231
diff
changeset
|
878 } |
|
5368bbe813cf
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parents:
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diff
changeset
|
879 else |
|
5368bbe813cf
refactoring of attachments
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parents:
231
diff
changeset
|
880 { |
|
5368bbe813cf
refactoring of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
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231
diff
changeset
|
881 return false; |
|
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parents:
231
diff
changeset
|
882 } |
|
192
c56dc32266e0
refactoring getfile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
191
diff
changeset
|
883 } |
|
c56dc32266e0
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parents:
191
diff
changeset
|
884 |
|
c56dc32266e0
refactoring getfile
Sebastien Jodogne <s.jodogne@gmail.com>
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191
diff
changeset
|
885 |
|
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191
diff
changeset
|
886 |
| 0 | 887 void ServerIndex::GetAllUuids(Json::Value& target, |
| 190 | 888 ResourceType resourceType) |
| 0 | 889 { |
|
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890 boost::mutex::scoped_lock lock(mutex_); |
| 202 | 891 db_->GetAllPublicIds(target, resourceType); |
| 0 | 892 } |
| 893 | |
| 894 | |
| 895 bool ServerIndex::GetChanges(Json::Value& target, | |
| 204 | 896 int64_t since, |
| 0 | 897 unsigned int maxResults) |
| 898 { | |
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899 boost::mutex::scoped_lock lock(mutex_); |
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900 db_->GetChanges(target, since, maxResults); |
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901 return true; |
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902 } |
| 0 | 903 |
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904 bool ServerIndex::GetLastChange(Json::Value& target) |
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905 { |
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906 boost::mutex::scoped_lock lock(mutex_); |
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907 db_->GetLastChange(target); |
| 204 | 908 return true; |
| 0 | 909 } |
| 231 | 910 |
| 911 void ServerIndex::LogExportedResource(const std::string& publicId, | |
| 912 const std::string& remoteModality) | |
| 913 { | |
| 914 boost::mutex::scoped_lock lock(mutex_); | |
| 915 | |
| 916 int64_t id; | |
| 917 ResourceType type; | |
| 918 if (!db_->LookupResource(publicId, id, type)) | |
| 919 { | |
| 920 throw OrthancException(ErrorCode_InternalError); | |
| 921 } | |
| 922 | |
| 923 std::string patientId; | |
| 924 std::string studyInstanceUid; | |
| 925 std::string seriesInstanceUid; | |
| 926 std::string sopInstanceUid; | |
| 927 | |
| 928 int64_t currentId = id; | |
| 929 ResourceType currentType = type; | |
| 930 | |
| 931 // Iteratively go up inside the patient/study/series/instance hierarchy | |
| 932 bool done = false; | |
| 933 while (!done) | |
| 934 { | |
| 935 DicomMap map; | |
| 936 db_->GetMainDicomTags(map, currentId); | |
| 937 | |
| 938 switch (currentType) | |
| 939 { | |
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940 case ResourceType_Patient: |
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941 patientId = map.GetValue(DICOM_TAG_PATIENT_ID).AsString(); |
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942 done = true; |
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943 break; |
| 231 | 944 |
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945 case ResourceType_Study: |
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946 studyInstanceUid = map.GetValue(DICOM_TAG_STUDY_INSTANCE_UID).AsString(); |
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947 currentType = ResourceType_Patient; |
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948 break; |
| 231 | 949 |
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950 case ResourceType_Series: |
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951 seriesInstanceUid = map.GetValue(DICOM_TAG_SERIES_INSTANCE_UID).AsString(); |
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952 currentType = ResourceType_Study; |
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953 break; |
| 231 | 954 |
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955 case ResourceType_Instance: |
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956 sopInstanceUid = map.GetValue(DICOM_TAG_SOP_INSTANCE_UID).AsString(); |
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957 currentType = ResourceType_Series; |
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958 break; |
| 231 | 959 |
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960 default: |
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961 throw OrthancException(ErrorCode_InternalError); |
| 231 | 962 } |
| 963 | |
| 964 // If we have not reached the Patient level, find the parent of | |
| 965 // the current resource | |
| 966 if (!done) | |
| 967 { | |
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968 bool ok = db_->LookupParent(currentId, currentId); |
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969 assert(ok); |
| 231 | 970 } |
| 971 } | |
| 972 | |
| 973 // No need for a SQLite::Transaction here, as we only insert 1 record | |
| 974 db_->LogExportedResource(type, | |
| 975 publicId, | |
| 976 remoteModality, | |
| 977 patientId, | |
| 978 studyInstanceUid, | |
| 979 seriesInstanceUid, | |
| 980 sopInstanceUid); | |
| 981 } | |
| 982 | |
| 983 | |
| 984 bool ServerIndex::GetExportedResources(Json::Value& target, | |
| 985 int64_t since, | |
| 986 unsigned int maxResults) | |
| 987 { | |
| 988 boost::mutex::scoped_lock lock(mutex_); | |
| 989 db_->GetExportedResources(target, since, maxResults); | |
| 990 return true; | |
| 991 } | |
|
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992 |
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993 bool ServerIndex::GetLastExportedResource(Json::Value& target) |
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994 { |
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995 boost::mutex::scoped_lock lock(mutex_); |
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996 db_->GetLastExportedResource(target); |
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997 return true; |
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998 } |
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999 |
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1000 |
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1001 bool ServerIndex::IsRecyclingNeeded(uint64_t instanceSize) |
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1002 { |
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1003 if (maximumStorageSize_ != 0) |
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1004 { |
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1005 uint64_t currentSize = currentStorageSize_ - listener_->GetSizeOfFilesToRemove(); |
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1006 assert(db_->GetTotalCompressedSize() == currentSize); |
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1007 |
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1008 if (currentSize + instanceSize > maximumStorageSize_) |
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1009 { |
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1010 return true; |
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1011 } |
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1012 } |
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1013 |
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1014 if (maximumPatients_ != 0) |
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1015 { |
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1016 uint64_t patientCount = db_->GetResourceCount(ResourceType_Patient); |
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1017 if (patientCount > maximumPatients_) |
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1018 { |
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1019 return true; |
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1020 } |
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1021 } |
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1022 |
|
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1023 return false; |
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1024 } |
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1025 |
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1026 |
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1027 void ServerIndex::Recycle(uint64_t instanceSize, |
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1028 const std::string& newPatientId) |
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1029 { |
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1030 if (!IsRecyclingNeeded(instanceSize)) |
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1031 { |
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1032 return; |
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1033 } |
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1034 |
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1035 // Check whether other DICOM instances from this patient are |
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1036 // already stored |
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1037 int64_t patientToAvoid; |
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1038 ResourceType type; |
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1039 bool hasPatientToAvoid = db_->LookupResource(newPatientId, patientToAvoid, type); |
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1040 |
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1041 if (hasPatientToAvoid && type != ResourceType_Patient) |
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1042 { |
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1043 throw OrthancException(ErrorCode_InternalError); |
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1044 } |
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1045 |
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1046 // Iteratively select patient to remove until there is enough |
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1047 // space in the DICOM store |
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1048 int64_t patientToRecycle; |
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1049 while (true) |
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1050 { |
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1051 // If other instances of this patient are already in the store, |
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1052 // we must avoid to recycle them |
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1053 bool ok = hasPatientToAvoid ? |
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1054 db_->SelectPatientToRecycle(patientToRecycle, patientToAvoid) : |
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1055 db_->SelectPatientToRecycle(patientToRecycle); |
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1056 |
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1057 if (!ok) |
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1058 { |
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1059 throw OrthancException(ErrorCode_FullStorage); |
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1060 } |
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1061 |
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1062 LOG(INFO) << "Recycling one patient"; |
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1063 db_->DeleteResource(patientToRecycle); |
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1064 |
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1065 if (!IsRecyclingNeeded(instanceSize)) |
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1066 { |
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1067 // OK, we're done |
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1068 break; |
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1069 } |
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1070 } |
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1071 } |
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1072 |
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1073 void ServerIndex::SetMaximumPatientCount(unsigned int count) |
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1074 { |
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1075 boost::mutex::scoped_lock lock(mutex_); |
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1076 maximumPatients_ = count; |
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1077 |
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1078 if (count == 0) |
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1079 { |
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1080 LOG(WARNING) << "No limit on the number of stored patients"; |
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1081 } |
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1082 else |
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1083 { |
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1084 LOG(WARNING) << "At most " << count << " patients will be stored"; |
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1085 } |
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1086 |
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1087 StandaloneRecycling(); |
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1088 } |
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1089 |
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1090 void ServerIndex::SetMaximumStorageSize(uint64_t size) |
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1091 { |
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1092 boost::mutex::scoped_lock lock(mutex_); |
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1093 maximumStorageSize_ = size; |
|
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1094 |
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1095 if (size == 0) |
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1096 { |
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1097 LOG(WARNING) << "No limit on the size of the storage area"; |
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1098 } |
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1099 else |
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1100 { |
|
440
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1101 LOG(WARNING) << "At most " << (size / MEGA_BYTES) << "MB will be used for the storage area"; |
|
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1102 } |
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1103 |
|
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1104 StandaloneRecycling(); |
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1105 } |
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1106 |
|
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1107 void ServerIndex::StandaloneRecycling() |
|
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1108 { |
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1109 // WARNING: No mutex here, do not include this as a public method |
|
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1110 Transaction t(*this); |
|
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1111 Recycle(0, ""); |
|
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1112 t.Commit(0); |
|
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1113 } |
|
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1114 |
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1115 |
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1116 bool ServerIndex::IsProtectedPatient(const std::string& publicId) |
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1117 { |
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1118 boost::mutex::scoped_lock lock(mutex_); |
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1119 |
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1120 // Lookup for the requested resource |
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1121 int64_t id; |
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1122 ResourceType type; |
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1123 if (!db_->LookupResource(publicId, id, type) || |
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1124 type != ResourceType_Patient) |
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1125 { |
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1126 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1127 } |
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1128 |
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1129 return db_->IsProtectedPatient(id); |
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1130 } |
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1131 |
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1132 |
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1133 void ServerIndex::SetProtectedPatient(const std::string& publicId, |
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1134 bool isProtected) |
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1135 { |
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1136 boost::mutex::scoped_lock lock(mutex_); |
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1137 |
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1138 // Lookup for the requested resource |
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1139 int64_t id; |
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1140 ResourceType type; |
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1141 if (!db_->LookupResource(publicId, id, type) || |
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1142 type != ResourceType_Patient) |
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1143 { |
|
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1144 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1145 } |
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1146 |
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1147 // No need for a SQLite::Transaction here, as we only make 1 write to the DB |
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1148 db_->SetProtectedPatient(id, isProtected); |
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1149 |
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1150 if (isProtected) |
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1151 LOG(INFO) << "Patient " << publicId << " has been protected"; |
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1152 else |
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1153 LOG(INFO) << "Patient " << publicId << " has been unprotected"; |
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1154 } |
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1155 |
| 304 | 1156 |
|
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1157 void ServerIndex::GetChildren(std::list<std::string>& result, |
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1158 const std::string& publicId) |
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1159 { |
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1160 result.clear(); |
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1161 |
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1162 boost::mutex::scoped_lock lock(mutex_); |
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1163 |
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1164 ResourceType type; |
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1165 int64_t resource; |
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1166 if (!db_->LookupResource(publicId, resource, type)) |
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1167 { |
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1168 throw OrthancException(ErrorCode_UnknownResource); |
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1169 } |
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1170 |
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1171 if (type == ResourceType_Instance) |
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1172 { |
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1173 // An instance cannot have a child |
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1174 throw OrthancException(ErrorCode_BadParameterType); |
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1175 } |
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1176 |
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1177 std::list<int64_t> tmp; |
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1178 db_->GetChildrenInternalId(tmp, resource); |
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1179 |
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1180 for (std::list<int64_t>::const_iterator |
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1181 it = tmp.begin(); it != tmp.end(); ++it) |
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1182 { |
|
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1183 result.push_back(db_->GetPublicId(*it)); |
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1184 } |
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1185 } |
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1186 |
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1187 |
| 304 | 1188 void ServerIndex::GetChildInstances(std::list<std::string>& result, |
| 1189 const std::string& publicId) | |
| 1190 { | |
| 1191 result.clear(); | |
| 1192 | |
| 1193 boost::mutex::scoped_lock lock(mutex_); | |
| 1194 | |
| 1195 ResourceType type; | |
| 1196 int64_t top; | |
| 1197 if (!db_->LookupResource(publicId, top, type)) | |
| 1198 { | |
| 1199 throw OrthancException(ErrorCode_UnknownResource); | |
| 1200 } | |
| 1201 | |
| 1202 if (type == ResourceType_Instance) | |
| 1203 { | |
| 1204 // The resource is already an instance: Do not go down the hierarchy | |
| 1205 result.push_back(publicId); | |
| 1206 return; | |
| 1207 } | |
| 1208 | |
| 1209 std::stack<int64_t> toExplore; | |
| 1210 toExplore.push(top); | |
| 1211 | |
| 1212 std::list<int64_t> tmp; | |
| 1213 | |
| 1214 while (!toExplore.empty()) | |
| 1215 { | |
| 1216 // Get the internal ID of the current resource | |
| 1217 int64_t resource = toExplore.top(); | |
| 1218 toExplore.pop(); | |
| 1219 | |
| 1220 if (db_->GetResourceType(resource) == ResourceType_Instance) | |
| 1221 { | |
| 1222 result.push_back(db_->GetPublicId(resource)); | |
| 1223 } | |
| 1224 else | |
| 1225 { | |
| 1226 // Tag all the children of this resource as to be explored | |
| 1227 db_->GetChildrenInternalId(tmp, resource); | |
| 1228 for (std::list<int64_t>::const_iterator | |
| 656 | 1229 it = tmp.begin(); it != tmp.end(); ++it) |
| 304 | 1230 { |
| 1231 toExplore.push(*it); | |
| 1232 } | |
| 1233 } | |
| 1234 } | |
| 1235 } | |
| 1236 | |
|
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1237 |
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1238 void ServerIndex::SetMetadata(const std::string& publicId, |
|
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1239 MetadataType type, |
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1240 const std::string& value) |
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1241 { |
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1242 boost::mutex::scoped_lock lock(mutex_); |
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1243 |
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1244 ResourceType rtype; |
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1245 int64_t id; |
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1246 if (!db_->LookupResource(publicId, id, rtype)) |
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1247 { |
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1248 throw OrthancException(ErrorCode_UnknownResource); |
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1249 } |
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1250 |
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1251 db_->SetMetadata(id, type, value); |
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1252 } |
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1253 |
| 438 | 1254 |
| 1255 void ServerIndex::DeleteMetadata(const std::string& publicId, | |
| 1256 MetadataType type) | |
| 1257 { | |
| 1258 boost::mutex::scoped_lock lock(mutex_); | |
| 1259 | |
| 1260 ResourceType rtype; | |
| 1261 int64_t id; | |
| 1262 if (!db_->LookupResource(publicId, id, rtype)) | |
| 1263 { | |
| 1264 throw OrthancException(ErrorCode_UnknownResource); | |
| 1265 } | |
| 1266 | |
| 1267 db_->DeleteMetadata(id, type); | |
| 1268 } | |
| 1269 | |
| 1270 | |
|
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1271 bool ServerIndex::LookupMetadata(std::string& target, |
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1272 const std::string& publicId, |
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1273 MetadataType type) |
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1274 { |
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1275 boost::mutex::scoped_lock lock(mutex_); |
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1276 |
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1277 ResourceType rtype; |
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1278 int64_t id; |
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1279 if (!db_->LookupResource(publicId, id, rtype)) |
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1280 { |
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1281 throw OrthancException(ErrorCode_UnknownResource); |
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1282 } |
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1283 |
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1284 return db_->LookupMetadata(target, id, type); |
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1285 } |
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1286 |
|
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1287 |
| 739 | 1288 void ServerIndex::ListAvailableMetadata(std::list<MetadataType>& target, |
|
436
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1289 const std::string& publicId) |
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1290 { |
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1291 boost::mutex::scoped_lock lock(mutex_); |
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1292 |
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1293 ResourceType rtype; |
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1294 int64_t id; |
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1295 if (!db_->LookupResource(publicId, id, rtype)) |
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1296 { |
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1297 throw OrthancException(ErrorCode_UnknownResource); |
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1298 } |
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1299 |
| 739 | 1300 db_->ListAvailableMetadata(target, id); |
|
436
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1301 } |
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1302 |
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1303 |
|
697
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|
1304 void ServerIndex::ListAvailableAttachments(std::list<FileContentType>& target, |
|
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|
1305 const std::string& publicId, |
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1306 ResourceType expectedType) |
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1307 { |
|
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1308 boost::mutex::scoped_lock lock(mutex_); |
|
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1309 |
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1310 ResourceType type; |
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1311 int64_t id; |
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1312 if (!db_->LookupResource(publicId, id, type) || |
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1313 expectedType != type) |
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1314 { |
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1315 throw OrthancException(ErrorCode_UnknownResource); |
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1316 } |
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1317 |
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1318 db_->ListAvailableAttachments(target, id); |
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1319 } |
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1320 |
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1321 |
|
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1322 bool ServerIndex::LookupParent(std::string& target, |
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1323 const std::string& publicId) |
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1324 { |
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1325 boost::mutex::scoped_lock lock(mutex_); |
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1326 |
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1327 ResourceType type; |
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1328 int64_t id; |
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1329 if (!db_->LookupResource(publicId, id, type)) |
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1330 { |
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1331 throw OrthancException(ErrorCode_UnknownResource); |
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1332 } |
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1333 |
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1334 int64_t parentId; |
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1335 if (db_->LookupParent(parentId, id)) |
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1336 { |
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1337 target = db_->GetPublicId(parentId); |
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1338 return true; |
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1339 } |
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1340 else |
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1341 { |
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1342 return false; |
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1343 } |
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1344 } |
| 310 | 1345 |
| 1346 | |
| 1347 uint64_t ServerIndex::IncrementGlobalSequence(GlobalProperty sequence) | |
| 1348 { | |
| 1349 boost::mutex::scoped_lock lock(mutex_); | |
| 311 | 1350 |
| 1351 std::auto_ptr<SQLite::Transaction> transaction(db_->StartTransaction()); | |
| 1352 | |
| 1353 transaction->Begin(); | |
| 1354 uint64_t seq = db_->IncrementGlobalSequence(sequence); | |
| 1355 transaction->Commit(); | |
| 1356 | |
| 1357 return seq; | |
| 310 | 1358 } |
| 315 | 1359 |
| 1360 | |
| 1361 | |
| 1362 void ServerIndex::LogChange(ChangeType changeType, | |
| 1363 const std::string& publicId) | |
| 1364 { | |
| 1365 boost::mutex::scoped_lock lock(mutex_); | |
| 1366 std::auto_ptr<SQLite::Transaction> transaction(db_->StartTransaction()); | |
| 1367 transaction->Begin(); | |
| 1368 | |
| 1369 int64_t id; | |
| 1370 ResourceType type; | |
| 1371 if (!db_->LookupResource(publicId, id, type)) | |
| 1372 { | |
| 1373 throw OrthancException(ErrorCode_UnknownResource); | |
| 1374 } | |
| 1375 | |
| 1376 db_->LogChange(changeType, id, type); | |
| 1377 | |
| 1378 transaction->Commit(); | |
| 1379 } | |
|
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1380 |
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1381 |
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1382 void ServerIndex::DeleteChanges() |
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1383 { |
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1384 boost::mutex::scoped_lock lock(mutex_); |
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1385 db_->ClearTable("Changes"); |
|
47d63c941902
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|
1386 } |
|
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diff
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|
1387 |
|
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diff
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|
1388 void ServerIndex::DeleteExportedResources() |
|
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|
1389 { |
|
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|
1390 boost::mutex::scoped_lock lock(mutex_); |
|
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|
1391 db_->ClearTable("ExportedResources"); |
|
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|
1392 } |
|
440
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|
1393 |
|
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|
1394 |
| 646 | 1395 void ServerIndex::GetStatisticsInternal(/* out */ uint64_t& compressedSize, |
| 1396 /* out */ uint64_t& uncompressedSize, | |
| 1397 /* out */ unsigned int& countStudies, | |
| 1398 /* out */ unsigned int& countSeries, | |
| 1399 /* out */ unsigned int& countInstances, | |
| 1400 /* in */ int64_t id, | |
| 1401 /* in */ ResourceType type) | |
|
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|
1402 { |
| 646 | 1403 std::stack<int64_t> toExplore; |
| 1404 toExplore.push(id); | |
|
440
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|
1405 |
| 646 | 1406 countInstances = 0; |
| 1407 countSeries = 0; | |
| 1408 countStudies = 0; | |
| 1409 compressedSize = 0; | |
| 1410 uncompressedSize = 0; | |
|
440
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|
1411 |
|
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diff
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|
1412 while (!toExplore.empty()) |
|
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|
1413 { |
|
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|
1414 // Get the internal ID of the current resource |
|
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|
1415 int64_t resource = toExplore.top(); |
|
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|
1416 toExplore.pop(); |
|
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|
1417 |
|
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diff
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|
1418 ResourceType thisType = db_->GetResourceType(resource); |
|
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|
1419 |
|
702
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|
1420 std::list<FileContentType> f; |
|
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|
1421 db_->ListAvailableAttachments(f, resource); |
|
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|
1422 |
|
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|
1423 for (std::list<FileContentType>::const_iterator |
|
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|
1424 it = f.begin(); it != f.end(); ++it) |
|
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|
1425 { |
|
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|
1426 FileInfo attachment; |
|
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diff
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|
1427 if (db_->LookupAttachment(attachment, resource, *it)) |
|
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|
1428 { |
|
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|
1429 compressedSize += attachment.GetCompressedSize(); |
|
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|
1430 uncompressedSize += attachment.GetUncompressedSize(); |
|
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|
1431 } |
|
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|
1432 } |
|
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|
1433 |
|
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|
1434 if (thisType == ResourceType_Instance) |
|
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|
1435 { |
|
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|
1436 countInstances++; |
|
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|
1437 } |
|
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|
1438 else |
|
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|
1439 { |
|
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|
1440 switch (thisType) |
|
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|
1441 { |
|
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|
1442 case ResourceType_Study: |
|
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|
1443 countStudies++; |
|
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|
1444 break; |
|
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|
1445 |
|
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|
1446 case ResourceType_Series: |
|
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|
1447 countSeries++; |
|
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|
1448 break; |
|
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diff
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|
1449 |
|
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diff
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|
1450 default: |
|
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|
1451 break; |
|
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|
1452 } |
|
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|
1453 |
|
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|
1454 // Tag all the children of this resource as to be explored |
|
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|
1455 std::list<int64_t> tmp; |
|
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|
1456 db_->GetChildrenInternalId(tmp, resource); |
|
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|
1457 for (std::list<int64_t>::const_iterator |
| 656 | 1458 it = tmp.begin(); it != tmp.end(); ++it) |
|
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|
1459 { |
|
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|
1460 toExplore.push(*it); |
|
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|
1461 } |
|
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|
1462 } |
|
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|
1463 } |
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|
1464 |
| 646 | 1465 if (countStudies == 0) |
| 1466 { | |
| 1467 countStudies = 1; | |
| 1468 } | |
| 1469 | |
| 1470 if (countSeries == 0) | |
| 1471 { | |
| 1472 countSeries = 1; | |
| 1473 } | |
| 1474 } | |
| 1475 | |
| 1476 | |
| 1477 | |
| 1478 void ServerIndex::GetStatistics(Json::Value& target, | |
| 1479 const std::string& publicId) | |
| 1480 { | |
| 1481 boost::mutex::scoped_lock lock(mutex_); | |
| 1482 | |
| 1483 ResourceType type; | |
| 1484 int64_t top; | |
| 1485 if (!db_->LookupResource(publicId, top, type)) | |
| 1486 { | |
| 1487 throw OrthancException(ErrorCode_UnknownResource); | |
| 1488 } | |
| 1489 | |
| 1490 uint64_t uncompressedSize; | |
| 1491 uint64_t compressedSize; | |
| 1492 unsigned int countStudies; | |
| 1493 unsigned int countSeries; | |
| 1494 unsigned int countInstances; | |
| 1495 GetStatisticsInternal(compressedSize, uncompressedSize, countStudies, | |
| 1496 countSeries, countInstances, top, type); | |
| 1497 | |
|
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|
1498 target = Json::objectValue; |
|
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|
1499 target["DiskSize"] = boost::lexical_cast<std::string>(compressedSize); |
|
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|
1500 target["DiskSizeMB"] = boost::lexical_cast<unsigned int>(compressedSize / MEGA_BYTES); |
|
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|
1501 target["UncompressedSize"] = boost::lexical_cast<std::string>(uncompressedSize); |
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|
1502 target["UncompressedSizeMB"] = boost::lexical_cast<unsigned int>(uncompressedSize / MEGA_BYTES); |
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|
1503 |
|
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|
1504 switch (type) |
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|
1505 { |
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|
1506 // Do NOT add "break" below this point! |
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|
1507 case ResourceType_Patient: |
|
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|
1508 target["CountStudies"] = countStudies; |
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|
1509 |
|
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|
1510 case ResourceType_Study: |
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|
1511 target["CountSeries"] = countSeries; |
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|
1512 |
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|
1513 case ResourceType_Series: |
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|
1514 target["CountInstances"] = countInstances; |
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|
1515 |
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|
1516 case ResourceType_Instance: |
|
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|
1517 default: |
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|
1518 break; |
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|
1519 } |
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|
1520 } |
|
511
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|
1521 |
|
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|
1522 |
| 646 | 1523 void ServerIndex::GetStatistics(/* out */ uint64_t& compressedSize, |
| 1524 /* out */ uint64_t& uncompressedSize, | |
| 1525 /* out */ unsigned int& countStudies, | |
| 1526 /* out */ unsigned int& countSeries, | |
| 1527 /* out */ unsigned int& countInstances, | |
| 1528 const std::string& publicId) | |
| 1529 { | |
| 1530 boost::mutex::scoped_lock lock(mutex_); | |
| 1531 | |
| 1532 ResourceType type; | |
| 1533 int64_t top; | |
| 1534 if (!db_->LookupResource(publicId, top, type)) | |
| 1535 { | |
| 1536 throw OrthancException(ErrorCode_UnknownResource); | |
| 1537 } | |
| 1538 | |
| 1539 GetStatisticsInternal(compressedSize, uncompressedSize, countStudies, | |
| 1540 countSeries, countInstances, top, type); | |
| 1541 } | |
| 1542 | |
| 1543 | |
|
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|
1544 void ServerIndex::UnstableResourcesMonitorThread(ServerIndex* that) |
|
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|
1545 { |
|
810
401a9633e492
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|
1546 int stableAge = Configuration::GetGlobalIntegerParameter("StableAge", 60); |
|
511
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|
1547 if (stableAge <= 0) |
|
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|
1548 { |
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|
1549 stableAge = 60; |
|
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1550 } |
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|
1551 |
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1552 LOG(INFO) << "Starting the monitor for stable resources (stable age = " << stableAge << ")"; |
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1553 |
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|
1554 while (!that->done_) |
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1555 { |
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1556 // Check for stable resources each second |
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1557 boost::this_thread::sleep(boost::posix_time::seconds(1)); |
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1558 |
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|
1559 boost::mutex::scoped_lock lock(that->mutex_); |
| 513 | 1560 |
|
511
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1561 while (!that->unstableResources_.IsEmpty() && |
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1562 that->unstableResources_.GetOldestPayload().GetAge() > static_cast<unsigned int>(stableAge)) |
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|
1563 { |
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1564 // This DICOM resource has not received any new instance for |
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1565 // some time. It can be considered as stable. |
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1566 |
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|
1567 UnstableResourcePayload payload; |
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1568 int64_t id = that->unstableResources_.RemoveOldest(payload); |
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1569 |
| 513 | 1570 // Ensure that the resource is still existing before logging the change |
| 1571 if (that->db_->IsExistingResource(id)) | |
|
511
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1572 { |
| 513 | 1573 switch (payload.type_) |
| 1574 { | |
| 1575 case Orthanc::ResourceType_Patient: | |
| 1576 that->db_->LogChange(ChangeType_StablePatient, id, ResourceType_Patient); | |
| 1577 break; | |
|
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1578 |
| 513 | 1579 case Orthanc::ResourceType_Study: |
| 1580 that->db_->LogChange(ChangeType_StableStudy, id, ResourceType_Study); | |
| 1581 break; | |
|
511
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1582 |
| 513 | 1583 case Orthanc::ResourceType_Series: |
| 1584 that->db_->LogChange(ChangeType_StableSeries, id, ResourceType_Series); | |
| 1585 break; | |
| 1586 | |
| 1587 default: | |
| 1588 throw OrthancException(ErrorCode_InternalError); | |
| 1589 } | |
| 1590 | |
| 1591 //LOG(INFO) << "Stable resource: " << EnumerationToString(payload.type_) << " " << id; | |
|
511
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1592 } |
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|
1593 } |
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|
1594 } |
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|
1595 |
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|
1596 LOG(INFO) << "Closing the monitor thread for stable resources"; |
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|
1597 } |
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|
1598 |
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|
1599 |
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|
1600 void ServerIndex::MarkAsUnstable(int64_t id, |
|
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|
1601 Orthanc::ResourceType type) |
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1602 { |
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1603 // WARNING: Before calling this method, "mutex_" must be locked. |
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1604 |
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|
1605 assert(type == Orthanc::ResourceType_Patient || |
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1606 type == Orthanc::ResourceType_Study || |
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1607 type == Orthanc::ResourceType_Series); |
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1608 |
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1609 unstableResources_.AddOrMakeMostRecent(id, type); |
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1610 //LOG(INFO) << "Unstable resource: " << EnumerationToString(type) << " " << id; |
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1611 } |
| 521 | 1612 |
| 1613 | |
| 1614 | |
| 1615 void ServerIndex::LookupTagValue(std::list<std::string>& result, | |
| 1616 DicomTag tag, | |
| 615 | 1617 const std::string& value, |
| 1618 ResourceType type) | |
| 1619 { | |
| 1620 result.clear(); | |
| 1621 | |
| 1622 boost::mutex::scoped_lock lock(mutex_); | |
| 1623 | |
| 1624 std::list<int64_t> id; | |
| 1625 db_->LookupTagValue(id, tag, value); | |
| 1626 | |
| 1627 for (std::list<int64_t>::const_iterator | |
| 656 | 1628 it = id.begin(); it != id.end(); ++it) |
| 615 | 1629 { |
| 1630 if (db_->GetResourceType(*it) == type) | |
| 1631 { | |
| 1632 result.push_back(db_->GetPublicId(*it)); | |
| 1633 } | |
| 1634 } | |
| 1635 } | |
| 1636 | |
| 1637 | |
| 1638 void ServerIndex::LookupTagValue(std::list<std::string>& result, | |
| 1639 DicomTag tag, | |
| 521 | 1640 const std::string& value) |
| 1641 { | |
| 1642 result.clear(); | |
| 1643 | |
| 1644 boost::mutex::scoped_lock lock(mutex_); | |
| 1645 | |
| 1646 std::list<int64_t> id; | |
| 1647 db_->LookupTagValue(id, tag, value); | |
| 1648 | |
| 1649 for (std::list<int64_t>::const_iterator | |
| 656 | 1650 it = id.begin(); it != id.end(); ++it) |
| 521 | 1651 { |
| 1652 result.push_back(db_->GetPublicId(*it)); | |
| 1653 } | |
| 1654 } | |
| 1655 | |
| 1656 | |
| 1657 void ServerIndex::LookupTagValue(std::list<std::string>& result, | |
| 1658 const std::string& value) | |
| 1659 { | |
| 1660 result.clear(); | |
| 1661 | |
| 1662 boost::mutex::scoped_lock lock(mutex_); | |
| 1663 | |
| 1664 std::list<int64_t> id; | |
| 1665 db_->LookupTagValue(id, value); | |
| 1666 | |
| 1667 for (std::list<int64_t>::const_iterator | |
| 656 | 1668 it = id.begin(); it != id.end(); ++it) |
| 521 | 1669 { |
| 1670 result.push_back(db_->GetPublicId(*it)); | |
| 1671 } | |
| 1672 } | |
|
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|
1673 |
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1674 |
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|
1675 StoreStatus ServerIndex::AddAttachment(const FileInfo& attachment, |
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1676 const std::string& publicId) |
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|
1677 { |
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|
1678 boost::mutex::scoped_lock lock(mutex_); |
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1679 |
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1680 Transaction t(*this); |
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1681 |
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|
1682 ResourceType resourceType; |
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1683 int64_t resourceId; |
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1684 if (!db_->LookupResource(publicId, resourceId, resourceType)) |
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1685 { |
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1686 return StoreStatus_Failure; // Inexistent resource |
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1687 } |
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1688 |
|
704
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|
1689 // Remove possible previous attachment |
|
699
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1690 db_->DeleteAttachment(resourceId, attachment.GetContentType()); |
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1691 |
|
704
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1692 // Locate the patient of the target resource |
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1693 int64_t patientId = resourceId; |
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|
1694 for (;;) |
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|
1695 { |
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|
1696 int64_t parent; |
|
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1697 if (db_->LookupParent(parent, patientId)) |
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|
1698 { |
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1699 // We have not reached the patient level yet |
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1700 patientId = parent; |
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1701 } |
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1702 else |
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1703 { |
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1704 // We have reached the patient level |
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1705 break; |
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1706 } |
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1707 } |
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1708 |
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1709 // Possibly apply the recycling mechanism while preserving this patient |
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1710 assert(db_->GetResourceType(patientId) == ResourceType_Patient); |
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1711 Recycle(attachment.GetCompressedSize(), db_->GetPublicId(patientId)); |
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1712 |
|
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1713 db_->AddAttachment(resourceId, attachment); |
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1714 |
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1715 t.Commit(attachment.GetCompressedSize()); |
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1716 |
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1717 return StoreStatus_Success; |
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1718 } |
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1719 |
|
702
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1720 |
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1721 void ServerIndex::DeleteAttachment(const std::string& publicId, |
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1722 FileContentType type) |
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1723 { |
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1724 boost::mutex::scoped_lock lock(mutex_); |
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1725 listener_->Reset(); |
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1726 |
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1727 Transaction t(*this); |
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1728 |
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|
1729 ResourceType rtype; |
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1730 int64_t id; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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1731 if (!db_->LookupResource(publicId, id, rtype)) |
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1732 { |
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1733 throw OrthancException(ErrorCode_UnknownResource); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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1734 } |
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1735 |
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1736 db_->DeleteAttachment(id, type); |
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1737 |
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1738 t.Commit(0); |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1739 } |
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1740 |
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1741 |
|
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1742 bool ServerIndex::GetMetadata(Json::Value& target, |
|
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1743 const std::string& publicId) |
|
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1744 { |
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1745 boost::mutex::scoped_lock lock(mutex_); |
|
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1746 |
|
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1747 target = Json::objectValue; |
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1748 |
|
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1749 ResourceType type; |
|
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1750 int64_t id; |
|
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1751 if (!db_->LookupResource(publicId, id, type)) |
|
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1752 { |
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1753 return false; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
1754 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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1755 |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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1756 std::list<MetadataType> metadata; |
|
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Sebastien Jodogne <s.jodogne@gmail.com>
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1757 db_->ListAvailableMetadata(metadata, id); |
|
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|
1758 |
|
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|
1759 for (std::list<MetadataType>::const_iterator |
|
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1760 it = metadata.begin(); it != metadata.end(); it++) |
|
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1761 { |
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1762 std::string key = EnumerationToString(*it); |
|
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1763 std::string value = db_->GetMetadata(id, *it); |
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1764 target[key] = value; |
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1765 } |
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1766 |
|
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1767 return true; |
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1768 } |
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1769 |
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1770 |
| 0 | 1771 } |