Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 1192:2036c3865990
thanks emsy
| author | Sebastien Jodogne <s.jodogne@gmail.com> |
|---|---|
| date | Thu, 16 Oct 2014 11:24:03 +0200 |
| parents | ac36589f699e |
| children | badc14fee61f |
| rev | line source |
|---|---|
| 0 | 1 /** |
| 62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
| 689 | 3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege, |
| 0 | 4 * Belgium |
| 5 * | |
| 6 * This program is free software: you can redistribute it and/or | |
| 7 * modify it under the terms of the GNU General Public License as | |
| 8 * published by the Free Software Foundation, either version 3 of the | |
| 9 * License, or (at your option) any later version. | |
| 136 | 10 * |
| 11 * In addition, as a special exception, the copyright holders of this | |
| 12 * program give permission to link the code of its release with the | |
| 13 * OpenSSL project's "OpenSSL" library (or with modified versions of it | |
| 14 * that use the same license as the "OpenSSL" library), and distribute | |
| 15 * the linked executables. You must obey the GNU General Public License | |
| 16 * in all respects for all of the code used other than "OpenSSL". If you | |
| 17 * modify file(s) with this exception, you may extend this exception to | |
| 18 * your version of the file(s), but you are not obligated to do so. If | |
| 19 * you do not wish to do so, delete this exception statement from your | |
| 20 * version. If you delete this exception statement from all source files | |
| 21 * in the program, then also delete it here. | |
| 0 | 22 * |
| 23 * This program is distributed in the hope that it will be useful, but | |
| 24 * WITHOUT ANY WARRANTY; without even the implied warranty of | |
| 25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU | |
| 26 * General Public License for more details. | |
| 27 * | |
| 28 * You should have received a copy of the GNU General Public License | |
| 29 * along with this program. If not, see <http://www.gnu.org/licenses/>. | |
| 30 **/ | |
| 31 | |
| 32 | |
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33 #include "PrecompiledHeadersServer.h" |
| 0 | 34 #include "ServerIndex.h" |
| 35 | |
| 6 | 36 #ifndef NOMINMAX |
| 2 | 37 #define NOMINMAX |
| 6 | 38 #endif |
| 39 | |
| 8 | 40 #include "EmbeddedResources.h" |
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41 #include "OrthancInitialization.h" |
| 0 | 42 #include "../Core/Toolbox.h" |
| 43 #include "../Core/Uuid.h" | |
| 44 #include "../Core/DicomFormat/DicomArray.h" | |
| 45 #include "../Core/SQLite/Transaction.h" | |
| 46 #include "FromDcmtkBridge.h" | |
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47 #include "ServerContext.h" |
| 0 | 48 |
| 49 #include <boost/lexical_cast.hpp> | |
| 50 #include <stdio.h> | |
| 108 | 51 #include <glog/logging.h> |
| 0 | 52 |
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53 static const uint64_t MEGA_BYTES = 1024 * 1024; |
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54 |
| 62 | 55 namespace Orthanc |
| 0 | 56 { |
| 57 namespace Internals | |
| 58 { | |
| 202 | 59 class ServerIndexListener : public IServerIndexListener |
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60 { |
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61 private: |
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62 struct FileToRemove |
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63 { |
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64 std::string uuid_; |
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65 FileContentType type_; |
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66 |
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67 FileToRemove(const FileInfo& info) : uuid_(info.GetUuid()), |
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68 type_(info.GetContentType()) |
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69 { |
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70 } |
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71 }; |
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72 |
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73 ServerContext& context_; |
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74 bool hasRemainingLevel_; |
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75 ResourceType remainingType_; |
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76 std::string remainingPublicId_; |
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77 std::list<FileToRemove> pendingFilesToRemove_; |
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78 uint64_t sizeOfFilesToRemove_; |
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79 |
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80 public: |
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81 ServerIndexListener(ServerContext& context) : |
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82 context_(context) |
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83 { |
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84 Reset(); |
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85 assert(ResourceType_Patient < ResourceType_Study && |
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86 ResourceType_Study < ResourceType_Series && |
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87 ResourceType_Series < ResourceType_Instance); |
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88 } |
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89 |
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90 void Reset() |
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91 { |
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92 sizeOfFilesToRemove_ = 0; |
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93 hasRemainingLevel_ = false; |
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94 pendingFilesToRemove_.clear(); |
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95 } |
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96 |
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97 uint64_t GetSizeOfFilesToRemove() |
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98 { |
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99 return sizeOfFilesToRemove_; |
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100 } |
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101 |
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102 void CommitFilesToRemove() |
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103 { |
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104 for (std::list<FileToRemove>::iterator |
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105 it = pendingFilesToRemove_.begin(); |
| 656 | 106 it != pendingFilesToRemove_.end(); ++it) |
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107 { |
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108 context_.RemoveFile(it->uuid_, it->type_); |
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109 } |
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110 } |
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111 |
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112 virtual void SignalRemainingAncestor(ResourceType parentType, |
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113 const std::string& publicId) |
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114 { |
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115 LOG(INFO) << "Remaining ancestor \"" << publicId << "\" (" << parentType << ")"; |
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116 |
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117 if (hasRemainingLevel_) |
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118 { |
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119 if (parentType < remainingType_) |
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120 { |
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121 remainingType_ = parentType; |
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122 remainingPublicId_ = publicId; |
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123 } |
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124 } |
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125 else |
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126 { |
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127 hasRemainingLevel_ = true; |
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128 remainingType_ = parentType; |
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129 remainingPublicId_ = publicId; |
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130 } |
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131 } |
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132 |
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133 virtual void SignalFileDeleted(const FileInfo& info) |
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134 { |
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135 assert(Toolbox::IsUuid(info.GetUuid())); |
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136 pendingFilesToRemove_.push_back(FileToRemove(info)); |
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137 sizeOfFilesToRemove_ += info.GetCompressedSize(); |
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138 } |
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139 |
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140 bool HasRemainingLevel() const |
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141 { |
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142 return hasRemainingLevel_; |
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143 } |
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144 |
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145 ResourceType GetRemainingType() const |
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146 { |
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147 assert(HasRemainingLevel()); |
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148 return remainingType_; |
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149 } |
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150 |
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151 const std::string& GetRemainingPublicId() const |
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152 { |
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153 assert(HasRemainingLevel()); |
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154 return remainingPublicId_; |
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155 } |
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156 }; |
| 0 | 157 } |
| 158 | |
| 159 | |
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160 class ServerIndex::Transaction |
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161 { |
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162 private: |
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163 ServerIndex& index_; |
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164 std::auto_ptr<SQLite::Transaction> transaction_; |
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165 bool isCommitted_; |
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166 |
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167 public: |
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168 Transaction(ServerIndex& index) : |
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169 index_(index), |
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170 isCommitted_(false) |
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171 { |
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172 assert(index_.currentStorageSize_ == index_.db_->GetTotalCompressedSize()); |
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173 |
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174 index_.listener_->Reset(); |
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175 transaction_.reset(index_.db_->StartTransaction()); |
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176 transaction_->Begin(); |
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177 } |
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178 |
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179 void Commit(uint64_t sizeOfAddedFiles) |
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180 { |
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181 if (!isCommitted_) |
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182 { |
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183 transaction_->Commit(); |
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184 |
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185 // We can remove the files once the SQLite transaction has |
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186 // been successfully committed. Some files might have to be |
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187 // deleted because of recycling. |
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188 index_.listener_->CommitFilesToRemove(); |
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189 |
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190 index_.currentStorageSize_ += sizeOfAddedFiles; |
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191 |
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192 assert(index_.currentStorageSize_ >= index_.listener_->GetSizeOfFilesToRemove()); |
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193 index_.currentStorageSize_ -= index_.listener_->GetSizeOfFilesToRemove(); |
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194 |
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195 assert(index_.currentStorageSize_ == index_.db_->GetTotalCompressedSize()); |
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196 |
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197 isCommitted_ = true; |
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198 } |
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199 } |
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200 }; |
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201 |
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202 |
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203 struct ServerIndex::UnstableResourcePayload |
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204 { |
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205 Orthanc::ResourceType type_; |
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206 boost::posix_time::ptime time_; |
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207 |
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208 UnstableResourcePayload() : type_(Orthanc::ResourceType_Instance) |
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209 { |
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210 } |
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211 |
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212 UnstableResourcePayload(Orthanc::ResourceType type) : type_(type) |
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213 { |
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214 time_ = boost::posix_time::second_clock::local_time(); |
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215 } |
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216 |
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217 unsigned int GetAge() const |
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218 { |
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219 return (boost::posix_time::second_clock::local_time() - time_).total_seconds(); |
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220 } |
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221 }; |
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222 |
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223 |
| 212 | 224 bool ServerIndex::DeleteResource(Json::Value& target, |
| 0 | 225 const std::string& uuid, |
| 202 | 226 ResourceType expectedType) |
| 0 | 227 { |
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228 boost::mutex::scoped_lock lock(mutex_); |
| 202 | 229 listener_->Reset(); |
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201
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230 |
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231 Transaction t(*this); |
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232 |
| 202 | 233 int64_t id; |
| 234 ResourceType type; | |
| 235 if (!db_->LookupResource(uuid, id, type) || | |
| 236 expectedType != type) | |
| 0 | 237 { |
| 238 return false; | |
| 239 } | |
| 202 | 240 |
| 241 db_->DeleteResource(id); | |
| 0 | 242 |
| 202 | 243 if (listener_->HasRemainingLevel()) |
| 0 | 244 { |
| 202 | 245 ResourceType type = listener_->GetRemainingType(); |
| 246 const std::string& uuid = listener_->GetRemainingPublicId(); | |
| 0 | 247 |
| 248 target["RemainingAncestor"] = Json::Value(Json::objectValue); | |
| 204 | 249 target["RemainingAncestor"]["Path"] = GetBasePath(type, uuid); |
|
434
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250 target["RemainingAncestor"]["Type"] = EnumerationToString(type); |
| 0 | 251 target["RemainingAncestor"]["ID"] = uuid; |
| 252 } | |
| 253 else | |
| 254 { | |
| 255 target["RemainingAncestor"] = Json::nullValue; | |
| 256 } | |
| 257 | |
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258 t.Commit(0); |
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264
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259 |
| 0 | 260 return true; |
| 261 } | |
| 262 | |
| 263 | |
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264 void ServerIndex::FlushThread(ServerIndex* that) |
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265 { |
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266 // By default, wait for 10 seconds before flushing |
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267 unsigned int sleep = 10; |
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268 |
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269 try |
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270 { |
| 744 | 271 boost::mutex::scoped_lock lock(that->mutex_); |
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272 std::string sleepString = that->db_->GetGlobalProperty(GlobalProperty_FlushSleep); |
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273 |
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274 if (Toolbox::IsInteger(sleepString)) |
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275 { |
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276 sleep = boost::lexical_cast<unsigned int>(sleepString); |
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277 } |
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278 } |
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279 catch (boost::bad_lexical_cast&) |
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280 { |
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281 } |
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282 |
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283 LOG(INFO) << "Starting the database flushing thread (sleep = " << sleep << ")"; |
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284 |
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285 unsigned int count = 0; |
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286 |
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287 while (!that->done_) |
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288 { |
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289 boost::this_thread::sleep(boost::posix_time::seconds(1)); |
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290 count++; |
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291 if (count < sleep) |
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292 { |
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293 continue; |
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294 } |
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295 |
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296 boost::mutex::scoped_lock lock(that->mutex_); |
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297 that->db_->FlushToDisk(); |
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298 count = 0; |
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299 } |
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300 |
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301 LOG(INFO) << "Stopping the database flushing thread"; |
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302 } |
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303 |
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304 |
| 433 | 305 static void ComputeExpectedNumberOfInstances(DatabaseWrapper& db, |
| 306 int64_t series, | |
| 307 const DicomMap& dicomSummary) | |
| 308 { | |
| 309 try | |
| 310 { | |
| 656 | 311 const DicomValue* value; |
| 312 const DicomValue* value2; | |
| 313 | |
| 433 | 314 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL && |
| 315 (value2 = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS)) != NULL) | |
| 316 { | |
| 317 // Patch for series with temporal positions thanks to Will Ryder | |
| 318 int64_t imagesInAcquisition = boost::lexical_cast<int64_t>(value->AsString()); | |
| 319 int64_t countTemporalPositions = boost::lexical_cast<int64_t>(value2->AsString()); | |
| 320 std::string expected = boost::lexical_cast<std::string>(imagesInAcquisition * countTemporalPositions); | |
| 321 db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, expected); | |
| 322 } | |
| 323 | |
| 324 else if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL && | |
| 325 (value2 = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_TIME_SLICES)) != NULL) | |
| 326 { | |
| 327 // Support of Cardio-PET images | |
| 328 int64_t numberOfSlices = boost::lexical_cast<int64_t>(value->AsString()); | |
| 329 int64_t numberOfTimeSlices = boost::lexical_cast<int64_t>(value2->AsString()); | |
| 330 std::string expected = boost::lexical_cast<std::string>(numberOfSlices * numberOfTimeSlices); | |
| 331 db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, expected); | |
| 332 } | |
| 333 | |
| 334 else if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL) | |
| 335 { | |
| 336 db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, value->AsString()); | |
| 337 } | |
| 338 } | |
| 339 catch (boost::bad_lexical_cast) | |
| 340 { | |
| 341 } | |
| 342 } | |
| 343 | |
| 344 | |
|
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345 ServerIndex::ServerIndex(ServerContext& context, |
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346 const std::string& dbPath) : |
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347 done_(false), |
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348 maximumStorageSize_(0), |
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349 maximumPatients_(0) |
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350 { |
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351 listener_.reset(new Internals::ServerIndexListener(context)); |
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352 |
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353 if (dbPath == ":memory:") |
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354 { |
| 202 | 355 db_.reset(new DatabaseWrapper(*listener_)); |
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356 } |
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357 else |
| 0 | 358 { |
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359 boost::filesystem::path p = dbPath; |
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360 |
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361 try |
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362 { |
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363 boost::filesystem::create_directories(p); |
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364 } |
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365 catch (boost::filesystem::filesystem_error) |
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366 { |
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367 } |
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368 |
| 202 | 369 db_.reset(new DatabaseWrapper(p.string() + "/index", *listener_)); |
| 0 | 370 } |
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371 |
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372 currentStorageSize_ = db_->GetTotalCompressedSize(); |
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373 |
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374 // Initial recycling if the parameters have changed since the last |
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375 // execution of Orthanc |
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376 StandaloneRecycling(); |
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377 |
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378 flushThread_ = boost::thread(FlushThread, this); |
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379 unstableResourcesMonitorThread_ = boost::thread(UnstableResourcesMonitorThread, this); |
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380 } |
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381 |
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382 |
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383 ServerIndex::~ServerIndex() |
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384 { |
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385 done_ = true; |
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386 |
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387 if (flushThread_.joinable()) |
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388 { |
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389 flushThread_.join(); |
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390 } |
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391 |
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392 if (unstableResourcesMonitorThread_.joinable()) |
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393 { |
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394 unstableResourcesMonitorThread_.join(); |
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395 } |
| 0 | 396 } |
| 397 | |
| 398 | |
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399 StoreStatus ServerIndex::Store(std::map<MetadataType, std::string>& instanceMetadata, |
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400 const DicomMap& dicomSummary, |
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401 const Attachments& attachments, |
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402 const std::string& remoteAet, |
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403 const MetadataMap& metadata) |
| 0 | 404 { |
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405 boost::mutex::scoped_lock lock(mutex_); |
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406 listener_->Reset(); |
| 0 | 407 |
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408 instanceMetadata.clear(); |
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409 |
| 178 | 410 DicomInstanceHasher hasher(dicomSummary); |
| 0 | 411 |
| 412 try | |
| 413 { | |
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414 Transaction t(*this); |
| 0 | 415 |
| 202 | 416 // Do nothing if the instance already exists |
| 0 | 417 { |
| 432 | 418 ResourceType type; |
| 419 int64_t tmp; | |
| 420 if (db_->LookupResource(hasher.HashInstance(), tmp, type)) | |
| 421 { | |
| 422 assert(type == ResourceType_Instance); | |
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423 db_->GetAllMetadata(instanceMetadata, tmp); |
| 432 | 424 return StoreStatus_AlreadyStored; |
| 425 } | |
| 0 | 426 } |
| 427 | |
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428 // Ensure there is enough room in the storage for the new instance |
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429 uint64_t instanceSize = 0; |
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430 for (Attachments::const_iterator it = attachments.begin(); |
| 656 | 431 it != attachments.end(); ++it) |
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432 { |
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433 instanceSize += it->GetCompressedSize(); |
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434 } |
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435 |
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436 Recycle(instanceSize, hasher.HashPatient()); |
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437 |
| 202 | 438 // Create the instance |
| 432 | 439 int64_t instance = db_->CreateResource(hasher.HashInstance(), ResourceType_Instance); |
| 202 | 440 |
| 441 DicomMap dicom; | |
| 442 dicomSummary.ExtractInstanceInformation(dicom); | |
| 443 db_->SetMainDicomTags(instance, dicom); | |
| 444 | |
| 432 | 445 // Detect up to which level the patient/study/series/instance |
| 446 // hierarchy must be created | |
| 447 int64_t patient = -1, study = -1, series = -1; | |
| 448 bool isNewPatient = false; | |
| 449 bool isNewStudy = false; | |
| 450 bool isNewSeries = false; | |
| 451 | |
| 0 | 452 { |
| 432 | 453 ResourceType dummy; |
| 454 | |
| 455 if (db_->LookupResource(hasher.HashSeries(), series, dummy)) | |
| 456 { | |
| 457 assert(dummy == ResourceType_Series); | |
| 458 // The patient, the study and the series already exist | |
| 459 | |
| 460 bool ok = (db_->LookupResource(hasher.HashPatient(), patient, dummy) && | |
| 461 db_->LookupResource(hasher.HashStudy(), study, dummy)); | |
| 462 assert(ok); | |
| 463 } | |
| 464 else if (db_->LookupResource(hasher.HashStudy(), study, dummy)) | |
| 465 { | |
| 466 assert(dummy == ResourceType_Study); | |
| 467 | |
| 468 // New series: The patient and the study already exist | |
| 469 isNewSeries = true; | |
| 470 | |
| 471 bool ok = db_->LookupResource(hasher.HashPatient(), patient, dummy); | |
| 472 assert(ok); | |
| 473 } | |
| 474 else if (db_->LookupResource(hasher.HashPatient(), patient, dummy)) | |
| 475 { | |
| 476 assert(dummy == ResourceType_Patient); | |
| 477 | |
| 478 // New study and series: The patient already exist | |
| 479 isNewStudy = true; | |
| 480 isNewSeries = true; | |
| 481 } | |
| 482 else | |
| 483 { | |
| 484 // New patient, study and series: Nothing exists | |
| 485 isNewPatient = true; | |
| 486 isNewStudy = true; | |
| 487 isNewSeries = true; | |
| 488 } | |
| 489 } | |
| 490 | |
| 491 // Create the series if needed | |
| 492 if (isNewSeries) | |
| 493 { | |
| 202 | 494 series = db_->CreateResource(hasher.HashSeries(), ResourceType_Series); |
| 495 dicomSummary.ExtractSeriesInformation(dicom); | |
| 496 db_->SetMainDicomTags(series, dicom); | |
| 432 | 497 } |
| 202 | 498 |
| 432 | 499 // Create the study if needed |
| 500 if (isNewStudy) | |
| 501 { | |
| 502 study = db_->CreateResource(hasher.HashStudy(), ResourceType_Study); | |
| 503 dicomSummary.ExtractStudyInformation(dicom); | |
| 504 db_->SetMainDicomTags(study, dicom); | |
| 505 } | |
| 506 | |
| 507 // Create the patient if needed | |
| 508 if (isNewPatient) | |
| 509 { | |
| 510 patient = db_->CreateResource(hasher.HashPatient(), ResourceType_Patient); | |
| 511 dicomSummary.ExtractPatientInformation(dicom); | |
| 512 db_->SetMainDicomTags(patient, dicom); | |
| 513 } | |
| 202 | 514 |
| 432 | 515 // Create the parent-to-child links |
| 516 db_->AttachChild(series, instance); | |
| 517 | |
| 518 if (isNewSeries) | |
| 519 { | |
| 520 db_->AttachChild(study, series); | |
| 0 | 521 } |
| 432 | 522 |
| 523 if (isNewStudy) | |
| 0 | 524 { |
| 432 | 525 db_->AttachChild(patient, study); |
| 0 | 526 } |
| 527 | |
| 432 | 528 // Sanity checks |
| 529 assert(patient != -1); | |
| 530 assert(study != -1); | |
| 531 assert(series != -1); | |
| 532 assert(instance != -1); | |
| 533 | |
| 202 | 534 // Attach the files to the newly created instance |
|
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535 for (Attachments::const_iterator it = attachments.begin(); |
| 656 | 536 it != attachments.end(); ++it) |
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537 { |
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538 db_->AddAttachment(instance, *it); |
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539 } |
| 202 | 540 |
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541 // Attach the user-specified metadata |
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542 for (MetadataMap::const_iterator |
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543 it = metadata.begin(); it != metadata.end(); ++it) |
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544 { |
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545 switch (it->first.first) |
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546 { |
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547 case ResourceType_Patient: |
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548 db_->SetMetadata(patient, it->first.second, it->second); |
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549 break; |
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550 |
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551 case ResourceType_Study: |
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552 db_->SetMetadata(study, it->first.second, it->second); |
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553 break; |
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554 |
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555 case ResourceType_Series: |
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556 db_->SetMetadata(series, it->first.second, it->second); |
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557 break; |
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558 |
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559 case ResourceType_Instance: |
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560 db_->SetMetadata(instance, it->first.second, it->second); |
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561 instanceMetadata[it->first.second] = it->second; |
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562 break; |
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563 |
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564 default: |
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565 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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566 } |
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567 } |
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568 |
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569 // Attach the auto-computed metadata for the patient/study/series levels |
| 432 | 570 std::string now = Toolbox::GetNowIsoString(); |
| 571 db_->SetMetadata(series, MetadataType_LastUpdate, now); | |
| 572 db_->SetMetadata(study, MetadataType_LastUpdate, now); | |
| 573 db_->SetMetadata(patient, MetadataType_LastUpdate, now); | |
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574 |
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575 // Attach the auto-computed metadata for the instance level, |
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576 // reflecting these additions into the input metadata map |
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577 db_->SetMetadata(instance, MetadataType_Instance_ReceptionDate, now); |
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578 instanceMetadata[MetadataType_Instance_ReceptionDate] = now; |
| 202 | 579 |
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580 db_->SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); |
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581 instanceMetadata[MetadataType_Instance_RemoteAet] = remoteAet; |
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582 |
| 202 | 583 const DicomValue* value; |
| 584 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || | |
| 585 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) | |
| 0 | 586 { |
| 202 | 587 db_->SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->AsString()); |
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588 instanceMetadata[MetadataType_Instance_IndexInSeries] = value->AsString(); |
| 0 | 589 } |
| 590 | |
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591 // Check whether the series of this new instance is now completed |
| 202 | 592 if (isNewSeries) |
| 593 { | |
| 433 | 594 ComputeExpectedNumberOfInstances(*db_, series, dicomSummary); |
| 202 | 595 } |
| 596 | |
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597 SeriesStatus seriesStatus = GetSeriesStatus(series); |
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598 if (seriesStatus == SeriesStatus_Complete) |
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599 { |
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600 db_->LogChange(ChangeType_CompletedSeries, series, ResourceType_Series); |
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601 } |
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602 |
|
511
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603 // Mark the parent resources of this instance as unstable |
| 1128 | 604 MarkAsUnstable(series, ResourceType_Series); |
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605 MarkAsUnstable(study, ResourceType_Study); |
| 1128 | 606 MarkAsUnstable(patient, ResourceType_Patient); |
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607 |
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608 t.Commit(instanceSize); |
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609 |
| 0 | 610 return StoreStatus_Success; |
| 611 } | |
| 62 | 612 catch (OrthancException& e) |
| 0 | 613 { |
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614 LOG(ERROR) << "EXCEPTION [" << e.What() << "]" |
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615 << " (SQLite status: " << db_->GetErrorMessage() << ")"; |
| 0 | 616 } |
| 617 | |
| 618 return StoreStatus_Failure; | |
| 619 } | |
| 620 | |
| 621 | |
| 238 | 622 void ServerIndex::ComputeStatistics(Json::Value& target) |
| 0 | 623 { |
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624 boost::mutex::scoped_lock lock(mutex_); |
| 238 | 625 target = Json::objectValue; |
| 0 | 626 |
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627 uint64_t cs = currentStorageSize_; |
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628 assert(cs == db_->GetTotalCompressedSize()); |
| 238 | 629 uint64_t us = db_->GetTotalUncompressedSize(); |
|
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630 target["TotalDiskSize"] = boost::lexical_cast<std::string>(cs); |
| 238 | 631 target["TotalUncompressedSize"] = boost::lexical_cast<std::string>(us); |
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632 target["TotalDiskSizeMB"] = boost::lexical_cast<unsigned int>(cs / MEGA_BYTES); |
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633 target["TotalUncompressedSizeMB"] = boost::lexical_cast<unsigned int>(us / MEGA_BYTES); |
| 238 | 634 |
| 635 target["CountPatients"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Patient)); | |
| 636 target["CountStudies"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Study)); | |
| 637 target["CountSeries"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Series)); | |
| 638 target["CountInstances"] = static_cast<unsigned int>(db_->GetResourceCount(ResourceType_Instance)); | |
| 639 } | |
| 640 | |
|
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641 |
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642 |
| 585 | 643 SeriesStatus ServerIndex::GetSeriesStatus(int64_t id) |
| 199 | 644 { |
| 645 // Get the expected number of instances in this series (from the metadata) | |
| 202 | 646 std::string s = db_->GetMetadata(id, MetadataType_Series_ExpectedNumberOfInstances); |
| 199 | 647 |
| 648 size_t expected; | |
| 649 try | |
| 650 { | |
| 651 expected = boost::lexical_cast<size_t>(s); | |
| 652 } | |
| 653 catch (boost::bad_lexical_cast&) | |
| 654 { | |
| 655 return SeriesStatus_Unknown; | |
| 656 } | |
| 657 | |
| 658 // Loop over the instances of this series | |
| 659 std::list<int64_t> children; | |
| 202 | 660 db_->GetChildrenInternalId(children, id); |
| 199 | 661 |
| 662 std::set<size_t> instances; | |
| 663 for (std::list<int64_t>::const_iterator | |
| 656 | 664 it = children.begin(); it != children.end(); ++it) |
| 199 | 665 { |
| 666 // Get the index of this instance in the series | |
| 202 | 667 s = db_->GetMetadata(*it, MetadataType_Instance_IndexInSeries); |
| 199 | 668 size_t index; |
| 669 try | |
| 670 { | |
| 671 index = boost::lexical_cast<size_t>(s); | |
| 672 } | |
| 673 catch (boost::bad_lexical_cast&) | |
| 674 { | |
| 675 return SeriesStatus_Unknown; | |
| 676 } | |
| 677 | |
| 656 | 678 if (!(index > 0 && index <= expected)) |
| 199 | 679 { |
| 680 // Out-of-range instance index | |
| 681 return SeriesStatus_Inconsistent; | |
| 682 } | |
| 683 | |
| 684 if (instances.find(index) != instances.end()) | |
| 685 { | |
| 686 // Twice the same instance index | |
| 687 return SeriesStatus_Inconsistent; | |
| 688 } | |
| 689 | |
| 690 instances.insert(index); | |
| 691 } | |
| 692 | |
| 693 if (instances.size() == expected) | |
| 694 { | |
| 695 return SeriesStatus_Complete; | |
| 696 } | |
| 697 else | |
| 698 { | |
| 699 return SeriesStatus_Missing; | |
| 700 } | |
| 701 } | |
| 702 | |
| 703 | |
| 704 | |
| 202 | 705 void ServerIndex::MainDicomTagsToJson(Json::Value& target, |
| 706 int64_t resourceId) | |
|
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707 { |
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|
708 DicomMap tags; |
| 202 | 709 db_->GetMainDicomTags(tags, resourceId); |
|
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710 target["MainDicomTags"] = Json::objectValue; |
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711 FromDcmtkBridge::ToJson(target["MainDicomTags"], tags); |
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712 } |
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713 |
|
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|
714 bool ServerIndex::LookupResource(Json::Value& result, |
| 199 | 715 const std::string& publicId, |
| 716 ResourceType expectedType) | |
|
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|
717 { |
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718 result = Json::objectValue; |
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719 |
|
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|
720 boost::mutex::scoped_lock lock(mutex_); |
| 199 | 721 |
|
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722 // Lookup for the requested resource |
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723 int64_t id; |
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724 ResourceType type; |
| 202 | 725 if (!db_->LookupResource(publicId, id, type) || |
| 199 | 726 type != expectedType) |
|
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727 { |
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|
728 return false; |
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|
729 } |
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|
730 |
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|
731 // Find the parent resource (if it exists) |
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732 if (type != ResourceType_Patient) |
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733 { |
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|
734 int64_t parentId; |
| 202 | 735 if (!db_->LookupParent(parentId, id)) |
|
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736 { |
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737 throw OrthancException(ErrorCode_InternalError); |
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738 } |
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739 |
| 202 | 740 std::string parent = db_->GetPublicId(parentId); |
|
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741 |
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742 switch (type) |
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743 { |
|
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|
744 case ResourceType_Study: |
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|
745 result["ParentPatient"] = parent; |
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|
746 break; |
|
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|
747 |
|
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748 case ResourceType_Series: |
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749 result["ParentStudy"] = parent; |
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|
750 break; |
|
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751 |
|
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|
752 case ResourceType_Instance: |
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753 result["ParentSeries"] = parent; |
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754 break; |
|
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755 |
|
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756 default: |
|
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|
757 throw OrthancException(ErrorCode_InternalError); |
|
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758 } |
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759 } |
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760 |
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761 // List the children resources |
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762 std::list<std::string> children; |
| 202 | 763 db_->GetChildrenPublicId(children, id); |
|
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764 |
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765 if (type != ResourceType_Instance) |
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766 { |
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767 Json::Value c = Json::arrayValue; |
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768 |
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769 for (std::list<std::string>::const_iterator |
| 656 | 770 it = children.begin(); it != children.end(); ++it) |
|
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771 { |
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|
772 c.append(*it); |
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773 } |
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changeset
|
774 |
|
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changeset
|
775 switch (type) |
|
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|
776 { |
|
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|
777 case ResourceType_Patient: |
|
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|
778 result["Studies"] = c; |
|
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|
779 break; |
|
198
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|
780 |
|
269
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|
781 case ResourceType_Study: |
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|
782 result["Series"] = c; |
|
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|
783 break; |
|
198
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changeset
|
784 |
|
269
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|
785 case ResourceType_Series: |
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786 result["Instances"] = c; |
|
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|
787 break; |
|
198
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changeset
|
788 |
|
269
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|
789 default: |
|
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|
790 throw OrthancException(ErrorCode_InternalError); |
|
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791 } |
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|
792 } |
|
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changeset
|
793 |
|
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changeset
|
794 // Set the resource type |
|
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|
795 switch (type) |
|
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changeset
|
796 { |
|
269
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|
797 case ResourceType_Patient: |
|
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|
798 result["Type"] = "Patient"; |
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|
799 break; |
|
198
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changeset
|
800 |
|
269
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changeset
|
801 case ResourceType_Study: |
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|
802 result["Type"] = "Study"; |
|
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|
803 break; |
| 199 | 804 |
|
269
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|
805 case ResourceType_Series: |
|
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|
806 { |
|
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changeset
|
807 result["Type"] = "Series"; |
|
434
ccf3a0a43dac
EnumerationDictionary
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parents:
433
diff
changeset
|
808 result["Status"] = EnumerationToString(GetSeriesStatus(id)); |
|
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changeset
|
809 |
|
269
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|
810 int i; |
|
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|
811 if (db_->GetMetadataAsInteger(i, id, MetadataType_Series_ExpectedNumberOfInstances)) |
|
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|
812 result["ExpectedNumberOfInstances"] = i; |
|
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|
813 else |
|
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changeset
|
814 result["ExpectedNumberOfInstances"] = Json::nullValue; |
|
200
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refactoring of read operations
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diff
changeset
|
815 |
|
269
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diff
changeset
|
816 break; |
|
200
9c58b2b03cf0
refactoring of read operations
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diff
changeset
|
817 } |
|
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refactoring of read operations
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diff
changeset
|
818 |
|
269
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changeset
|
819 case ResourceType_Instance: |
|
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|
820 { |
|
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|
821 result["Type"] = "Instance"; |
|
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|
822 |
|
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|
823 FileInfo attachment; |
|
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diff
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|
824 if (!db_->LookupAttachment(attachment, id, FileContentType_Dicom)) |
|
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|
825 { |
|
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|
826 throw OrthancException(ErrorCode_InternalError); |
|
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|
827 } |
|
200
9c58b2b03cf0
refactoring of read operations
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diff
changeset
|
828 |
|
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|
829 result["FileSize"] = static_cast<unsigned int>(attachment.GetUncompressedSize()); |
|
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diff
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|
830 result["FileUuid"] = attachment.GetUuid(); |
|
200
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refactoring of read operations
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diff
changeset
|
831 |
|
269
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|
832 int i; |
|
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|
833 if (db_->GetMetadataAsInteger(i, id, MetadataType_Instance_IndexInSeries)) |
|
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|
834 result["IndexInSeries"] = i; |
|
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diff
changeset
|
835 else |
|
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changeset
|
836 result["IndexInSeries"] = Json::nullValue; |
|
198
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|
837 |
|
269
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diff
changeset
|
838 break; |
|
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changeset
|
839 } |
|
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changeset
|
840 |
|
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|
841 default: |
|
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changeset
|
842 throw OrthancException(ErrorCode_InternalError); |
|
198
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|
843 } |
|
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|
844 |
|
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|
845 // Record the remaining information |
|
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changeset
|
846 result["ID"] = publicId; |
| 202 | 847 MainDicomTagsToJson(result, id); |
|
198
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|
848 |
| 315 | 849 std::string tmp; |
| 850 | |
| 851 tmp = db_->GetMetadata(id, MetadataType_AnonymizedFrom); | |
| 852 if (tmp.size() != 0) | |
| 853 result["AnonymizedFrom"] = tmp; | |
| 854 | |
| 855 tmp = db_->GetMetadata(id, MetadataType_ModifiedFrom); | |
| 856 if (tmp.size() != 0) | |
| 857 result["ModifiedFrom"] = tmp; | |
| 858 | |
|
511
3b735fdf320b
monitoring of stable patients/studies/series
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parents:
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diff
changeset
|
859 if (type == ResourceType_Patient || |
|
3b735fdf320b
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diff
changeset
|
860 type == ResourceType_Study || |
|
3b735fdf320b
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parents:
440
diff
changeset
|
861 type == ResourceType_Series) |
|
3b735fdf320b
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440
diff
changeset
|
862 { |
|
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
863 result["IsStable"] = !unstableResources_.Contains(id); |
|
1148
ac36589f699e
LastUpdate metadata is now always returned for patients, studies and series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1139
diff
changeset
|
864 |
|
ac36589f699e
LastUpdate metadata is now always returned for patients, studies and series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1139
diff
changeset
|
865 tmp = db_->GetMetadata(id, MetadataType_LastUpdate); |
|
ac36589f699e
LastUpdate metadata is now always returned for patients, studies and series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1139
diff
changeset
|
866 if (tmp.size() != 0) |
|
ac36589f699e
LastUpdate metadata is now always returned for patients, studies and series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1139
diff
changeset
|
867 result["LastUpdate"] = tmp; |
|
511
3b735fdf320b
monitoring of stable patients/studies/series
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diff
changeset
|
868 } |
|
3b735fdf320b
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440
diff
changeset
|
869 |
|
198
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diff
changeset
|
870 return true; |
|
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diff
changeset
|
871 } |
|
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diff
changeset
|
872 |
| 0 | 873 |
|
232
5368bbe813cf
refactoring of attachments
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231
diff
changeset
|
874 bool ServerIndex::LookupAttachment(FileInfo& attachment, |
|
5368bbe813cf
refactoring of attachments
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diff
changeset
|
875 const std::string& instanceUuid, |
| 233 | 876 FileContentType contentType) |
| 0 | 877 { |
|
206
4453a010d0db
flush to disk thread
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parents:
205
diff
changeset
|
878 boost::mutex::scoped_lock lock(mutex_); |
| 0 | 879 |
|
193
a1b9d1e1497b
failed attempt to compile with linux standard base
Sebastien Jodogne <s.jodogne@gmail.com>
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192
diff
changeset
|
880 int64_t id; |
|
a1b9d1e1497b
failed attempt to compile with linux standard base
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192
diff
changeset
|
881 ResourceType type; |
| 701 | 882 if (!db_->LookupResource(instanceUuid, id, type)) |
|
192
c56dc32266e0
refactoring getfile
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191
diff
changeset
|
883 { |
|
1113
ba5c0908600c
Refactoring of HttpOutput ("Content-Length" header is now always sent)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1102
diff
changeset
|
884 throw OrthancException(ErrorCode_UnknownResource); |
|
192
c56dc32266e0
refactoring getfile
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191
diff
changeset
|
885 } |
|
193
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886 |
|
232
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887 if (db_->LookupAttachment(attachment, id, contentType)) |
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888 { |
| 233 | 889 assert(attachment.GetContentType() == contentType); |
|
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890 return true; |
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891 } |
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892 else |
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893 { |
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894 return false; |
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895 } |
|
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896 } |
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897 |
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898 |
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899 |
| 0 | 900 void ServerIndex::GetAllUuids(Json::Value& target, |
| 190 | 901 ResourceType resourceType) |
| 0 | 902 { |
|
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903 boost::mutex::scoped_lock lock(mutex_); |
| 202 | 904 db_->GetAllPublicIds(target, resourceType); |
| 0 | 905 } |
| 906 | |
| 907 | |
| 908 bool ServerIndex::GetChanges(Json::Value& target, | |
| 204 | 909 int64_t since, |
| 0 | 910 unsigned int maxResults) |
| 911 { | |
|
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912 boost::mutex::scoped_lock lock(mutex_); |
|
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913 db_->GetChanges(target, since, maxResults); |
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914 return true; |
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915 } |
| 0 | 916 |
|
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917 bool ServerIndex::GetLastChange(Json::Value& target) |
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918 { |
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919 boost::mutex::scoped_lock lock(mutex_); |
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920 db_->GetLastChange(target); |
| 204 | 921 return true; |
| 0 | 922 } |
| 231 | 923 |
| 924 void ServerIndex::LogExportedResource(const std::string& publicId, | |
| 925 const std::string& remoteModality) | |
| 926 { | |
| 927 boost::mutex::scoped_lock lock(mutex_); | |
| 928 | |
| 929 int64_t id; | |
| 930 ResourceType type; | |
| 931 if (!db_->LookupResource(publicId, id, type)) | |
| 932 { | |
| 933 throw OrthancException(ErrorCode_InternalError); | |
| 934 } | |
| 935 | |
| 936 std::string patientId; | |
| 937 std::string studyInstanceUid; | |
| 938 std::string seriesInstanceUid; | |
| 939 std::string sopInstanceUid; | |
| 940 | |
| 941 int64_t currentId = id; | |
| 942 ResourceType currentType = type; | |
| 943 | |
| 944 // Iteratively go up inside the patient/study/series/instance hierarchy | |
| 945 bool done = false; | |
| 946 while (!done) | |
| 947 { | |
| 948 DicomMap map; | |
| 949 db_->GetMainDicomTags(map, currentId); | |
| 950 | |
| 951 switch (currentType) | |
| 952 { | |
|
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953 case ResourceType_Patient: |
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954 patientId = map.GetValue(DICOM_TAG_PATIENT_ID).AsString(); |
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955 done = true; |
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956 break; |
| 231 | 957 |
|
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958 case ResourceType_Study: |
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959 studyInstanceUid = map.GetValue(DICOM_TAG_STUDY_INSTANCE_UID).AsString(); |
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960 currentType = ResourceType_Patient; |
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961 break; |
| 231 | 962 |
|
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963 case ResourceType_Series: |
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964 seriesInstanceUid = map.GetValue(DICOM_TAG_SERIES_INSTANCE_UID).AsString(); |
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965 currentType = ResourceType_Study; |
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966 break; |
| 231 | 967 |
|
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968 case ResourceType_Instance: |
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969 sopInstanceUid = map.GetValue(DICOM_TAG_SOP_INSTANCE_UID).AsString(); |
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970 currentType = ResourceType_Series; |
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971 break; |
| 231 | 972 |
|
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973 default: |
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974 throw OrthancException(ErrorCode_InternalError); |
| 231 | 975 } |
| 976 | |
| 977 // If we have not reached the Patient level, find the parent of | |
| 978 // the current resource | |
| 979 if (!done) | |
| 980 { | |
|
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981 bool ok = db_->LookupParent(currentId, currentId); |
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982 assert(ok); |
| 231 | 983 } |
| 984 } | |
| 985 | |
| 986 // No need for a SQLite::Transaction here, as we only insert 1 record | |
| 987 db_->LogExportedResource(type, | |
| 988 publicId, | |
| 989 remoteModality, | |
| 990 patientId, | |
| 991 studyInstanceUid, | |
| 992 seriesInstanceUid, | |
| 993 sopInstanceUid); | |
| 994 } | |
| 995 | |
| 996 | |
| 997 bool ServerIndex::GetExportedResources(Json::Value& target, | |
| 998 int64_t since, | |
| 999 unsigned int maxResults) | |
| 1000 { | |
| 1001 boost::mutex::scoped_lock lock(mutex_); | |
| 1002 db_->GetExportedResources(target, since, maxResults); | |
| 1003 return true; | |
| 1004 } | |
|
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1005 |
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1006 bool ServerIndex::GetLastExportedResource(Json::Value& target) |
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1007 { |
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1008 boost::mutex::scoped_lock lock(mutex_); |
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1009 db_->GetLastExportedResource(target); |
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1010 return true; |
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1011 } |
|
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1012 |
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1013 |
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1014 bool ServerIndex::IsRecyclingNeeded(uint64_t instanceSize) |
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1015 { |
|
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1016 if (maximumStorageSize_ != 0) |
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1017 { |
|
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1018 uint64_t currentSize = currentStorageSize_ - listener_->GetSizeOfFilesToRemove(); |
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1019 assert(db_->GetTotalCompressedSize() == currentSize); |
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1020 |
|
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1021 if (currentSize + instanceSize > maximumStorageSize_) |
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1022 { |
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1023 return true; |
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1024 } |
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1025 } |
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1026 |
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1027 if (maximumPatients_ != 0) |
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1028 { |
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1029 uint64_t patientCount = db_->GetResourceCount(ResourceType_Patient); |
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1030 if (patientCount > maximumPatients_) |
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1031 { |
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1032 return true; |
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1033 } |
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1034 } |
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1035 |
|
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1036 return false; |
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1037 } |
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1038 |
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1039 |
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1040 void ServerIndex::Recycle(uint64_t instanceSize, |
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1041 const std::string& newPatientId) |
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1042 { |
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1043 if (!IsRecyclingNeeded(instanceSize)) |
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1044 { |
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1045 return; |
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1046 } |
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1047 |
|
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1048 // Check whether other DICOM instances from this patient are |
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1049 // already stored |
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1050 int64_t patientToAvoid; |
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1051 ResourceType type; |
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1052 bool hasPatientToAvoid = db_->LookupResource(newPatientId, patientToAvoid, type); |
|
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1053 |
|
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1054 if (hasPatientToAvoid && type != ResourceType_Patient) |
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1055 { |
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1056 throw OrthancException(ErrorCode_InternalError); |
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1057 } |
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1058 |
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1059 // Iteratively select patient to remove until there is enough |
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1060 // space in the DICOM store |
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1061 int64_t patientToRecycle; |
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1062 while (true) |
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1063 { |
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1064 // If other instances of this patient are already in the store, |
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1065 // we must avoid to recycle them |
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1066 bool ok = hasPatientToAvoid ? |
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1067 db_->SelectPatientToRecycle(patientToRecycle, patientToAvoid) : |
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1068 db_->SelectPatientToRecycle(patientToRecycle); |
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1069 |
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1070 if (!ok) |
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1071 { |
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1072 throw OrthancException(ErrorCode_FullStorage); |
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1073 } |
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1074 |
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1075 LOG(INFO) << "Recycling one patient"; |
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1076 db_->DeleteResource(patientToRecycle); |
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1077 |
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1078 if (!IsRecyclingNeeded(instanceSize)) |
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1079 { |
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1080 // OK, we're done |
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1081 break; |
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1082 } |
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1083 } |
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1084 } |
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1085 |
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1086 void ServerIndex::SetMaximumPatientCount(unsigned int count) |
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1087 { |
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1088 boost::mutex::scoped_lock lock(mutex_); |
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1089 maximumPatients_ = count; |
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1090 |
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1091 if (count == 0) |
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1092 { |
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1093 LOG(WARNING) << "No limit on the number of stored patients"; |
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1094 } |
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1095 else |
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1096 { |
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1097 LOG(WARNING) << "At most " << count << " patients will be stored"; |
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1098 } |
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1099 |
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1100 StandaloneRecycling(); |
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1101 } |
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1102 |
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1103 void ServerIndex::SetMaximumStorageSize(uint64_t size) |
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1104 { |
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1105 boost::mutex::scoped_lock lock(mutex_); |
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1106 maximumStorageSize_ = size; |
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1107 |
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1108 if (size == 0) |
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1109 { |
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1110 LOG(WARNING) << "No limit on the size of the storage area"; |
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1111 } |
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1112 else |
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1113 { |
|
440
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1114 LOG(WARNING) << "At most " << (size / MEGA_BYTES) << "MB will be used for the storage area"; |
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1115 } |
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1116 |
|
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1117 StandaloneRecycling(); |
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1118 } |
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1119 |
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1120 void ServerIndex::StandaloneRecycling() |
|
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1121 { |
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1122 // WARNING: No mutex here, do not include this as a public method |
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1123 Transaction t(*this); |
|
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1124 Recycle(0, ""); |
|
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1125 t.Commit(0); |
|
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1126 } |
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1127 |
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1128 |
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1129 bool ServerIndex::IsProtectedPatient(const std::string& publicId) |
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1130 { |
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1131 boost::mutex::scoped_lock lock(mutex_); |
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1132 |
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1133 // Lookup for the requested resource |
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1134 int64_t id; |
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1135 ResourceType type; |
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1136 if (!db_->LookupResource(publicId, id, type) || |
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1137 type != ResourceType_Patient) |
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1138 { |
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1139 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1140 } |
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1141 |
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1142 return db_->IsProtectedPatient(id); |
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1143 } |
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1144 |
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1145 |
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1146 void ServerIndex::SetProtectedPatient(const std::string& publicId, |
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1147 bool isProtected) |
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1148 { |
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1149 boost::mutex::scoped_lock lock(mutex_); |
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1150 |
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1151 // Lookup for the requested resource |
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1152 int64_t id; |
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1153 ResourceType type; |
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1154 if (!db_->LookupResource(publicId, id, type) || |
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1155 type != ResourceType_Patient) |
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1156 { |
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1157 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1158 } |
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1159 |
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1160 // No need for a SQLite::Transaction here, as we only make 1 write to the DB |
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1161 db_->SetProtectedPatient(id, isProtected); |
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1162 |
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1163 if (isProtected) |
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1164 LOG(INFO) << "Patient " << publicId << " has been protected"; |
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1165 else |
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1166 LOG(INFO) << "Patient " << publicId << " has been unprotected"; |
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1167 } |
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1168 |
| 304 | 1169 |
|
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1170 void ServerIndex::GetChildren(std::list<std::string>& result, |
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1171 const std::string& publicId) |
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1172 { |
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1173 result.clear(); |
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1174 |
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1175 boost::mutex::scoped_lock lock(mutex_); |
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1176 |
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1177 ResourceType type; |
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1178 int64_t resource; |
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1179 if (!db_->LookupResource(publicId, resource, type)) |
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1180 { |
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1181 throw OrthancException(ErrorCode_UnknownResource); |
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1182 } |
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1183 |
|
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1184 if (type == ResourceType_Instance) |
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1185 { |
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1186 // An instance cannot have a child |
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1187 throw OrthancException(ErrorCode_BadParameterType); |
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1188 } |
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1189 |
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1190 std::list<int64_t> tmp; |
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1191 db_->GetChildrenInternalId(tmp, resource); |
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1192 |
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1193 for (std::list<int64_t>::const_iterator |
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1194 it = tmp.begin(); it != tmp.end(); ++it) |
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1195 { |
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1196 result.push_back(db_->GetPublicId(*it)); |
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1197 } |
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1198 } |
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1199 |
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1200 |
| 304 | 1201 void ServerIndex::GetChildInstances(std::list<std::string>& result, |
| 1202 const std::string& publicId) | |
| 1203 { | |
| 1204 result.clear(); | |
| 1205 | |
| 1206 boost::mutex::scoped_lock lock(mutex_); | |
| 1207 | |
| 1208 ResourceType type; | |
| 1209 int64_t top; | |
| 1210 if (!db_->LookupResource(publicId, top, type)) | |
| 1211 { | |
| 1212 throw OrthancException(ErrorCode_UnknownResource); | |
| 1213 } | |
| 1214 | |
| 1215 if (type == ResourceType_Instance) | |
| 1216 { | |
| 1217 // The resource is already an instance: Do not go down the hierarchy | |
| 1218 result.push_back(publicId); | |
| 1219 return; | |
| 1220 } | |
| 1221 | |
| 1222 std::stack<int64_t> toExplore; | |
| 1223 toExplore.push(top); | |
| 1224 | |
| 1225 std::list<int64_t> tmp; | |
| 1226 | |
| 1227 while (!toExplore.empty()) | |
| 1228 { | |
| 1229 // Get the internal ID of the current resource | |
| 1230 int64_t resource = toExplore.top(); | |
| 1231 toExplore.pop(); | |
| 1232 | |
| 1233 if (db_->GetResourceType(resource) == ResourceType_Instance) | |
| 1234 { | |
| 1235 result.push_back(db_->GetPublicId(resource)); | |
| 1236 } | |
| 1237 else | |
| 1238 { | |
| 1239 // Tag all the children of this resource as to be explored | |
| 1240 db_->GetChildrenInternalId(tmp, resource); | |
| 1241 for (std::list<int64_t>::const_iterator | |
| 656 | 1242 it = tmp.begin(); it != tmp.end(); ++it) |
| 304 | 1243 { |
| 1244 toExplore.push(*it); | |
| 1245 } | |
| 1246 } | |
| 1247 } | |
| 1248 } | |
| 1249 | |
|
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1250 |
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1251 void ServerIndex::SetMetadata(const std::string& publicId, |
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1252 MetadataType type, |
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1253 const std::string& value) |
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1254 { |
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1255 boost::mutex::scoped_lock lock(mutex_); |
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1256 |
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1257 ResourceType rtype; |
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1258 int64_t id; |
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1259 if (!db_->LookupResource(publicId, id, rtype)) |
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1260 { |
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1261 throw OrthancException(ErrorCode_UnknownResource); |
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1262 } |
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1263 |
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1264 db_->SetMetadata(id, type, value); |
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1265 } |
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1266 |
| 438 | 1267 |
| 1268 void ServerIndex::DeleteMetadata(const std::string& publicId, | |
| 1269 MetadataType type) | |
| 1270 { | |
| 1271 boost::mutex::scoped_lock lock(mutex_); | |
| 1272 | |
| 1273 ResourceType rtype; | |
| 1274 int64_t id; | |
| 1275 if (!db_->LookupResource(publicId, id, rtype)) | |
| 1276 { | |
| 1277 throw OrthancException(ErrorCode_UnknownResource); | |
| 1278 } | |
| 1279 | |
| 1280 db_->DeleteMetadata(id, type); | |
| 1281 } | |
| 1282 | |
| 1283 | |
|
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1284 bool ServerIndex::LookupMetadata(std::string& target, |
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1285 const std::string& publicId, |
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1286 MetadataType type) |
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1287 { |
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1288 boost::mutex::scoped_lock lock(mutex_); |
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1289 |
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1290 ResourceType rtype; |
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1291 int64_t id; |
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1292 if (!db_->LookupResource(publicId, id, rtype)) |
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1293 { |
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1294 throw OrthancException(ErrorCode_UnknownResource); |
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1295 } |
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1296 |
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1297 return db_->LookupMetadata(target, id, type); |
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1298 } |
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1299 |
|
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1300 |
| 739 | 1301 void ServerIndex::ListAvailableMetadata(std::list<MetadataType>& target, |
|
436
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1302 const std::string& publicId) |
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1303 { |
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1304 boost::mutex::scoped_lock lock(mutex_); |
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1305 |
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1306 ResourceType rtype; |
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1307 int64_t id; |
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1308 if (!db_->LookupResource(publicId, id, rtype)) |
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1309 { |
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1310 throw OrthancException(ErrorCode_UnknownResource); |
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1311 } |
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1312 |
| 739 | 1313 db_->ListAvailableMetadata(target, id); |
|
436
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1314 } |
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1315 |
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1316 |
|
697
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|
1317 void ServerIndex::ListAvailableAttachments(std::list<FileContentType>& target, |
|
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|
1318 const std::string& publicId, |
|
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|
1319 ResourceType expectedType) |
|
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1320 { |
|
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|
1321 boost::mutex::scoped_lock lock(mutex_); |
|
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1322 |
|
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1323 ResourceType type; |
|
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1324 int64_t id; |
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1325 if (!db_->LookupResource(publicId, id, type) || |
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1326 expectedType != type) |
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1327 { |
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1328 throw OrthancException(ErrorCode_UnknownResource); |
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1329 } |
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1330 |
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1331 db_->ListAvailableAttachments(target, id); |
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1332 } |
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1333 |
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1334 |
|
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1335 bool ServerIndex::LookupParent(std::string& target, |
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1336 const std::string& publicId) |
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1337 { |
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1338 boost::mutex::scoped_lock lock(mutex_); |
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1339 |
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1340 ResourceType type; |
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1341 int64_t id; |
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1342 if (!db_->LookupResource(publicId, id, type)) |
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1343 { |
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1344 throw OrthancException(ErrorCode_UnknownResource); |
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1345 } |
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1346 |
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1347 int64_t parentId; |
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1348 if (db_->LookupParent(parentId, id)) |
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1349 { |
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1350 target = db_->GetPublicId(parentId); |
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1351 return true; |
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1352 } |
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1353 else |
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1354 { |
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1355 return false; |
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1356 } |
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|
1357 } |
| 310 | 1358 |
| 1359 | |
| 1360 uint64_t ServerIndex::IncrementGlobalSequence(GlobalProperty sequence) | |
| 1361 { | |
| 1362 boost::mutex::scoped_lock lock(mutex_); | |
| 311 | 1363 |
| 1364 std::auto_ptr<SQLite::Transaction> transaction(db_->StartTransaction()); | |
| 1365 | |
| 1366 transaction->Begin(); | |
| 1367 uint64_t seq = db_->IncrementGlobalSequence(sequence); | |
| 1368 transaction->Commit(); | |
| 1369 | |
| 1370 return seq; | |
| 310 | 1371 } |
| 315 | 1372 |
| 1373 | |
| 1374 | |
| 1375 void ServerIndex::LogChange(ChangeType changeType, | |
| 1376 const std::string& publicId) | |
| 1377 { | |
| 1378 boost::mutex::scoped_lock lock(mutex_); | |
| 1379 std::auto_ptr<SQLite::Transaction> transaction(db_->StartTransaction()); | |
| 1380 transaction->Begin(); | |
| 1381 | |
| 1382 int64_t id; | |
| 1383 ResourceType type; | |
| 1384 if (!db_->LookupResource(publicId, id, type)) | |
| 1385 { | |
| 1386 throw OrthancException(ErrorCode_UnknownResource); | |
| 1387 } | |
| 1388 | |
| 1389 db_->LogChange(changeType, id, type); | |
| 1390 | |
| 1391 transaction->Commit(); | |
| 1392 } | |
|
413
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diff
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|
1393 |
|
47d63c941902
clearing /exports and /changes
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diff
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|
1394 |
|
47d63c941902
clearing /exports and /changes
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diff
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|
1395 void ServerIndex::DeleteChanges() |
|
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diff
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|
1396 { |
|
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diff
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|
1397 boost::mutex::scoped_lock lock(mutex_); |
|
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diff
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|
1398 db_->ClearTable("Changes"); |
|
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diff
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|
1399 } |
|
47d63c941902
clearing /exports and /changes
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diff
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|
1400 |
|
47d63c941902
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diff
changeset
|
1401 void ServerIndex::DeleteExportedResources() |
|
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diff
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|
1402 { |
|
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diff
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|
1403 boost::mutex::scoped_lock lock(mutex_); |
|
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diff
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|
1404 db_->ClearTable("ExportedResources"); |
|
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diff
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|
1405 } |
|
440
23e5b35e3c5c
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diff
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|
1406 |
|
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diff
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|
1407 |
| 646 | 1408 void ServerIndex::GetStatisticsInternal(/* out */ uint64_t& compressedSize, |
| 1409 /* out */ uint64_t& uncompressedSize, | |
| 1410 /* out */ unsigned int& countStudies, | |
| 1411 /* out */ unsigned int& countSeries, | |
| 1412 /* out */ unsigned int& countInstances, | |
| 1413 /* in */ int64_t id, | |
| 1414 /* in */ ResourceType type) | |
|
440
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diff
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|
1415 { |
| 646 | 1416 std::stack<int64_t> toExplore; |
| 1417 toExplore.push(id); | |
|
440
23e5b35e3c5c
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diff
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|
1418 |
| 646 | 1419 countInstances = 0; |
| 1420 countSeries = 0; | |
| 1421 countStudies = 0; | |
| 1422 compressedSize = 0; | |
| 1423 uncompressedSize = 0; | |
|
440
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diff
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|
1424 |
|
23e5b35e3c5c
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diff
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|
1425 while (!toExplore.empty()) |
|
23e5b35e3c5c
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diff
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|
1426 { |
|
23e5b35e3c5c
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diff
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|
1427 // Get the internal ID of the current resource |
|
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diff
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|
1428 int64_t resource = toExplore.top(); |
|
23e5b35e3c5c
statistics for patient/studies/series/instances
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diff
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|
1429 toExplore.pop(); |
|
23e5b35e3c5c
statistics for patient/studies/series/instances
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diff
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|
1430 |
|
23e5b35e3c5c
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diff
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|
1431 ResourceType thisType = db_->GetResourceType(resource); |
|
23e5b35e3c5c
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diff
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|
1432 |
|
702
7592a48e97e4
delete custom attachment
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
1433 std::list<FileContentType> f; |
|
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parents:
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diff
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|
1434 db_->ListAvailableAttachments(f, resource); |
|
7592a48e97e4
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diff
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|
1435 |
|
7592a48e97e4
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diff
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|
1436 for (std::list<FileContentType>::const_iterator |
|
7592a48e97e4
delete custom attachment
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diff
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|
1437 it = f.begin(); it != f.end(); ++it) |
|
7592a48e97e4
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diff
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|
1438 { |
|
7592a48e97e4
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diff
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|
1439 FileInfo attachment; |
|
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delete custom attachment
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parents:
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diff
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|
1440 if (db_->LookupAttachment(attachment, resource, *it)) |
|
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diff
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|
1441 { |
|
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diff
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|
1442 compressedSize += attachment.GetCompressedSize(); |
|
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diff
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|
1443 uncompressedSize += attachment.GetUncompressedSize(); |
|
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diff
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|
1444 } |
|
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diff
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|
1445 } |
|
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diff
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|
1446 |
|
440
23e5b35e3c5c
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diff
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|
1447 if (thisType == ResourceType_Instance) |
|
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|
1448 { |
|
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|
1449 countInstances++; |
|
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|
1450 } |
|
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diff
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|
1451 else |
|
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diff
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|
1452 { |
|
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diff
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|
1453 switch (thisType) |
|
23e5b35e3c5c
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diff
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|
1454 { |
|
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diff
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|
1455 case ResourceType_Study: |
|
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|
1456 countStudies++; |
|
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diff
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|
1457 break; |
|
23e5b35e3c5c
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diff
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|
1458 |
|
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diff
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|
1459 case ResourceType_Series: |
|
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|
1460 countSeries++; |
|
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diff
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|
1461 break; |
|
23e5b35e3c5c
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diff
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|
1462 |
|
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diff
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|
1463 default: |
|
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diff
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|
1464 break; |
|
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diff
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|
1465 } |
|
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diff
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|
1466 |
|
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|
1467 // Tag all the children of this resource as to be explored |
|
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|
1468 std::list<int64_t> tmp; |
|
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diff
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|
1469 db_->GetChildrenInternalId(tmp, resource); |
|
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diff
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|
1470 for (std::list<int64_t>::const_iterator |
| 656 | 1471 it = tmp.begin(); it != tmp.end(); ++it) |
|
440
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diff
changeset
|
1472 { |
|
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diff
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|
1473 toExplore.push(*it); |
|
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diff
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|
1474 } |
|
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diff
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|
1475 } |
|
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diff
changeset
|
1476 } |
|
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diff
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|
1477 |
| 646 | 1478 if (countStudies == 0) |
| 1479 { | |
| 1480 countStudies = 1; | |
| 1481 } | |
| 1482 | |
| 1483 if (countSeries == 0) | |
| 1484 { | |
| 1485 countSeries = 1; | |
| 1486 } | |
| 1487 } | |
| 1488 | |
| 1489 | |
| 1490 | |
| 1491 void ServerIndex::GetStatistics(Json::Value& target, | |
| 1492 const std::string& publicId) | |
| 1493 { | |
| 1494 boost::mutex::scoped_lock lock(mutex_); | |
| 1495 | |
| 1496 ResourceType type; | |
| 1497 int64_t top; | |
| 1498 if (!db_->LookupResource(publicId, top, type)) | |
| 1499 { | |
| 1500 throw OrthancException(ErrorCode_UnknownResource); | |
| 1501 } | |
| 1502 | |
| 1503 uint64_t uncompressedSize; | |
| 1504 uint64_t compressedSize; | |
| 1505 unsigned int countStudies; | |
| 1506 unsigned int countSeries; | |
| 1507 unsigned int countInstances; | |
| 1508 GetStatisticsInternal(compressedSize, uncompressedSize, countStudies, | |
| 1509 countSeries, countInstances, top, type); | |
| 1510 | |
|
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|
1511 target = Json::objectValue; |
|
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|
1512 target["DiskSize"] = boost::lexical_cast<std::string>(compressedSize); |
|
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|
1513 target["DiskSizeMB"] = boost::lexical_cast<unsigned int>(compressedSize / MEGA_BYTES); |
|
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|
1514 target["UncompressedSize"] = boost::lexical_cast<std::string>(uncompressedSize); |
|
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|
1515 target["UncompressedSizeMB"] = boost::lexical_cast<unsigned int>(uncompressedSize / MEGA_BYTES); |
|
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changeset
|
1516 |
|
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changeset
|
1517 switch (type) |
|
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|
1518 { |
|
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|
1519 // Do NOT add "break" below this point! |
|
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changeset
|
1520 case ResourceType_Patient: |
|
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|
1521 target["CountStudies"] = countStudies; |
|
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|
1522 |
|
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changeset
|
1523 case ResourceType_Study: |
|
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|
1524 target["CountSeries"] = countSeries; |
|
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changeset
|
1525 |
|
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changeset
|
1526 case ResourceType_Series: |
|
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|
1527 target["CountInstances"] = countInstances; |
|
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changeset
|
1528 |
|
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changeset
|
1529 case ResourceType_Instance: |
|
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diff
changeset
|
1530 default: |
|
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diff
changeset
|
1531 break; |
|
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changeset
|
1532 } |
|
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diff
changeset
|
1533 } |
|
511
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|
1534 |
|
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1535 |
| 646 | 1536 void ServerIndex::GetStatistics(/* out */ uint64_t& compressedSize, |
| 1537 /* out */ uint64_t& uncompressedSize, | |
| 1538 /* out */ unsigned int& countStudies, | |
| 1539 /* out */ unsigned int& countSeries, | |
| 1540 /* out */ unsigned int& countInstances, | |
| 1541 const std::string& publicId) | |
| 1542 { | |
| 1543 boost::mutex::scoped_lock lock(mutex_); | |
| 1544 | |
| 1545 ResourceType type; | |
| 1546 int64_t top; | |
| 1547 if (!db_->LookupResource(publicId, top, type)) | |
| 1548 { | |
| 1549 throw OrthancException(ErrorCode_UnknownResource); | |
| 1550 } | |
| 1551 | |
| 1552 GetStatisticsInternal(compressedSize, uncompressedSize, countStudies, | |
| 1553 countSeries, countInstances, top, type); | |
| 1554 } | |
| 1555 | |
| 1556 | |
|
511
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1557 void ServerIndex::UnstableResourcesMonitorThread(ServerIndex* that) |
|
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1558 { |
|
810
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|
1559 int stableAge = Configuration::GetGlobalIntegerParameter("StableAge", 60); |
|
511
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1560 if (stableAge <= 0) |
|
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1561 { |
|
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1562 stableAge = 60; |
|
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1563 } |
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|
1564 |
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|
1565 LOG(INFO) << "Starting the monitor for stable resources (stable age = " << stableAge << ")"; |
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1566 |
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|
1567 while (!that->done_) |
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1568 { |
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1569 // Check for stable resources each second |
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1570 boost::this_thread::sleep(boost::posix_time::seconds(1)); |
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|
1571 |
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|
1572 boost::mutex::scoped_lock lock(that->mutex_); |
| 513 | 1573 |
|
511
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1574 while (!that->unstableResources_.IsEmpty() && |
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1575 that->unstableResources_.GetOldestPayload().GetAge() > static_cast<unsigned int>(stableAge)) |
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|
1576 { |
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1577 // This DICOM resource has not received any new instance for |
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1578 // some time. It can be considered as stable. |
|
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|
1579 |
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|
1580 UnstableResourcePayload payload; |
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1581 int64_t id = that->unstableResources_.RemoveOldest(payload); |
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1582 |
| 513 | 1583 // Ensure that the resource is still existing before logging the change |
| 1584 if (that->db_->IsExistingResource(id)) | |
|
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1585 { |
| 513 | 1586 switch (payload.type_) |
| 1587 { | |
| 1588 case Orthanc::ResourceType_Patient: | |
| 1589 that->db_->LogChange(ChangeType_StablePatient, id, ResourceType_Patient); | |
| 1590 break; | |
|
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1591 |
| 513 | 1592 case Orthanc::ResourceType_Study: |
| 1593 that->db_->LogChange(ChangeType_StableStudy, id, ResourceType_Study); | |
| 1594 break; | |
|
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1595 |
| 513 | 1596 case Orthanc::ResourceType_Series: |
| 1597 that->db_->LogChange(ChangeType_StableSeries, id, ResourceType_Series); | |
| 1598 break; | |
| 1599 | |
| 1600 default: | |
| 1601 throw OrthancException(ErrorCode_InternalError); | |
| 1602 } | |
| 1603 | |
| 1604 //LOG(INFO) << "Stable resource: " << EnumerationToString(payload.type_) << " " << id; | |
|
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1605 } |
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1606 } |
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1607 } |
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|
1608 |
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|
1609 LOG(INFO) << "Closing the monitor thread for stable resources"; |
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1610 } |
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|
1611 |
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|
1612 |
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|
1613 void ServerIndex::MarkAsUnstable(int64_t id, |
|
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|
1614 Orthanc::ResourceType type) |
|
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1615 { |
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|
1616 // WARNING: Before calling this method, "mutex_" must be locked. |
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1617 |
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|
1618 assert(type == Orthanc::ResourceType_Patient || |
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|
1619 type == Orthanc::ResourceType_Study || |
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1620 type == Orthanc::ResourceType_Series); |
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1621 |
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|
1622 unstableResources_.AddOrMakeMostRecent(id, type); |
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1623 //LOG(INFO) << "Unstable resource: " << EnumerationToString(type) << " " << id; |
|
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|
1624 } |
| 521 | 1625 |
| 1626 | |
| 1627 | |
| 1628 void ServerIndex::LookupTagValue(std::list<std::string>& result, | |
| 1629 DicomTag tag, | |
| 615 | 1630 const std::string& value, |
| 1631 ResourceType type) | |
| 1632 { | |
| 1633 result.clear(); | |
| 1634 | |
| 1635 boost::mutex::scoped_lock lock(mutex_); | |
| 1636 | |
| 1637 std::list<int64_t> id; | |
| 1638 db_->LookupTagValue(id, tag, value); | |
| 1639 | |
| 1640 for (std::list<int64_t>::const_iterator | |
| 656 | 1641 it = id.begin(); it != id.end(); ++it) |
| 615 | 1642 { |
| 1643 if (db_->GetResourceType(*it) == type) | |
| 1644 { | |
| 1645 result.push_back(db_->GetPublicId(*it)); | |
| 1646 } | |
| 1647 } | |
| 1648 } | |
| 1649 | |
| 1650 | |
| 1651 void ServerIndex::LookupTagValue(std::list<std::string>& result, | |
| 1652 DicomTag tag, | |
| 521 | 1653 const std::string& value) |
| 1654 { | |
| 1655 result.clear(); | |
| 1656 | |
| 1657 boost::mutex::scoped_lock lock(mutex_); | |
| 1658 | |
| 1659 std::list<int64_t> id; | |
| 1660 db_->LookupTagValue(id, tag, value); | |
| 1661 | |
| 1662 for (std::list<int64_t>::const_iterator | |
| 656 | 1663 it = id.begin(); it != id.end(); ++it) |
| 521 | 1664 { |
| 1665 result.push_back(db_->GetPublicId(*it)); | |
| 1666 } | |
| 1667 } | |
| 1668 | |
| 1669 | |
|
1139
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diff
changeset
|
1670 void ServerIndex::LookupTagValue(std::list< std::pair<ResourceType, std::string> >& result, |
| 521 | 1671 const std::string& value) |
| 1672 { | |
| 1673 result.clear(); | |
| 1674 | |
| 1675 boost::mutex::scoped_lock lock(mutex_); | |
| 1676 | |
| 1677 std::list<int64_t> id; | |
| 1678 db_->LookupTagValue(id, value); | |
| 1679 | |
| 1680 for (std::list<int64_t>::const_iterator | |
| 656 | 1681 it = id.begin(); it != id.end(); ++it) |
| 521 | 1682 { |
|
1139
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|
1683 result.push_back(std::make_pair(db_->GetResourceType(*it), |
|
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|
1684 db_->GetPublicId(*it))); |
| 521 | 1685 } |
| 1686 } | |
|
699
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|
1687 |
|
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|
1688 |
|
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|
1689 StoreStatus ServerIndex::AddAttachment(const FileInfo& attachment, |
|
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|
1690 const std::string& publicId) |
|
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|
1691 { |
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|
1692 boost::mutex::scoped_lock lock(mutex_); |
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|
1693 |
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|
1694 Transaction t(*this); |
|
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1695 |
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1696 ResourceType resourceType; |
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1697 int64_t resourceId; |
|
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1698 if (!db_->LookupResource(publicId, resourceId, resourceType)) |
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1699 { |
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1700 return StoreStatus_Failure; // Inexistent resource |
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1701 } |
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1702 |
|
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|
1703 // Remove possible previous attachment |
|
699
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1704 db_->DeleteAttachment(resourceId, attachment.GetContentType()); |
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1705 |
|
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|
1706 // Locate the patient of the target resource |
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1707 int64_t patientId = resourceId; |
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1708 for (;;) |
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1709 { |
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1710 int64_t parent; |
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1711 if (db_->LookupParent(parent, patientId)) |
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1712 { |
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1713 // We have not reached the patient level yet |
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1714 patientId = parent; |
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1715 } |
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|
1716 else |
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|
1717 { |
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1718 // We have reached the patient level |
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1719 break; |
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1720 } |
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1721 } |
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|
1722 |
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1723 // Possibly apply the recycling mechanism while preserving this patient |
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1724 assert(db_->GetResourceType(patientId) == ResourceType_Patient); |
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1725 Recycle(attachment.GetCompressedSize(), db_->GetPublicId(patientId)); |
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1726 |
|
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|
1727 db_->AddAttachment(resourceId, attachment); |
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1728 |
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1729 t.Commit(attachment.GetCompressedSize()); |
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1730 |
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1731 return StoreStatus_Success; |
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1732 } |
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|
1733 |
|
702
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|
1734 |
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|
1735 void ServerIndex::DeleteAttachment(const std::string& publicId, |
|
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|
1736 FileContentType type) |
|
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|
1737 { |
|
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|
1738 boost::mutex::scoped_lock lock(mutex_); |
|
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1739 listener_->Reset(); |
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1740 |
|
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1741 Transaction t(*this); |
|
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1742 |
|
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1743 ResourceType rtype; |
|
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1744 int64_t id; |
|
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1745 if (!db_->LookupResource(publicId, id, rtype)) |
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|
1746 { |
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1747 throw OrthancException(ErrorCode_UnknownResource); |
|
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1748 } |
|
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|
1749 |
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|
1750 db_->DeleteAttachment(id, type); |
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1751 |
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|
1752 t.Commit(0); |
|
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1753 } |
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|
1754 |
|
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1755 |
|
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|
1756 bool ServerIndex::GetMetadata(Json::Value& target, |
|
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1757 const std::string& publicId) |
|
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1758 { |
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|
1759 boost::mutex::scoped_lock lock(mutex_); |
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|
1760 |
|
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|
1761 target = Json::objectValue; |
|
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1762 |
|
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|
1763 ResourceType type; |
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1764 int64_t id; |
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1765 if (!db_->LookupResource(publicId, id, type)) |
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|
1766 { |
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|
1767 return false; |
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|
1768 } |
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|
1769 |
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1770 std::list<MetadataType> metadata; |
|
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|
1771 db_->ListAvailableMetadata(metadata, id); |
|
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|
1772 |
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|
1773 for (std::list<MetadataType>::const_iterator |
|
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1774 it = metadata.begin(); it != metadata.end(); it++) |
|
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|
1775 { |
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|
1776 std::string key = EnumerationToString(*it); |
|
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|
1777 std::string value = db_->GetMetadata(id, *it); |
|
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|
1778 target[key] = value; |
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|
1779 } |
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|
1780 |
|
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|
1781 return true; |
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|
1782 } |
|
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|
1783 |
|
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|
1784 |
| 0 | 1785 } |