Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 1002:b067017a8a5b lua-scripting
anonymization refactoring
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 04 Jul 2014 16:31:14 +0200 |
parents | 84513f2ee1f3 |
children | a226e0959d8b |
rev | line source |
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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 { |
206
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217 boost::mutex::scoped_lock lock(mutex_); |
202 | 218 listener_->Reset(); |
201
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219 |
278
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220 Transaction t(*this); |
201
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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); |
434
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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 | |
278
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247 t.Commit(0); |
264
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248 |
0 | 249 return true; |
250 } | |
251 | |
252 | |
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253 void ServerIndex::FlushThread(ServerIndex* that) |
206
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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_) |
206
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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, |
269
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332 const std::string& dbPath) : |
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333 done_(false), |
269
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334 maximumStorageSize_(0), |
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335 maximumPatients_(0) |
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336 { |
226
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337 listener_.reset(new Internals::ServerIndexListener(context)); |
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338 |
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339 if (dbPath == ":memory:") |
180
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340 { |
202 | 341 db_.reset(new DatabaseWrapper(*listener_)); |
180
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342 } |
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343 else |
0 | 344 { |
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345 boost::filesystem::path p = dbPath; |
180
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346 |
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347 try |
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348 { |
201
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349 boost::filesystem::create_directories(p); |
180
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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 const 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-computer metadata |
432 | 554 std::string now = Toolbox::GetNowIsoString(); |
555 db_->SetMetadata(instance, MetadataType_Instance_ReceptionDate, now); | |
556 db_->SetMetadata(series, MetadataType_LastUpdate, now); | |
557 db_->SetMetadata(study, MetadataType_LastUpdate, now); | |
558 db_->SetMetadata(patient, MetadataType_LastUpdate, now); | |
202 | 559 db_->SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); |
560 | |
561 const DicomValue* value; | |
562 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || | |
563 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) | |
0 | 564 { |
202 | 565 db_->SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->AsString()); |
0 | 566 } |
567 | |
202 | 568 if (isNewSeries) |
569 { | |
433 | 570 ComputeExpectedNumberOfInstances(*db_, series, dicomSummary); |
202 | 571 } |
572 | |
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573 // Check whether the series of this new instance is now completed |
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574 SeriesStatus seriesStatus = GetSeriesStatus(series); |
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575 if (seriesStatus == SeriesStatus_Complete) |
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576 { |
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577 db_->LogChange(ChangeType_CompletedSeries, series, ResourceType_Series); |
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578 } |
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579 |
511
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580 // Mark the parent resources of this instance as unstable |
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581 MarkAsUnstable(patient, ResourceType_Patient); |
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582 MarkAsUnstable(study, ResourceType_Study); |
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583 MarkAsUnstable(series, ResourceType_Series); |
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584 |
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585 t.Commit(instanceSize); |
268
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586 |
0 | 587 return StoreStatus_Success; |
588 } | |
62 | 589 catch (OrthancException& e) |
0 | 590 { |
268
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591 LOG(ERROR) << "EXCEPTION [" << e.What() << "]" |
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592 << " (SQLite status: " << db_->GetErrorMessage() << ")"; |
0 | 593 } |
594 | |
595 return StoreStatus_Failure; | |
596 } | |
597 | |
598 | |
238 | 599 void ServerIndex::ComputeStatistics(Json::Value& target) |
0 | 600 { |
206
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601 boost::mutex::scoped_lock lock(mutex_); |
238 | 602 target = Json::objectValue; |
0 | 603 |
278
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604 uint64_t cs = currentStorageSize_; |
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605 assert(cs == db_->GetTotalCompressedSize()); |
238 | 606 uint64_t us = db_->GetTotalUncompressedSize(); |
440
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607 target["TotalDiskSize"] = boost::lexical_cast<std::string>(cs); |
238 | 608 target["TotalUncompressedSize"] = boost::lexical_cast<std::string>(us); |
440
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609 target["TotalDiskSizeMB"] = boost::lexical_cast<unsigned int>(cs / MEGA_BYTES); |
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610 target["TotalUncompressedSizeMB"] = boost::lexical_cast<unsigned int>(us / MEGA_BYTES); |
238 | 611 |
612 target["CountPatients"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Patient)); | |
613 target["CountStudies"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Study)); | |
614 target["CountSeries"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Series)); | |
615 target["CountInstances"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Instance)); | |
616 } | |
617 | |
187
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618 |
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619 |
585 | 620 SeriesStatus ServerIndex::GetSeriesStatus(int64_t id) |
199 | 621 { |
622 // Get the expected number of instances in this series (from the metadata) | |
202 | 623 std::string s = db_->GetMetadata(id, MetadataType_Series_ExpectedNumberOfInstances); |
199 | 624 |
625 size_t expected; | |
626 try | |
627 { | |
628 expected = boost::lexical_cast<size_t>(s); | |
629 } | |
630 catch (boost::bad_lexical_cast&) | |
631 { | |
632 return SeriesStatus_Unknown; | |
633 } | |
634 | |
635 // Loop over the instances of this series | |
636 std::list<int64_t> children; | |
202 | 637 db_->GetChildrenInternalId(children, id); |
199 | 638 |
639 std::set<size_t> instances; | |
640 for (std::list<int64_t>::const_iterator | |
656 | 641 it = children.begin(); it != children.end(); ++it) |
199 | 642 { |
643 // Get the index of this instance in the series | |
202 | 644 s = db_->GetMetadata(*it, MetadataType_Instance_IndexInSeries); |
199 | 645 size_t index; |
646 try | |
647 { | |
648 index = boost::lexical_cast<size_t>(s); | |
649 } | |
650 catch (boost::bad_lexical_cast&) | |
651 { | |
652 return SeriesStatus_Unknown; | |
653 } | |
654 | |
656 | 655 if (!(index > 0 && index <= expected)) |
199 | 656 { |
657 // Out-of-range instance index | |
658 return SeriesStatus_Inconsistent; | |
659 } | |
660 | |
661 if (instances.find(index) != instances.end()) | |
662 { | |
663 // Twice the same instance index | |
664 return SeriesStatus_Inconsistent; | |
665 } | |
666 | |
667 instances.insert(index); | |
668 } | |
669 | |
670 if (instances.size() == expected) | |
671 { | |
672 return SeriesStatus_Complete; | |
673 } | |
674 else | |
675 { | |
676 return SeriesStatus_Missing; | |
677 } | |
678 } | |
679 | |
680 | |
681 | |
202 | 682 void ServerIndex::MainDicomTagsToJson(Json::Value& target, |
683 int64_t resourceId) | |
198
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684 { |
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685 DicomMap tags; |
202 | 686 db_->GetMainDicomTags(tags, resourceId); |
198
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687 target["MainDicomTags"] = Json::objectValue; |
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688 FromDcmtkBridge::ToJson(target["MainDicomTags"], tags); |
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689 } |
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690 |
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691 bool ServerIndex::LookupResource(Json::Value& result, |
199 | 692 const std::string& publicId, |
693 ResourceType expectedType) | |
198
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694 { |
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695 result = Json::objectValue; |
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696 |
206
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697 boost::mutex::scoped_lock lock(mutex_); |
199 | 698 |
198
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699 // Lookup for the requested resource |
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700 int64_t id; |
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701 ResourceType type; |
202 | 702 if (!db_->LookupResource(publicId, id, type) || |
199 | 703 type != expectedType) |
198
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704 { |
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705 return false; |
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706 } |
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707 |
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708 // Find the parent resource (if it exists) |
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709 if (type != ResourceType_Patient) |
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710 { |
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711 int64_t parentId; |
202 | 712 if (!db_->LookupParent(parentId, id)) |
198
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713 { |
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714 throw OrthancException(ErrorCode_InternalError); |
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715 } |
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716 |
202 | 717 std::string parent = db_->GetPublicId(parentId); |
198
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718 |
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719 switch (type) |
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720 { |
269
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|
721 case ResourceType_Study: |
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722 result["ParentPatient"] = parent; |
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723 break; |
198
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724 |
269
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725 case ResourceType_Series: |
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726 result["ParentStudy"] = parent; |
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727 break; |
198
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728 |
269
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729 case ResourceType_Instance: |
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730 result["ParentSeries"] = parent; |
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731 break; |
198
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732 |
269
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733 default: |
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734 throw OrthancException(ErrorCode_InternalError); |
198
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735 } |
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736 } |
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737 |
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738 // List the children resources |
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739 std::list<std::string> children; |
202 | 740 db_->GetChildrenPublicId(children, id); |
198
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741 |
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742 if (type != ResourceType_Instance) |
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743 { |
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744 Json::Value c = Json::arrayValue; |
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745 |
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746 for (std::list<std::string>::const_iterator |
656 | 747 it = children.begin(); it != children.end(); ++it) |
198
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748 { |
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749 c.append(*it); |
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750 } |
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751 |
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752 switch (type) |
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753 { |
269
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|
754 case ResourceType_Patient: |
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755 result["Studies"] = c; |
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756 break; |
198
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757 |
269
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758 case ResourceType_Study: |
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759 result["Series"] = c; |
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760 break; |
198
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761 |
269
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|
762 case ResourceType_Series: |
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763 result["Instances"] = c; |
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764 break; |
198
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765 |
269
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766 default: |
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767 throw OrthancException(ErrorCode_InternalError); |
198
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768 } |
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769 } |
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770 |
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771 // Set the resource type |
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772 switch (type) |
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773 { |
269
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774 case ResourceType_Patient: |
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775 result["Type"] = "Patient"; |
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776 break; |
198
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777 |
269
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changeset
|
778 case ResourceType_Study: |
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779 result["Type"] = "Study"; |
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780 break; |
199 | 781 |
269
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782 case ResourceType_Series: |
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783 { |
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784 result["Type"] = "Series"; |
434
ccf3a0a43dac
EnumerationDictionary
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diff
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|
785 result["Status"] = EnumerationToString(GetSeriesStatus(id)); |
198
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786 |
269
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787 int i; |
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788 if (db_->GetMetadataAsInteger(i, id, MetadataType_Series_ExpectedNumberOfInstances)) |
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789 result["ExpectedNumberOfInstances"] = i; |
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790 else |
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791 result["ExpectedNumberOfInstances"] = Json::nullValue; |
200
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diff
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792 |
269
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|
793 break; |
200
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|
794 } |
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|
795 |
269
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796 case ResourceType_Instance: |
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797 { |
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798 result["Type"] = "Instance"; |
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799 |
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800 FileInfo attachment; |
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801 if (!db_->LookupAttachment(attachment, id, FileContentType_Dicom)) |
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802 { |
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803 throw OrthancException(ErrorCode_InternalError); |
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804 } |
200
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805 |
269
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806 result["FileSize"] = static_cast<unsigned int>(attachment.GetUncompressedSize()); |
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807 result["FileUuid"] = attachment.GetUuid(); |
200
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808 |
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809 int i; |
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810 if (db_->GetMetadataAsInteger(i, id, MetadataType_Instance_IndexInSeries)) |
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811 result["IndexInSeries"] = i; |
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812 else |
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813 result["IndexInSeries"] = Json::nullValue; |
198
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814 |
269
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815 break; |
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816 } |
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817 |
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818 default: |
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819 throw OrthancException(ErrorCode_InternalError); |
198
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820 } |
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821 |
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822 // Record the remaining information |
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823 result["ID"] = publicId; |
202 | 824 MainDicomTagsToJson(result, id); |
198
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825 |
315 | 826 std::string tmp; |
827 | |
828 tmp = db_->GetMetadata(id, MetadataType_AnonymizedFrom); | |
829 if (tmp.size() != 0) | |
830 result["AnonymizedFrom"] = tmp; | |
831 | |
832 tmp = db_->GetMetadata(id, MetadataType_ModifiedFrom); | |
833 if (tmp.size() != 0) | |
834 result["ModifiedFrom"] = tmp; | |
835 | |
511
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|
836 if (type == ResourceType_Patient || |
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|
837 type == ResourceType_Study || |
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|
838 type == ResourceType_Series) |
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|
839 { |
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|
840 result["IsStable"] = !unstableResources_.Contains(id); |
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|
841 } |
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|
842 |
198
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843 return true; |
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844 } |
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845 |
0 | 846 |
232
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diff
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|
847 bool ServerIndex::LookupAttachment(FileInfo& attachment, |
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diff
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|
848 const std::string& instanceUuid, |
233 | 849 FileContentType contentType) |
0 | 850 { |
206
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diff
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|
851 boost::mutex::scoped_lock lock(mutex_); |
0 | 852 |
193
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diff
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|
853 int64_t id; |
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diff
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|
854 ResourceType type; |
701 | 855 if (!db_->LookupResource(instanceUuid, id, type)) |
192
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|
856 { |
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diff
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|
857 throw OrthancException(ErrorCode_InternalError); |
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diff
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|
858 } |
193
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diff
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|
859 |
232
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diff
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|
860 if (db_->LookupAttachment(attachment, id, contentType)) |
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|
861 { |
233 | 862 assert(attachment.GetContentType() == contentType); |
232
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diff
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|
863 return true; |
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231
diff
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|
864 } |
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diff
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|
865 else |
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diff
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|
866 { |
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diff
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|
867 return false; |
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231
diff
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|
868 } |
192
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diff
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|
869 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
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191
diff
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|
870 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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191
diff
changeset
|
871 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
872 |
0 | 873 void ServerIndex::GetAllUuids(Json::Value& target, |
190 | 874 ResourceType resourceType) |
0 | 875 { |
206
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diff
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|
876 boost::mutex::scoped_lock lock(mutex_); |
202 | 877 db_->GetAllPublicIds(target, resourceType); |
0 | 878 } |
879 | |
880 | |
881 bool ServerIndex::GetChanges(Json::Value& target, | |
204 | 882 int64_t since, |
0 | 883 unsigned int maxResults) |
884 { | |
206
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diff
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|
885 boost::mutex::scoped_lock lock(mutex_); |
237
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diff
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|
886 db_->GetChanges(target, since, maxResults); |
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|
887 return true; |
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|
888 } |
0 | 889 |
237
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|
890 bool ServerIndex::GetLastChange(Json::Value& target) |
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|
891 { |
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|
892 boost::mutex::scoped_lock lock(mutex_); |
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|
893 db_->GetLastChange(target); |
204 | 894 return true; |
0 | 895 } |
231 | 896 |
897 void ServerIndex::LogExportedResource(const std::string& publicId, | |
898 const std::string& remoteModality) | |
899 { | |
900 boost::mutex::scoped_lock lock(mutex_); | |
901 | |
902 int64_t id; | |
903 ResourceType type; | |
904 if (!db_->LookupResource(publicId, id, type)) | |
905 { | |
906 throw OrthancException(ErrorCode_InternalError); | |
907 } | |
908 | |
909 std::string patientId; | |
910 std::string studyInstanceUid; | |
911 std::string seriesInstanceUid; | |
912 std::string sopInstanceUid; | |
913 | |
914 int64_t currentId = id; | |
915 ResourceType currentType = type; | |
916 | |
917 // Iteratively go up inside the patient/study/series/instance hierarchy | |
918 bool done = false; | |
919 while (!done) | |
920 { | |
921 DicomMap map; | |
922 db_->GetMainDicomTags(map, currentId); | |
923 | |
924 switch (currentType) | |
925 { | |
269
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|
926 case ResourceType_Patient: |
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|
927 patientId = map.GetValue(DICOM_TAG_PATIENT_ID).AsString(); |
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928 done = true; |
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|
929 break; |
231 | 930 |
269
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|
931 case ResourceType_Study: |
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|
932 studyInstanceUid = map.GetValue(DICOM_TAG_STUDY_INSTANCE_UID).AsString(); |
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|
933 currentType = ResourceType_Patient; |
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|
934 break; |
231 | 935 |
269
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|
936 case ResourceType_Series: |
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|
937 seriesInstanceUid = map.GetValue(DICOM_TAG_SERIES_INSTANCE_UID).AsString(); |
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938 currentType = ResourceType_Study; |
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939 break; |
231 | 940 |
269
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|
941 case ResourceType_Instance: |
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|
942 sopInstanceUid = map.GetValue(DICOM_TAG_SOP_INSTANCE_UID).AsString(); |
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943 currentType = ResourceType_Series; |
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944 break; |
231 | 945 |
269
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|
946 default: |
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|
947 throw OrthancException(ErrorCode_InternalError); |
231 | 948 } |
949 | |
950 // If we have not reached the Patient level, find the parent of | |
951 // the current resource | |
952 if (!done) | |
953 { | |
375
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diff
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|
954 bool ok = db_->LookupParent(currentId, currentId); |
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|
955 assert(ok); |
231 | 956 } |
957 } | |
958 | |
959 // No need for a SQLite::Transaction here, as we only insert 1 record | |
960 db_->LogExportedResource(type, | |
961 publicId, | |
962 remoteModality, | |
963 patientId, | |
964 studyInstanceUid, | |
965 seriesInstanceUid, | |
966 sopInstanceUid); | |
967 } | |
968 | |
969 | |
970 bool ServerIndex::GetExportedResources(Json::Value& target, | |
971 int64_t since, | |
972 unsigned int maxResults) | |
973 { | |
974 boost::mutex::scoped_lock lock(mutex_); | |
975 db_->GetExportedResources(target, since, maxResults); | |
976 return true; | |
977 } | |
237
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diff
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|
978 |
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|
979 bool ServerIndex::GetLastExportedResource(Json::Value& target) |
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980 { |
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981 boost::mutex::scoped_lock lock(mutex_); |
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982 db_->GetLastExportedResource(target); |
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983 return true; |
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984 } |
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985 |
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986 |
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987 bool ServerIndex::IsRecyclingNeeded(uint64_t instanceSize) |
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988 { |
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989 if (maximumStorageSize_ != 0) |
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990 { |
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991 uint64_t currentSize = currentStorageSize_ - listener_->GetSizeOfFilesToRemove(); |
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992 assert(db_->GetTotalCompressedSize() == currentSize); |
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993 |
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994 if (currentSize + instanceSize > maximumStorageSize_) |
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995 { |
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996 return true; |
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997 } |
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998 } |
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999 |
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1000 if (maximumPatients_ != 0) |
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1001 { |
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1002 uint64_t patientCount = db_->GetResourceCount(ResourceType_Patient); |
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1003 if (patientCount > maximumPatients_) |
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1004 { |
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1005 return true; |
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1006 } |
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1007 } |
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1008 |
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1009 return false; |
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1010 } |
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1011 |
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1012 |
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1013 void ServerIndex::Recycle(uint64_t instanceSize, |
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1014 const std::string& newPatientId) |
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1015 { |
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1016 if (!IsRecyclingNeeded(instanceSize)) |
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1017 { |
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1018 return; |
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1019 } |
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1020 |
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1021 // Check whether other DICOM instances from this patient are |
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1022 // already stored |
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1023 int64_t patientToAvoid; |
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1024 ResourceType type; |
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1025 bool hasPatientToAvoid = db_->LookupResource(newPatientId, patientToAvoid, type); |
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1026 |
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1027 if (hasPatientToAvoid && type != ResourceType_Patient) |
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1028 { |
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1029 throw OrthancException(ErrorCode_InternalError); |
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1030 } |
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1031 |
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1032 // Iteratively select patient to remove until there is enough |
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1033 // space in the DICOM store |
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1034 int64_t patientToRecycle; |
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1035 while (true) |
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1036 { |
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1037 // If other instances of this patient are already in the store, |
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1038 // we must avoid to recycle them |
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1039 bool ok = hasPatientToAvoid ? |
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1040 db_->SelectPatientToRecycle(patientToRecycle, patientToAvoid) : |
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1041 db_->SelectPatientToRecycle(patientToRecycle); |
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1042 |
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1043 if (!ok) |
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1044 { |
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1045 throw OrthancException(ErrorCode_FullStorage); |
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1046 } |
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1047 |
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1048 LOG(INFO) << "Recycling one patient"; |
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1049 db_->DeleteResource(patientToRecycle); |
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1050 |
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1051 if (!IsRecyclingNeeded(instanceSize)) |
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1052 { |
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1053 // OK, we're done |
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1054 break; |
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1055 } |
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1056 } |
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1057 } |
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1058 |
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1059 void ServerIndex::SetMaximumPatientCount(unsigned int count) |
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1060 { |
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1061 boost::mutex::scoped_lock lock(mutex_); |
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1062 maximumPatients_ = count; |
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1063 |
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1064 if (count == 0) |
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1065 { |
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1066 LOG(WARNING) << "No limit on the number of stored patients"; |
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1067 } |
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1068 else |
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1069 { |
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1070 LOG(WARNING) << "At most " << count << " patients will be stored"; |
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1071 } |
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1072 |
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1073 StandaloneRecycling(); |
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1074 } |
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1075 |
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1076 void ServerIndex::SetMaximumStorageSize(uint64_t size) |
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1077 { |
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1078 boost::mutex::scoped_lock lock(mutex_); |
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1079 maximumStorageSize_ = size; |
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1080 |
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1081 if (size == 0) |
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1082 { |
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1083 LOG(WARNING) << "No limit on the size of the storage area"; |
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1084 } |
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1085 else |
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1086 { |
440
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1087 LOG(WARNING) << "At most " << (size / MEGA_BYTES) << "MB will be used for the storage area"; |
270
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1088 } |
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1089 |
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1090 StandaloneRecycling(); |
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1091 } |
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1092 |
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1093 void ServerIndex::StandaloneRecycling() |
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1094 { |
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1095 // WARNING: No mutex here, do not include this as a public method |
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1096 Transaction t(*this); |
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1097 Recycle(0, ""); |
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1098 t.Commit(0); |
269
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1099 } |
272
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|
1100 |
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1101 |
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1102 bool ServerIndex::IsProtectedPatient(const std::string& publicId) |
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1103 { |
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1104 boost::mutex::scoped_lock lock(mutex_); |
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1105 |
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1106 // Lookup for the requested resource |
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1107 int64_t id; |
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1108 ResourceType type; |
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1109 if (!db_->LookupResource(publicId, id, type) || |
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1110 type != ResourceType_Patient) |
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1111 { |
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1112 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1113 } |
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1114 |
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1115 return db_->IsProtectedPatient(id); |
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1116 } |
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1117 |
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1118 |
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1119 void ServerIndex::SetProtectedPatient(const std::string& publicId, |
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1120 bool isProtected) |
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1121 { |
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1122 boost::mutex::scoped_lock lock(mutex_); |
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1123 |
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1124 // Lookup for the requested resource |
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1125 int64_t id; |
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1126 ResourceType type; |
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1127 if (!db_->LookupResource(publicId, id, type) || |
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1128 type != ResourceType_Patient) |
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1129 { |
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1130 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1131 } |
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1132 |
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1133 // No need for a SQLite::Transaction here, as we only make 1 write to the DB |
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1134 db_->SetProtectedPatient(id, isProtected); |
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1135 |
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1136 if (isProtected) |
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1137 LOG(INFO) << "Patient " << publicId << " has been protected"; |
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1138 else |
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1139 LOG(INFO) << "Patient " << publicId << " has been unprotected"; |
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1140 } |
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1141 |
304 | 1142 |
714
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1143 void ServerIndex::GetChildren(std::list<std::string>& result, |
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1144 const std::string& publicId) |
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1145 { |
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1146 result.clear(); |
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1147 |
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1148 boost::mutex::scoped_lock lock(mutex_); |
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1149 |
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1150 ResourceType type; |
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1151 int64_t resource; |
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1152 if (!db_->LookupResource(publicId, resource, type)) |
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1153 { |
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1154 throw OrthancException(ErrorCode_UnknownResource); |
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1155 } |
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1156 |
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1157 if (type == ResourceType_Instance) |
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1158 { |
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1159 // An instance cannot have a child |
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1160 throw OrthancException(ErrorCode_BadParameterType); |
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1161 } |
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1162 |
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1163 std::list<int64_t> tmp; |
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1164 db_->GetChildrenInternalId(tmp, resource); |
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1165 |
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1166 for (std::list<int64_t>::const_iterator |
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1167 it = tmp.begin(); it != tmp.end(); ++it) |
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1168 { |
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1169 result.push_back(db_->GetPublicId(*it)); |
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1170 } |
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1171 } |
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1172 |
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1173 |
304 | 1174 void ServerIndex::GetChildInstances(std::list<std::string>& result, |
1175 const std::string& publicId) | |
1176 { | |
1177 result.clear(); | |
1178 | |
1179 boost::mutex::scoped_lock lock(mutex_); | |
1180 | |
1181 ResourceType type; | |
1182 int64_t top; | |
1183 if (!db_->LookupResource(publicId, top, type)) | |
1184 { | |
1185 throw OrthancException(ErrorCode_UnknownResource); | |
1186 } | |
1187 | |
1188 if (type == ResourceType_Instance) | |
1189 { | |
1190 // The resource is already an instance: Do not go down the hierarchy | |
1191 result.push_back(publicId); | |
1192 return; | |
1193 } | |
1194 | |
1195 std::stack<int64_t> toExplore; | |
1196 toExplore.push(top); | |
1197 | |
1198 std::list<int64_t> tmp; | |
1199 | |
1200 while (!toExplore.empty()) | |
1201 { | |
1202 // Get the internal ID of the current resource | |
1203 int64_t resource = toExplore.top(); | |
1204 toExplore.pop(); | |
1205 | |
1206 if (db_->GetResourceType(resource) == ResourceType_Instance) | |
1207 { | |
1208 result.push_back(db_->GetPublicId(resource)); | |
1209 } | |
1210 else | |
1211 { | |
1212 // Tag all the children of this resource as to be explored | |
1213 db_->GetChildrenInternalId(tmp, resource); | |
1214 for (std::list<int64_t>::const_iterator | |
656 | 1215 it = tmp.begin(); it != tmp.end(); ++it) |
304 | 1216 { |
1217 toExplore.push(*it); | |
1218 } | |
1219 } | |
1220 } | |
1221 } | |
1222 | |
306
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1223 |
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1224 void ServerIndex::SetMetadata(const std::string& publicId, |
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1225 MetadataType type, |
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1226 const std::string& value) |
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1227 { |
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1228 boost::mutex::scoped_lock lock(mutex_); |
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1229 |
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1230 ResourceType rtype; |
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1231 int64_t id; |
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1232 if (!db_->LookupResource(publicId, id, rtype)) |
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1233 { |
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1234 throw OrthancException(ErrorCode_UnknownResource); |
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1235 } |
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1236 |
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1237 db_->SetMetadata(id, type, value); |
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1238 } |
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1239 |
438 | 1240 |
1241 void ServerIndex::DeleteMetadata(const std::string& publicId, | |
1242 MetadataType type) | |
1243 { | |
1244 boost::mutex::scoped_lock lock(mutex_); | |
1245 | |
1246 ResourceType rtype; | |
1247 int64_t id; | |
1248 if (!db_->LookupResource(publicId, id, rtype)) | |
1249 { | |
1250 throw OrthancException(ErrorCode_UnknownResource); | |
1251 } | |
1252 | |
1253 db_->DeleteMetadata(id, type); | |
1254 } | |
1255 | |
1256 | |
306
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1257 bool ServerIndex::LookupMetadata(std::string& target, |
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1258 const std::string& publicId, |
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1259 MetadataType type) |
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1260 { |
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1261 boost::mutex::scoped_lock lock(mutex_); |
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1262 |
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1263 ResourceType rtype; |
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1264 int64_t id; |
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1265 if (!db_->LookupResource(publicId, id, rtype)) |
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1266 { |
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1267 throw OrthancException(ErrorCode_UnknownResource); |
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1268 } |
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1269 |
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1270 return db_->LookupMetadata(target, id, type); |
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1271 } |
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1272 |
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1273 |
739 | 1274 void ServerIndex::ListAvailableMetadata(std::list<MetadataType>& target, |
436
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1275 const std::string& publicId) |
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1276 { |
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1277 boost::mutex::scoped_lock lock(mutex_); |
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1278 |
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1279 ResourceType rtype; |
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1280 int64_t id; |
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1281 if (!db_->LookupResource(publicId, id, rtype)) |
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1282 { |
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1283 throw OrthancException(ErrorCode_UnknownResource); |
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1284 } |
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1285 |
739 | 1286 db_->ListAvailableMetadata(target, id); |
436
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1287 } |
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1288 |
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1289 |
697
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1290 void ServerIndex::ListAvailableAttachments(std::list<FileContentType>& target, |
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1291 const std::string& publicId, |
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1292 ResourceType expectedType) |
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1293 { |
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1294 boost::mutex::scoped_lock lock(mutex_); |
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1295 |
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1296 ResourceType type; |
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1297 int64_t id; |
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1298 if (!db_->LookupResource(publicId, id, type) || |
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1299 expectedType != type) |
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1300 { |
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1301 throw OrthancException(ErrorCode_UnknownResource); |
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1302 } |
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1303 |
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1304 db_->ListAvailableAttachments(target, id); |
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1305 } |
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1306 |
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1307 |
306
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1308 bool ServerIndex::LookupParent(std::string& target, |
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1309 const std::string& publicId) |
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1310 { |
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1311 boost::mutex::scoped_lock lock(mutex_); |
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1312 |
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1313 ResourceType type; |
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1314 int64_t id; |
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1315 if (!db_->LookupResource(publicId, id, type)) |
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1316 { |
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1317 throw OrthancException(ErrorCode_UnknownResource); |
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1318 } |
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1319 |
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1320 int64_t parentId; |
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1321 if (db_->LookupParent(parentId, id)) |
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1322 { |
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1323 target = db_->GetPublicId(parentId); |
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1324 return true; |
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1325 } |
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1326 else |
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1327 { |
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1328 return false; |
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1329 } |
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1330 } |
310 | 1331 |
1332 | |
1333 uint64_t ServerIndex::IncrementGlobalSequence(GlobalProperty sequence) | |
1334 { | |
1335 boost::mutex::scoped_lock lock(mutex_); | |
311 | 1336 |
1337 std::auto_ptr<SQLite::Transaction> transaction(db_->StartTransaction()); | |
1338 | |
1339 transaction->Begin(); | |
1340 uint64_t seq = db_->IncrementGlobalSequence(sequence); | |
1341 transaction->Commit(); | |
1342 | |
1343 return seq; | |
310 | 1344 } |
315 | 1345 |
1346 | |
1347 | |
1348 void ServerIndex::LogChange(ChangeType changeType, | |
1349 const std::string& publicId) | |
1350 { | |
1351 boost::mutex::scoped_lock lock(mutex_); | |
1352 std::auto_ptr<SQLite::Transaction> transaction(db_->StartTransaction()); | |
1353 transaction->Begin(); | |
1354 | |
1355 int64_t id; | |
1356 ResourceType type; | |
1357 if (!db_->LookupResource(publicId, id, type)) | |
1358 { | |
1359 throw OrthancException(ErrorCode_UnknownResource); | |
1360 } | |
1361 | |
1362 db_->LogChange(changeType, id, type); | |
1363 | |
1364 transaction->Commit(); | |
1365 } | |
413
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1366 |
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1367 |
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|
1368 void ServerIndex::DeleteChanges() |
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1369 { |
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|
1370 boost::mutex::scoped_lock lock(mutex_); |
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1371 db_->ClearTable("Changes"); |
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|
1372 } |
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|
1373 |
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1374 void ServerIndex::DeleteExportedResources() |
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1375 { |
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|
1376 boost::mutex::scoped_lock lock(mutex_); |
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1377 db_->ClearTable("ExportedResources"); |
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1378 } |
440
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1379 |
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1380 |
646 | 1381 void ServerIndex::GetStatisticsInternal(/* out */ uint64_t& compressedSize, |
1382 /* out */ uint64_t& uncompressedSize, | |
1383 /* out */ unsigned int& countStudies, | |
1384 /* out */ unsigned int& countSeries, | |
1385 /* out */ unsigned int& countInstances, | |
1386 /* in */ int64_t id, | |
1387 /* in */ ResourceType type) | |
440
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1388 { |
646 | 1389 std::stack<int64_t> toExplore; |
1390 toExplore.push(id); | |
440
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1391 |
646 | 1392 countInstances = 0; |
1393 countSeries = 0; | |
1394 countStudies = 0; | |
1395 compressedSize = 0; | |
1396 uncompressedSize = 0; | |
440
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1397 |
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1398 while (!toExplore.empty()) |
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1399 { |
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1400 // Get the internal ID of the current resource |
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1401 int64_t resource = toExplore.top(); |
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1402 toExplore.pop(); |
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1403 |
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1404 ResourceType thisType = db_->GetResourceType(resource); |
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1405 |
702
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1406 std::list<FileContentType> f; |
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1407 db_->ListAvailableAttachments(f, resource); |
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1408 |
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1409 for (std::list<FileContentType>::const_iterator |
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1410 it = f.begin(); it != f.end(); ++it) |
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1411 { |
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1412 FileInfo attachment; |
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1413 if (db_->LookupAttachment(attachment, resource, *it)) |
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1414 { |
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1415 compressedSize += attachment.GetCompressedSize(); |
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1416 uncompressedSize += attachment.GetUncompressedSize(); |
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1417 } |
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1418 } |
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1419 |
440
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1420 if (thisType == ResourceType_Instance) |
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1421 { |
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1422 countInstances++; |
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1423 } |
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1424 else |
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1425 { |
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1426 switch (thisType) |
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1427 { |
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1428 case ResourceType_Study: |
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1429 countStudies++; |
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1430 break; |
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1431 |
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1432 case ResourceType_Series: |
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1433 countSeries++; |
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1434 break; |
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1435 |
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1436 default: |
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1437 break; |
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1438 } |
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1439 |
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1440 // Tag all the children of this resource as to be explored |
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1441 std::list<int64_t> tmp; |
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1442 db_->GetChildrenInternalId(tmp, resource); |
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1443 for (std::list<int64_t>::const_iterator |
656 | 1444 it = tmp.begin(); it != tmp.end(); ++it) |
440
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1445 { |
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1446 toExplore.push(*it); |
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1447 } |
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1448 } |
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1449 } |
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1450 |
646 | 1451 if (countStudies == 0) |
1452 { | |
1453 countStudies = 1; | |
1454 } | |
1455 | |
1456 if (countSeries == 0) | |
1457 { | |
1458 countSeries = 1; | |
1459 } | |
1460 } | |
1461 | |
1462 | |
1463 | |
1464 void ServerIndex::GetStatistics(Json::Value& target, | |
1465 const std::string& publicId) | |
1466 { | |
1467 boost::mutex::scoped_lock lock(mutex_); | |
1468 | |
1469 ResourceType type; | |
1470 int64_t top; | |
1471 if (!db_->LookupResource(publicId, top, type)) | |
1472 { | |
1473 throw OrthancException(ErrorCode_UnknownResource); | |
1474 } | |
1475 | |
1476 uint64_t uncompressedSize; | |
1477 uint64_t compressedSize; | |
1478 unsigned int countStudies; | |
1479 unsigned int countSeries; | |
1480 unsigned int countInstances; | |
1481 GetStatisticsInternal(compressedSize, uncompressedSize, countStudies, | |
1482 countSeries, countInstances, top, type); | |
1483 | |
440
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1484 target = Json::objectValue; |
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1485 target["DiskSize"] = boost::lexical_cast<std::string>(compressedSize); |
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1486 target["DiskSizeMB"] = boost::lexical_cast<unsigned int>(compressedSize / MEGA_BYTES); |
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1487 target["UncompressedSize"] = boost::lexical_cast<std::string>(uncompressedSize); |
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1488 target["UncompressedSizeMB"] = boost::lexical_cast<unsigned int>(uncompressedSize / MEGA_BYTES); |
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1489 |
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1490 switch (type) |
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1491 { |
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1492 // Do NOT add "break" below this point! |
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1493 case ResourceType_Patient: |
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1494 target["CountStudies"] = countStudies; |
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1495 |
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1496 case ResourceType_Study: |
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1497 target["CountSeries"] = countSeries; |
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1498 |
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1499 case ResourceType_Series: |
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1500 target["CountInstances"] = countInstances; |
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1501 |
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1502 case ResourceType_Instance: |
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1503 default: |
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1504 break; |
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1505 } |
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1506 } |
511
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1507 |
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1508 |
646 | 1509 void ServerIndex::GetStatistics(/* out */ uint64_t& compressedSize, |
1510 /* out */ uint64_t& uncompressedSize, | |
1511 /* out */ unsigned int& countStudies, | |
1512 /* out */ unsigned int& countSeries, | |
1513 /* out */ unsigned int& countInstances, | |
1514 const std::string& publicId) | |
1515 { | |
1516 boost::mutex::scoped_lock lock(mutex_); | |
1517 | |
1518 ResourceType type; | |
1519 int64_t top; | |
1520 if (!db_->LookupResource(publicId, top, type)) | |
1521 { | |
1522 throw OrthancException(ErrorCode_UnknownResource); | |
1523 } | |
1524 | |
1525 GetStatisticsInternal(compressedSize, uncompressedSize, countStudies, | |
1526 countSeries, countInstances, top, type); | |
1527 } | |
1528 | |
1529 | |
511
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1530 void ServerIndex::UnstableResourcesMonitorThread(ServerIndex* that) |
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1531 { |
810
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1532 int stableAge = Configuration::GetGlobalIntegerParameter("StableAge", 60); |
511
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1533 if (stableAge <= 0) |
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1534 { |
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1535 stableAge = 60; |
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1536 } |
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1537 |
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1538 LOG(INFO) << "Starting the monitor for stable resources (stable age = " << stableAge << ")"; |
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1539 |
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1540 while (!that->done_) |
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1541 { |
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1542 // Check for stable resources each second |
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1543 boost::this_thread::sleep(boost::posix_time::seconds(1)); |
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1544 |
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1545 boost::mutex::scoped_lock lock(that->mutex_); |
513 | 1546 |
511
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1547 while (!that->unstableResources_.IsEmpty() && |
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1548 that->unstableResources_.GetOldestPayload().GetAge() > static_cast<unsigned int>(stableAge)) |
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1549 { |
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1550 // This DICOM resource has not received any new instance for |
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1551 // some time. It can be considered as stable. |
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1552 |
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1553 UnstableResourcePayload payload; |
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1554 int64_t id = that->unstableResources_.RemoveOldest(payload); |
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1555 |
513 | 1556 // Ensure that the resource is still existing before logging the change |
1557 if (that->db_->IsExistingResource(id)) | |
511
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1558 { |
513 | 1559 switch (payload.type_) |
1560 { | |
1561 case Orthanc::ResourceType_Patient: | |
1562 that->db_->LogChange(ChangeType_StablePatient, id, ResourceType_Patient); | |
1563 break; | |
511
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1564 |
513 | 1565 case Orthanc::ResourceType_Study: |
1566 that->db_->LogChange(ChangeType_StableStudy, id, ResourceType_Study); | |
1567 break; | |
511
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1568 |
513 | 1569 case Orthanc::ResourceType_Series: |
1570 that->db_->LogChange(ChangeType_StableSeries, id, ResourceType_Series); | |
1571 break; | |
1572 | |
1573 default: | |
1574 throw OrthancException(ErrorCode_InternalError); | |
1575 } | |
1576 | |
1577 //LOG(INFO) << "Stable resource: " << EnumerationToString(payload.type_) << " " << id; | |
511
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1578 } |
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1579 } |
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1580 } |
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1581 |
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1582 LOG(INFO) << "Closing the monitor thread for stable resources"; |
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1583 } |
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1584 |
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1585 |
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1586 void ServerIndex::MarkAsUnstable(int64_t id, |
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1587 Orthanc::ResourceType type) |
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1588 { |
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1589 // WARNING: Before calling this method, "mutex_" must be locked. |
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1590 |
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1591 assert(type == Orthanc::ResourceType_Patient || |
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1592 type == Orthanc::ResourceType_Study || |
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1593 type == Orthanc::ResourceType_Series); |
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1594 |
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1595 unstableResources_.AddOrMakeMostRecent(id, type); |
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1596 //LOG(INFO) << "Unstable resource: " << EnumerationToString(type) << " " << id; |
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1597 } |
521 | 1598 |
1599 | |
1600 | |
1601 void ServerIndex::LookupTagValue(std::list<std::string>& result, | |
1602 DicomTag tag, | |
615 | 1603 const std::string& value, |
1604 ResourceType type) | |
1605 { | |
1606 result.clear(); | |
1607 | |
1608 boost::mutex::scoped_lock lock(mutex_); | |
1609 | |
1610 std::list<int64_t> id; | |
1611 db_->LookupTagValue(id, tag, value); | |
1612 | |
1613 for (std::list<int64_t>::const_iterator | |
656 | 1614 it = id.begin(); it != id.end(); ++it) |
615 | 1615 { |
1616 if (db_->GetResourceType(*it) == type) | |
1617 { | |
1618 result.push_back(db_->GetPublicId(*it)); | |
1619 } | |
1620 } | |
1621 } | |
1622 | |
1623 | |
1624 void ServerIndex::LookupTagValue(std::list<std::string>& result, | |
1625 DicomTag tag, | |
521 | 1626 const std::string& value) |
1627 { | |
1628 result.clear(); | |
1629 | |
1630 boost::mutex::scoped_lock lock(mutex_); | |
1631 | |
1632 std::list<int64_t> id; | |
1633 db_->LookupTagValue(id, tag, value); | |
1634 | |
1635 for (std::list<int64_t>::const_iterator | |
656 | 1636 it = id.begin(); it != id.end(); ++it) |
521 | 1637 { |
1638 result.push_back(db_->GetPublicId(*it)); | |
1639 } | |
1640 } | |
1641 | |
1642 | |
1643 void ServerIndex::LookupTagValue(std::list<std::string>& result, | |
1644 const std::string& value) | |
1645 { | |
1646 result.clear(); | |
1647 | |
1648 boost::mutex::scoped_lock lock(mutex_); | |
1649 | |
1650 std::list<int64_t> id; | |
1651 db_->LookupTagValue(id, value); | |
1652 | |
1653 for (std::list<int64_t>::const_iterator | |
656 | 1654 it = id.begin(); it != id.end(); ++it) |
521 | 1655 { |
1656 result.push_back(db_->GetPublicId(*it)); | |
1657 } | |
1658 } | |
699
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1659 |
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1660 |
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1661 StoreStatus ServerIndex::AddAttachment(const FileInfo& attachment, |
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1662 const std::string& publicId) |
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1663 { |
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1664 boost::mutex::scoped_lock lock(mutex_); |
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1665 |
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|
1666 Transaction t(*this); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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697
diff
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|
1667 |
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diff
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|
1668 ResourceType resourceType; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1669 int64_t resourceId; |
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add attachments to resources
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1670 if (!db_->LookupResource(publicId, resourceId, resourceType)) |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
697
diff
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|
1671 { |
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parents:
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diff
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|
1672 return StoreStatus_Failure; // Inexistent resource |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
697
diff
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|
1673 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
697
diff
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|
1674 |
704
4789da60d655
recycling with custom attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
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|
1675 // Remove possible previous attachment |
699
2929e17f8447
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1676 db_->DeleteAttachment(resourceId, attachment.GetContentType()); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
697
diff
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|
1677 |
704
4789da60d655
recycling with custom attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1678 // Locate the patient of the target resource |
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recycling with custom attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
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|
1679 int64_t patientId = resourceId; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1680 for (;;) |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
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|
1681 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
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|
1682 int64_t parent; |
4789da60d655
recycling with custom attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1683 if (db_->LookupParent(parent, patientId)) |
4789da60d655
recycling with custom attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
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|
1684 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1685 // We have not reached the patient level yet |
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recycling with custom attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1686 patientId = parent; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1687 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1688 else |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1689 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1690 // We have reached the patient level |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
1691 break; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1692 } |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1693 } |
4789da60d655
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1694 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1695 // Possibly apply the recycling mechanism while preserving this patient |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
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|
1696 assert(db_->GetResourceType(patientId) == ResourceType_Patient); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
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|
1697 Recycle(attachment.GetCompressedSize(), db_->GetPublicId(patientId)); |
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recycling with custom attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
702
diff
changeset
|
1698 |
699
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
1699 db_->AddAttachment(resourceId, attachment); |
2929e17f8447
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
697
diff
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|
1700 |
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Sebastien Jodogne <s.jodogne@gmail.com>
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697
diff
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|
1701 t.Commit(attachment.GetCompressedSize()); |
2929e17f8447
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
697
diff
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|
1702 |
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697
diff
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|
1703 return StoreStatus_Success; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
697
diff
changeset
|
1704 } |
2929e17f8447
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
697
diff
changeset
|
1705 |
702
7592a48e97e4
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
701
diff
changeset
|
1706 |
7592a48e97e4
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
701
diff
changeset
|
1707 void ServerIndex::DeleteAttachment(const std::string& publicId, |
7592a48e97e4
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
701
diff
changeset
|
1708 FileContentType type) |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
701
diff
changeset
|
1709 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
701
diff
changeset
|
1710 boost::mutex::scoped_lock lock(mutex_); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
701
diff
changeset
|
1711 listener_->Reset(); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
701
diff
changeset
|
1712 |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
701
diff
changeset
|
1713 Transaction t(*this); |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1714 |
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701
diff
changeset
|
1715 ResourceType rtype; |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
1716 int64_t id; |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
701
diff
changeset
|
1717 if (!db_->LookupResource(publicId, id, rtype)) |
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Sebastien Jodogne <s.jodogne@gmail.com>
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701
diff
changeset
|
1718 { |
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
701
diff
changeset
|
1719 throw OrthancException(ErrorCode_UnknownResource); |
7592a48e97e4
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parents:
701
diff
changeset
|
1720 } |
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parents:
701
diff
changeset
|
1721 |
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diff
changeset
|
1722 db_->DeleteAttachment(id, type); |
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diff
changeset
|
1723 |
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diff
changeset
|
1724 t.Commit(0); |
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parents:
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diff
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|
1725 } |
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diff
changeset
|
1726 |
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diff
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|
1727 |
1002
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parents:
831
diff
changeset
|
1728 bool ServerIndex::GetMetadata(Json::Value& target, |
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diff
changeset
|
1729 const std::string& publicId) |
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|
1730 { |
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diff
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|
1731 boost::mutex::scoped_lock lock(mutex_); |
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diff
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|
1732 |
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|
1733 target = Json::objectValue; |
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|
1734 |
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|
1735 ResourceType type; |
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|
1736 int64_t id; |
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diff
changeset
|
1737 if (!db_->LookupResource(publicId, id, type)) |
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diff
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|
1738 { |
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diff
changeset
|
1739 return false; |
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diff
changeset
|
1740 } |
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diff
changeset
|
1741 |
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diff
changeset
|
1742 std::list<MetadataType> metadata; |
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diff
changeset
|
1743 db_->ListAvailableMetadata(metadata, id); |
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diff
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|
1744 |
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diff
changeset
|
1745 for (std::list<MetadataType>::const_iterator |
b067017a8a5b
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diff
changeset
|
1746 it = metadata.begin(); it != metadata.end(); it++) |
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diff
changeset
|
1747 { |
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diff
changeset
|
1748 std::string key = EnumerationToString(*it); |
b067017a8a5b
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diff
changeset
|
1749 std::string value = db_->GetMetadata(id, *it); |
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diff
changeset
|
1750 target[key] = value; |
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diff
changeset
|
1751 } |
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diff
changeset
|
1752 |
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|
1753 return true; |
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diff
changeset
|
1754 } |
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diff
changeset
|
1755 |
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diff
changeset
|
1756 |
0 | 1757 } |