Mercurial > hg > orthanc
annotate OrthancServer/ServerIndex.cpp @ 1759:e268412adcf1 db-changes
removal of old implementation of search
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 28 Oct 2015 12:59:18 +0100 |
parents | 98abb8d7f905 |
children | 613df4362575 |
rev | line source |
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0 | 1 /** |
62 | 2 * Orthanc - A Lightweight, RESTful DICOM Store |
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
0 | 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 | |
1198 | 40 #include "ServerIndexChange.h" |
8 | 41 #include "EmbeddedResources.h" |
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42 #include "OrthancInitialization.h" |
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43 #include "ServerToolbox.h" |
0 | 44 #include "../Core/Toolbox.h" |
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45 #include "../Core/Logging.h" |
0 | 46 #include "../Core/Uuid.h" |
47 #include "../Core/DicomFormat/DicomArray.h" | |
1747 | 48 #include "Search/LookupIdentifierQuery.h" |
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49 #include "Search/LookupResource.h" |
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50 |
0 | 51 #include "FromDcmtkBridge.h" |
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52 #include "ServerContext.h" |
0 | 53 |
54 #include <boost/lexical_cast.hpp> | |
55 #include <stdio.h> | |
56 | |
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57 static const uint64_t MEGA_BYTES = 1024 * 1024; |
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58 |
62 | 59 namespace Orthanc |
0 | 60 { |
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61 class ServerIndex::Listener : public IDatabaseListener |
0 | 62 { |
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63 private: |
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64 struct FileToRemove |
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65 { |
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66 private: |
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67 std::string uuid_; |
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68 FileContentType type_; |
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69 |
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70 public: |
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71 FileToRemove(const FileInfo& info) : uuid_(info.GetUuid()), |
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72 type_(info.GetContentType()) |
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73 { |
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74 } |
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75 |
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76 const std::string& GetUuid() const |
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77 { |
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78 return uuid_; |
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79 } |
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80 |
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81 FileContentType GetContentType() const |
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82 { |
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83 return type_; |
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84 } |
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85 }; |
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86 |
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87 ServerContext& context_; |
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88 bool hasRemainingLevel_; |
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89 ResourceType remainingType_; |
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90 std::string remainingPublicId_; |
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91 std::list<FileToRemove> pendingFilesToRemove_; |
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92 std::list<ServerIndexChange> pendingChanges_; |
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93 uint64_t sizeOfFilesToRemove_; |
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94 bool insideTransaction_; |
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95 |
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96 void Reset() |
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97 { |
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98 sizeOfFilesToRemove_ = 0; |
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99 hasRemainingLevel_ = false; |
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100 pendingFilesToRemove_.clear(); |
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101 pendingChanges_.clear(); |
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102 } |
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103 |
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104 public: |
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105 Listener(ServerContext& context) : context_(context), |
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106 insideTransaction_(false) |
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107 { |
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108 Reset(); |
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109 assert(ResourceType_Patient < ResourceType_Study && |
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110 ResourceType_Study < ResourceType_Series && |
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111 ResourceType_Series < ResourceType_Instance); |
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112 } |
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113 |
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114 void StartTransaction() |
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115 { |
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116 Reset(); |
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117 insideTransaction_ = true; |
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118 } |
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119 |
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120 void EndTransaction() |
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121 { |
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122 insideTransaction_ = false; |
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123 } |
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124 |
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125 uint64_t GetSizeOfFilesToRemove() |
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126 { |
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127 return sizeOfFilesToRemove_; |
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128 } |
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129 |
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130 void CommitFilesToRemove() |
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131 { |
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132 for (std::list<FileToRemove>::const_iterator |
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133 it = pendingFilesToRemove_.begin(); |
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134 it != pendingFilesToRemove_.end(); ++it) |
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135 { |
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136 context_.RemoveFile(it->GetUuid(), it->GetContentType()); |
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137 } |
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138 } |
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139 |
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140 void CommitChanges() |
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141 { |
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142 for (std::list<ServerIndexChange>::const_iterator |
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143 it = pendingChanges_.begin(); |
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144 it != pendingChanges_.end(); ++it) |
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145 { |
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146 context_.SignalChange(*it); |
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147 } |
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148 } |
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149 |
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150 virtual void SignalRemainingAncestor(ResourceType parentType, |
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151 const std::string& publicId) |
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152 { |
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153 VLOG(1) << "Remaining ancestor \"" << publicId << "\" (" << parentType << ")"; |
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154 |
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155 if (hasRemainingLevel_) |
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156 { |
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157 if (parentType < remainingType_) |
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158 { |
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159 remainingType_ = parentType; |
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160 remainingPublicId_ = publicId; |
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161 } |
1158 | 162 } |
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163 else |
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164 { |
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165 hasRemainingLevel_ = true; |
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166 remainingType_ = parentType; |
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167 remainingPublicId_ = publicId; |
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168 } |
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169 } |
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170 |
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171 virtual void SignalFileDeleted(const FileInfo& info) |
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172 { |
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173 assert(Toolbox::IsUuid(info.GetUuid())); |
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174 pendingFilesToRemove_.push_back(FileToRemove(info)); |
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175 sizeOfFilesToRemove_ += info.GetCompressedSize(); |
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176 } |
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177 |
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178 virtual void SignalChange(const ServerIndexChange& change) |
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179 { |
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180 VLOG(1) << "Change related to resource " << change.GetPublicId() << " of type " |
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181 << EnumerationToString(change.GetResourceType()) << ": " |
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182 << EnumerationToString(change.GetChangeType()); |
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183 |
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184 if (insideTransaction_) |
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185 { |
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186 pendingChanges_.push_back(change); |
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187 } |
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188 else |
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189 { |
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190 context_.SignalChange(change); |
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191 } |
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192 } |
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193 |
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194 bool HasRemainingLevel() const |
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195 { |
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196 return hasRemainingLevel_; |
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197 } |
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198 |
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199 ResourceType GetRemainingType() const |
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200 { |
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201 assert(HasRemainingLevel()); |
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202 return remainingType_; |
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203 } |
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204 |
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205 const std::string& GetRemainingPublicId() const |
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206 { |
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207 assert(HasRemainingLevel()); |
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208 return remainingPublicId_; |
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209 } |
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210 }; |
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212 | |
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213 class ServerIndex::Transaction |
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214 { |
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215 private: |
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216 ServerIndex& index_; |
1235 | 217 std::auto_ptr<SQLite::ITransaction> transaction_; |
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218 bool isCommitted_; |
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219 |
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220 public: |
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221 Transaction(ServerIndex& index) : |
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222 index_(index), |
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223 isCommitted_(false) |
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224 { |
1247 | 225 transaction_.reset(index_.db_.StartTransaction()); |
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226 transaction_->Begin(); |
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227 |
1270 | 228 assert(index_.currentStorageSize_ == index_.db_.GetTotalCompressedSize()); |
229 | |
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230 index_.listener_->StartTransaction(); |
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231 } |
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232 |
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233 ~Transaction() |
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234 { |
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235 index_.listener_->EndTransaction(); |
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236 |
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237 if (!isCommitted_) |
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238 { |
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239 transaction_->Rollback(); |
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240 } |
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241 } |
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242 |
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243 void Commit(uint64_t sizeOfAddedFiles) |
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244 { |
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245 if (!isCommitted_) |
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246 { |
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247 transaction_->Commit(); |
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248 |
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249 // We can remove the files once the SQLite transaction has |
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250 // been successfully committed. Some files might have to be |
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251 // deleted because of recycling. |
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252 index_.listener_->CommitFilesToRemove(); |
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253 |
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254 index_.currentStorageSize_ += sizeOfAddedFiles; |
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255 |
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256 assert(index_.currentStorageSize_ >= index_.listener_->GetSizeOfFilesToRemove()); |
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257 index_.currentStorageSize_ -= index_.listener_->GetSizeOfFilesToRemove(); |
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258 |
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259 // Send all the pending changes to the Orthanc plugins |
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260 index_.listener_->CommitChanges(); |
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261 |
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262 isCommitted_ = true; |
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263 } |
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264 } |
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265 }; |
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266 |
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267 |
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268 class ServerIndex::UnstableResourcePayload |
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269 { |
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270 private: |
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271 ResourceType type_; |
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272 std::string publicId_; |
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273 boost::posix_time::ptime time_; |
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274 |
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275 public: |
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276 UnstableResourcePayload() : type_(ResourceType_Instance) |
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277 { |
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278 } |
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279 |
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280 UnstableResourcePayload(Orthanc::ResourceType type, |
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281 const std::string& publicId) : |
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282 type_(type), |
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283 publicId_(publicId) |
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284 { |
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285 time_ = boost::posix_time::second_clock::local_time(); |
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286 } |
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287 |
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288 unsigned int GetAge() const |
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289 { |
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290 return (boost::posix_time::second_clock::local_time() - time_).total_seconds(); |
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291 } |
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292 |
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293 ResourceType GetResourceType() const |
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294 { |
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295 return type_; |
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296 } |
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297 |
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298 const std::string& GetPublicId() const |
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299 { |
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300 return publicId_; |
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301 } |
511
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302 }; |
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303 |
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304 |
212 | 305 bool ServerIndex::DeleteResource(Json::Value& target, |
0 | 306 const std::string& uuid, |
202 | 307 ResourceType expectedType) |
0 | 308 { |
206
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309 boost::mutex::scoped_lock lock(mutex_); |
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310 |
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311 Transaction t(*this); |
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312 |
202 | 313 int64_t id; |
314 ResourceType type; | |
1294 | 315 if (!db_.LookupResource(id, type, uuid) || |
202 | 316 expectedType != type) |
0 | 317 { |
318 return false; | |
319 } | |
202 | 320 |
1247 | 321 db_.DeleteResource(id); |
0 | 322 |
202 | 323 if (listener_->HasRemainingLevel()) |
0 | 324 { |
202 | 325 ResourceType type = listener_->GetRemainingType(); |
326 const std::string& uuid = listener_->GetRemainingPublicId(); | |
0 | 327 |
328 target["RemainingAncestor"] = Json::Value(Json::objectValue); | |
204 | 329 target["RemainingAncestor"]["Path"] = GetBasePath(type, uuid); |
434
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330 target["RemainingAncestor"]["Type"] = EnumerationToString(type); |
0 | 331 target["RemainingAncestor"]["ID"] = uuid; |
332 } | |
333 else | |
334 { | |
335 target["RemainingAncestor"] = Json::nullValue; | |
336 } | |
337 | |
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338 t.Commit(0); |
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339 |
0 | 340 return true; |
341 } | |
342 | |
343 | |
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344 void ServerIndex::FlushThread(ServerIndex* that) |
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345 { |
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346 // By default, wait for 10 seconds before flushing |
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347 unsigned int sleep = 10; |
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348 |
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349 try |
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350 { |
744 | 351 boost::mutex::scoped_lock lock(that->mutex_); |
1239 | 352 std::string sleepString; |
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353 |
1247 | 354 if (that->db_.LookupGlobalProperty(sleepString, GlobalProperty_FlushSleep) && |
1239 | 355 Toolbox::IsInteger(sleepString)) |
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356 { |
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357 sleep = boost::lexical_cast<unsigned int>(sleepString); |
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358 } |
511
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359 } |
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360 catch (boost::bad_lexical_cast&) |
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361 { |
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362 } |
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363 |
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364 LOG(INFO) << "Starting the database flushing thread (sleep = " << sleep << ")"; |
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365 |
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366 unsigned int count = 0; |
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367 |
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368 while (!that->done_) |
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369 { |
511
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370 boost::this_thread::sleep(boost::posix_time::seconds(1)); |
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371 count++; |
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372 if (count < sleep) |
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373 { |
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374 continue; |
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375 } |
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376 |
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377 boost::mutex::scoped_lock lock(that->mutex_); |
1247 | 378 that->db_.FlushToDisk(); |
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379 count = 0; |
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380 } |
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381 |
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382 LOG(INFO) << "Stopping the database flushing thread"; |
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383 } |
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384 |
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385 |
1247 | 386 static void ComputeExpectedNumberOfInstances(IDatabaseWrapper& db, |
433 | 387 int64_t series, |
388 const DicomMap& dicomSummary) | |
389 { | |
390 try | |
391 { | |
656 | 392 const DicomValue* value; |
393 const DicomValue* value2; | |
394 | |
433 | 395 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGES_IN_ACQUISITION)) != NULL && |
396 (value2 = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_TEMPORAL_POSITIONS)) != NULL) | |
397 { | |
398 // Patch for series with temporal positions thanks to Will Ryder | |
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399 int64_t imagesInAcquisition = boost::lexical_cast<int64_t>(value->GetContent()); |
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400 int64_t countTemporalPositions = boost::lexical_cast<int64_t>(value2->GetContent()); |
433 | 401 std::string expected = boost::lexical_cast<std::string>(imagesInAcquisition * countTemporalPositions); |
402 db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, expected); | |
403 } | |
404 | |
405 else if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_SLICES)) != NULL && | |
406 (value2 = dicomSummary.TestAndGetValue(DICOM_TAG_NUMBER_OF_TIME_SLICES)) != NULL) | |
407 { | |
408 // Support of Cardio-PET images | |
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409 int64_t numberOfSlices = boost::lexical_cast<int64_t>(value->GetContent()); |
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410 int64_t numberOfTimeSlices = boost::lexical_cast<int64_t>(value2->GetContent()); |
433 | 411 std::string expected = boost::lexical_cast<std::string>(numberOfSlices * numberOfTimeSlices); |
412 db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, expected); | |
413 } | |
414 | |
415 else if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_CARDIAC_NUMBER_OF_IMAGES)) != NULL) | |
416 { | |
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417 db.SetMetadata(series, MetadataType_Series_ExpectedNumberOfInstances, value->GetContent()); |
433 | 418 } |
419 } | |
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420 catch (OrthancException&) |
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421 { |
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422 } |
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423 catch (boost::bad_lexical_cast&) |
433 | 424 { |
425 } | |
426 } | |
427 | |
428 | |
1237 | 429 |
430 | |
1238 | 431 bool ServerIndex::GetMetadataAsInteger(int64_t& result, |
1237 | 432 int64_t id, |
433 MetadataType type) | |
434 { | |
1238 | 435 std::string s; |
1247 | 436 if (!db_.LookupMetadata(s, id, type)) |
1237 | 437 { |
438 return false; | |
439 } | |
440 | |
441 try | |
442 { | |
1238 | 443 result = boost::lexical_cast<int64_t>(s); |
1237 | 444 return true; |
445 } | |
446 catch (boost::bad_lexical_cast&) | |
447 { | |
448 return false; | |
449 } | |
450 } | |
451 | |
452 | |
1297 | 453 void ServerIndex::LogChange(int64_t internalId, |
454 ChangeType changeType, | |
455 ResourceType resourceType, | |
456 const std::string& publicId) | |
457 { | |
458 ServerIndexChange change(changeType, resourceType, publicId); | |
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459 |
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460 if (changeType <= ChangeType_INTERNAL_LastLogged) |
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461 { |
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462 db_.LogChange(internalId, change); |
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463 } |
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464 |
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465 assert(listener_.get() != NULL); |
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466 listener_->SignalChange(change); |
1297 | 467 } |
468 | |
1237 | 469 |
470 uint64_t ServerIndex::IncrementGlobalSequenceInternal(GlobalProperty property) | |
471 { | |
472 std::string oldValue; | |
473 | |
1247 | 474 if (db_.LookupGlobalProperty(oldValue, property)) |
1237 | 475 { |
476 uint64_t oldNumber; | |
477 | |
478 try | |
479 { | |
480 oldNumber = boost::lexical_cast<uint64_t>(oldValue); | |
1247 | 481 db_.SetGlobalProperty(property, boost::lexical_cast<std::string>(oldNumber + 1)); |
1237 | 482 return oldNumber + 1; |
483 } | |
484 catch (boost::bad_lexical_cast&) | |
485 { | |
486 throw OrthancException(ErrorCode_InternalError); | |
487 } | |
488 } | |
489 else | |
490 { | |
491 // Initialize the sequence at "1" | |
1247 | 492 db_.SetGlobalProperty(property, "1"); |
1237 | 493 return 1; |
494 } | |
495 } | |
496 | |
497 | |
498 | |
1299 | 499 int64_t ServerIndex::CreateResource(const std::string& publicId, |
500 ResourceType type) | |
501 { | |
502 int64_t id = db_.CreateResource(publicId, type); | |
503 | |
504 ChangeType changeType; | |
505 switch (type) | |
506 { | |
507 case ResourceType_Patient: | |
508 changeType = ChangeType_NewPatient; | |
509 break; | |
510 | |
511 case ResourceType_Study: | |
512 changeType = ChangeType_NewStudy; | |
513 break; | |
514 | |
515 case ResourceType_Series: | |
516 changeType = ChangeType_NewSeries; | |
517 break; | |
518 | |
519 case ResourceType_Instance: | |
520 changeType = ChangeType_NewInstance; | |
521 break; | |
522 | |
523 default: | |
524 throw OrthancException(ErrorCode_InternalError); | |
525 } | |
526 | |
527 ServerIndexChange change(changeType, type, publicId); | |
528 db_.LogChange(id, change); | |
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529 |
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530 assert(listener_.get() != NULL); |
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531 listener_->SignalChange(change); |
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532 |
1299 | 533 return id; |
534 } | |
535 | |
1286 | 536 |
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537 ServerIndex::ServerIndex(ServerContext& context, |
1247 | 538 IDatabaseWrapper& db) : |
511
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539 done_(false), |
1247 | 540 db_(db), |
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541 maximumStorageSize_(0), |
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542 maximumPatients_(0) |
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543 { |
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544 listener_.reset(new Listener(context)); |
1247 | 545 db_.SetListener(*listener_); |
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546 |
1247 | 547 currentStorageSize_ = db_.GetTotalCompressedSize(); |
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548 |
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549 // Initial recycling if the parameters have changed since the last |
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550 // execution of Orthanc |
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551 StandaloneRecycling(); |
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552 |
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553 if (db.HasFlushToDisk()) |
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554 { |
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555 flushThread_ = boost::thread(FlushThread, this); |
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556 } |
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557 |
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558 unstableResourcesMonitorThread_ = boost::thread(UnstableResourcesMonitorThread, this); |
206
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559 } |
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560 |
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561 |
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562 |
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563 ServerIndex::~ServerIndex() |
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564 { |
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565 if (!done_) |
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566 { |
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567 LOG(ERROR) << "INTERNAL ERROR: ServerIndex::Stop() should be invoked manually to avoid mess in the destruction order!"; |
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568 Stop(); |
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569 } |
0 | 570 } |
571 | |
572 | |
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573 |
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574 void ServerIndex::Stop() |
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575 { |
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576 if (!done_) |
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577 { |
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578 done_ = true; |
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579 |
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580 if (db_.HasFlushToDisk() && |
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581 flushThread_.joinable()) |
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582 { |
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583 flushThread_.join(); |
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584 } |
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585 |
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586 if (unstableResourcesMonitorThread_.joinable()) |
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587 { |
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588 unstableResourcesMonitorThread_.join(); |
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589 } |
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590 } |
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591 } |
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592 |
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593 |
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594 |
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595 StoreStatus ServerIndex::Store(std::map<MetadataType, std::string>& instanceMetadata, |
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596 const DicomMap& dicomSummary, |
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597 const Attachments& attachments, |
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598 const std::string& remoteAet, |
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599 const MetadataMap& metadata) |
0 | 600 { |
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601 boost::mutex::scoped_lock lock(mutex_); |
0 | 602 |
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603 instanceMetadata.clear(); |
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604 |
178 | 605 DicomInstanceHasher hasher(dicomSummary); |
0 | 606 |
607 try | |
608 { | |
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609 Transaction t(*this); |
0 | 610 |
202 | 611 // Do nothing if the instance already exists |
0 | 612 { |
432 | 613 ResourceType type; |
614 int64_t tmp; | |
1294 | 615 if (db_.LookupResource(tmp, type, hasher.HashInstance())) |
432 | 616 { |
617 assert(type == ResourceType_Instance); | |
1247 | 618 db_.GetAllMetadata(instanceMetadata, tmp); |
432 | 619 return StoreStatus_AlreadyStored; |
620 } | |
0 | 621 } |
622 | |
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623 // Ensure there is enough room in the storage for the new instance |
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624 uint64_t instanceSize = 0; |
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625 for (Attachments::const_iterator it = attachments.begin(); |
656 | 626 it != attachments.end(); ++it) |
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627 { |
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628 instanceSize += it->GetCompressedSize(); |
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629 } |
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630 |
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631 Recycle(instanceSize, hasher.HashPatient()); |
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632 |
202 | 633 // Create the instance |
1299 | 634 int64_t instance = CreateResource(hasher.HashInstance(), ResourceType_Instance); |
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635 Toolbox::SetMainDicomTags(db_, instance, ResourceType_Instance, dicomSummary); |
202 | 636 |
432 | 637 // Detect up to which level the patient/study/series/instance |
638 // hierarchy must be created | |
639 int64_t patient = -1, study = -1, series = -1; | |
640 bool isNewPatient = false; | |
641 bool isNewStudy = false; | |
642 bool isNewSeries = false; | |
643 | |
0 | 644 { |
432 | 645 ResourceType dummy; |
646 | |
1294 | 647 if (db_.LookupResource(series, dummy, hasher.HashSeries())) |
432 | 648 { |
649 assert(dummy == ResourceType_Series); | |
650 // The patient, the study and the series already exist | |
651 | |
1294 | 652 bool ok = (db_.LookupResource(patient, dummy, hasher.HashPatient()) && |
653 db_.LookupResource(study, dummy, hasher.HashStudy())); | |
432 | 654 assert(ok); |
655 } | |
1294 | 656 else if (db_.LookupResource(study, dummy, hasher.HashStudy())) |
432 | 657 { |
658 assert(dummy == ResourceType_Study); | |
659 | |
660 // New series: The patient and the study already exist | |
661 isNewSeries = true; | |
662 | |
1294 | 663 bool ok = db_.LookupResource(patient, dummy, hasher.HashPatient()); |
432 | 664 assert(ok); |
665 } | |
1294 | 666 else if (db_.LookupResource(patient, dummy, hasher.HashPatient())) |
432 | 667 { |
668 assert(dummy == ResourceType_Patient); | |
669 | |
670 // New study and series: The patient already exist | |
671 isNewStudy = true; | |
672 isNewSeries = true; | |
673 } | |
674 else | |
675 { | |
676 // New patient, study and series: Nothing exists | |
677 isNewPatient = true; | |
678 isNewStudy = true; | |
679 isNewSeries = true; | |
680 } | |
681 } | |
682 | |
683 // Create the series if needed | |
684 if (isNewSeries) | |
685 { | |
1299 | 686 series = CreateResource(hasher.HashSeries(), ResourceType_Series); |
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687 Toolbox::SetMainDicomTags(db_, series, ResourceType_Series, dicomSummary); |
432 | 688 } |
202 | 689 |
432 | 690 // Create the study if needed |
691 if (isNewStudy) | |
692 { | |
1299 | 693 study = CreateResource(hasher.HashStudy(), ResourceType_Study); |
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694 Toolbox::SetMainDicomTags(db_, study, ResourceType_Study, dicomSummary); |
432 | 695 } |
696 | |
697 // Create the patient if needed | |
698 if (isNewPatient) | |
699 { | |
1299 | 700 patient = CreateResource(hasher.HashPatient(), ResourceType_Patient); |
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701 Toolbox::SetMainDicomTags(db_, patient, ResourceType_Patient, dicomSummary); |
432 | 702 } |
202 | 703 |
432 | 704 // Create the parent-to-child links |
1247 | 705 db_.AttachChild(series, instance); |
432 | 706 |
707 if (isNewSeries) | |
708 { | |
1247 | 709 db_.AttachChild(study, series); |
0 | 710 } |
432 | 711 |
712 if (isNewStudy) | |
0 | 713 { |
1247 | 714 db_.AttachChild(patient, study); |
0 | 715 } |
716 | |
432 | 717 // Sanity checks |
718 assert(patient != -1); | |
719 assert(study != -1); | |
720 assert(series != -1); | |
721 assert(instance != -1); | |
722 | |
202 | 723 // Attach the files to the newly created instance |
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724 for (Attachments::const_iterator it = attachments.begin(); |
656 | 725 it != attachments.end(); ++it) |
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726 { |
1247 | 727 db_.AddAttachment(instance, *it); |
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728 } |
202 | 729 |
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730 // Attach the user-specified metadata |
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731 for (MetadataMap::const_iterator |
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732 it = metadata.begin(); it != metadata.end(); ++it) |
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733 { |
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734 switch (it->first.first) |
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735 { |
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736 case ResourceType_Patient: |
1247 | 737 db_.SetMetadata(patient, it->first.second, it->second); |
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738 break; |
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739 |
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740 case ResourceType_Study: |
1247 | 741 db_.SetMetadata(study, it->first.second, it->second); |
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742 break; |
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743 |
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744 case ResourceType_Series: |
1247 | 745 db_.SetMetadata(series, it->first.second, it->second); |
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746 break; |
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747 |
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748 case ResourceType_Instance: |
1247 | 749 db_.SetMetadata(instance, it->first.second, it->second); |
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750 instanceMetadata[it->first.second] = it->second; |
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751 break; |
1002
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anonymization refactoring
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parents:
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diff
changeset
|
752 |
1006
649d47854314
proper handling of metadata in Store
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parents:
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diff
changeset
|
753 default: |
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
754 throw OrthancException(ErrorCode_ParameterOutOfRange); |
1002
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anonymization refactoring
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parents:
831
diff
changeset
|
755 } |
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diff
changeset
|
756 } |
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anonymization refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
757 |
1004
a226e0959d8b
DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
758 // Attach the auto-computed metadata for the patient/study/series levels |
432 | 759 std::string now = Toolbox::GetNowIsoString(); |
1247 | 760 db_.SetMetadata(series, MetadataType_LastUpdate, now); |
761 db_.SetMetadata(study, MetadataType_LastUpdate, now); | |
762 db_.SetMetadata(patient, MetadataType_LastUpdate, now); | |
1004
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DicomInstanceToStore
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parents:
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diff
changeset
|
763 |
a226e0959d8b
DicomInstanceToStore
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1002
diff
changeset
|
764 // Attach the auto-computed metadata for the instance level, |
a226e0959d8b
DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
765 // reflecting these additions into the input metadata map |
1247 | 766 db_.SetMetadata(instance, MetadataType_Instance_ReceptionDate, now); |
1006
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1004
diff
changeset
|
767 instanceMetadata[MetadataType_Instance_ReceptionDate] = now; |
202 | 768 |
1247 | 769 db_.SetMetadata(instance, MetadataType_Instance_RemoteAet, remoteAet); |
1006
649d47854314
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Sebastien Jodogne <s.jodogne@gmail.com>
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1004
diff
changeset
|
770 instanceMetadata[MetadataType_Instance_RemoteAet] = remoteAet; |
1004
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DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
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|
771 |
202 | 772 const DicomValue* value; |
773 if ((value = dicomSummary.TestAndGetValue(DICOM_TAG_INSTANCE_NUMBER)) != NULL || | |
774 (value = dicomSummary.TestAndGetValue(DICOM_TAG_IMAGE_INDEX)) != NULL) | |
0 | 775 { |
1737
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parents:
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diff
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|
776 if (!value->IsNull() && |
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777 !value->IsBinary()) |
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|
778 { |
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diff
changeset
|
779 db_.SetMetadata(instance, MetadataType_Instance_IndexInSeries, value->GetContent()); |
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diff
changeset
|
780 instanceMetadata[MetadataType_Instance_IndexInSeries] = value->GetContent(); |
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diff
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|
781 } |
0 | 782 } |
783 | |
1004
a226e0959d8b
DicomInstanceToStore
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parents:
1002
diff
changeset
|
784 // Check whether the series of this new instance is now completed |
202 | 785 if (isNewSeries) |
786 { | |
1247 | 787 ComputeExpectedNumberOfInstances(db_, series, dicomSummary); |
202 | 788 } |
789 | |
205
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parents:
204
diff
changeset
|
790 SeriesStatus seriesStatus = GetSeriesStatus(series); |
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|
791 if (seriesStatus == SeriesStatus_Complete) |
6ab754744446
logging of completed series
Sebastien Jodogne <s.jodogne@gmail.com>
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|
792 { |
1237 | 793 LogChange(series, ChangeType_CompletedSeries, ResourceType_Series, hasher.HashSeries()); |
205
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diff
changeset
|
794 } |
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logging of completed series
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parents:
204
diff
changeset
|
795 |
511
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
796 // Mark the parent resources of this instance as unstable |
1177
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Plugins can monitor changes through callbacks
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
797 MarkAsUnstable(series, ResourceType_Series, hasher.HashSeries()); |
5b2d8c280ac2
Plugins can monitor changes through callbacks
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1162
diff
changeset
|
798 MarkAsUnstable(study, ResourceType_Study, hasher.HashStudy()); |
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diff
changeset
|
799 MarkAsUnstable(patient, ResourceType_Patient, hasher.HashPatient()); |
511
3b735fdf320b
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diff
changeset
|
800 |
278
771f12042be9
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diff
changeset
|
801 t.Commit(instanceSize); |
268
4bc02e2254ec
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264
diff
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|
802 |
0 | 803 return StoreStatus_Success; |
804 } | |
62 | 805 catch (OrthancException& e) |
0 | 806 { |
1247 | 807 LOG(ERROR) << "EXCEPTION [" << e.What() << "]"; |
0 | 808 } |
809 | |
810 return StoreStatus_Failure; | |
811 } | |
812 | |
813 | |
238 | 814 void ServerIndex::ComputeStatistics(Json::Value& target) |
0 | 815 { |
206
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816 boost::mutex::scoped_lock lock(mutex_); |
238 | 817 target = Json::objectValue; |
0 | 818 |
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|
819 uint64_t cs = currentStorageSize_; |
1247 | 820 assert(cs == db_.GetTotalCompressedSize()); |
821 uint64_t us = db_.GetTotalUncompressedSize(); | |
440
23e5b35e3c5c
statistics for patient/studies/series/instances
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
438
diff
changeset
|
822 target["TotalDiskSize"] = boost::lexical_cast<std::string>(cs); |
238 | 823 target["TotalUncompressedSize"] = boost::lexical_cast<std::string>(us); |
1310
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custom database back-end
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1306
diff
changeset
|
824 target["TotalDiskSizeMB"] = static_cast<unsigned int>(cs / MEGA_BYTES); |
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Sebastien Jodogne <s.jodogne@gmail.com>
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|
825 target["TotalUncompressedSizeMB"] = static_cast<unsigned int>(us / MEGA_BYTES); |
238 | 826 |
1247 | 827 target["CountPatients"] = static_cast<unsigned int>(db_.GetResourceCount(ResourceType_Patient)); |
828 target["CountStudies"] = static_cast<unsigned int>(db_.GetResourceCount(ResourceType_Study)); | |
829 target["CountSeries"] = static_cast<unsigned int>(db_.GetResourceCount(ResourceType_Series)); | |
830 target["CountInstances"] = static_cast<unsigned int>(db_.GetResourceCount(ResourceType_Instance)); | |
238 | 831 } |
832 | |
187
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|
833 |
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|
834 |
585 | 835 SeriesStatus ServerIndex::GetSeriesStatus(int64_t id) |
199 | 836 { |
837 // Get the expected number of instances in this series (from the metadata) | |
1238 | 838 int64_t expected; |
839 if (!GetMetadataAsInteger(expected, id, MetadataType_Series_ExpectedNumberOfInstances)) | |
199 | 840 { |
841 return SeriesStatus_Unknown; | |
842 } | |
843 | |
844 // Loop over the instances of this series | |
845 std::list<int64_t> children; | |
1247 | 846 db_.GetChildrenInternalId(children, id); |
199 | 847 |
1238 | 848 std::set<int64_t> instances; |
199 | 849 for (std::list<int64_t>::const_iterator |
656 | 850 it = children.begin(); it != children.end(); ++it) |
199 | 851 { |
852 // Get the index of this instance in the series | |
1238 | 853 int64_t index; |
854 if (!GetMetadataAsInteger(index, *it, MetadataType_Instance_IndexInSeries)) | |
199 | 855 { |
856 return SeriesStatus_Unknown; | |
857 } | |
858 | |
656 | 859 if (!(index > 0 && index <= expected)) |
199 | 860 { |
861 // Out-of-range instance index | |
862 return SeriesStatus_Inconsistent; | |
863 } | |
864 | |
865 if (instances.find(index) != instances.end()) | |
866 { | |
867 // Twice the same instance index | |
868 return SeriesStatus_Inconsistent; | |
869 } | |
870 | |
871 instances.insert(index); | |
872 } | |
873 | |
1238 | 874 if (static_cast<int64_t>(instances.size()) == expected) |
199 | 875 { |
876 return SeriesStatus_Complete; | |
877 } | |
878 else | |
879 { | |
880 return SeriesStatus_Missing; | |
881 } | |
882 } | |
883 | |
884 | |
202 | 885 void ServerIndex::MainDicomTagsToJson(Json::Value& target, |
1668
de1413733c97
reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
886 int64_t resourceId, |
de1413733c97
reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
887 ResourceType resourceType) |
198
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|
888 { |
663cc6c46d0a
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parents:
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diff
changeset
|
889 DicomMap tags; |
1247 | 890 db_.GetMainDicomTags(tags, resourceId); |
1676
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
891 |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
892 if (resourceType == ResourceType_Study) |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
893 { |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
894 DicomMap t1, t2; |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
895 tags.ExtractStudyInformation(t1); |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
896 tags.ExtractPatientInformation(t2); |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
897 |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
898 target["MainDicomTags"] = Json::objectValue; |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
899 FromDcmtkBridge::ToJson(target["MainDicomTags"], t1, true); |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
900 |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
901 target["PatientMainDicomTags"] = Json::objectValue; |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
902 FromDcmtkBridge::ToJson(target["PatientMainDicomTags"], t2, true); |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
903 } |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
904 else |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
905 { |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
906 target["MainDicomTags"] = Json::objectValue; |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1668
diff
changeset
|
907 FromDcmtkBridge::ToJson(target["MainDicomTags"], tags, true); |
f079f3efe33b
patient tags reported in studies
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
908 } |
198
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
909 } |
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
910 |
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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diff
changeset
|
911 bool ServerIndex::LookupResource(Json::Value& result, |
199 | 912 const std::string& publicId, |
913 ResourceType expectedType) | |
198
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before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
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|
914 { |
663cc6c46d0a
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parents:
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diff
changeset
|
915 result = Json::objectValue; |
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diff
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|
916 |
206
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flush to disk thread
Sebastien Jodogne <s.jodogne@gmail.com>
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205
diff
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|
917 boost::mutex::scoped_lock lock(mutex_); |
199 | 918 |
198
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diff
changeset
|
919 // Lookup for the requested resource |
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parents:
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diff
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|
920 int64_t id; |
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parents:
197
diff
changeset
|
921 ResourceType type; |
1294 | 922 if (!db_.LookupResource(id, type, publicId) || |
199 | 923 type != expectedType) |
198
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diff
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|
924 { |
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parents:
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diff
changeset
|
925 return false; |
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diff
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|
926 } |
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diff
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|
927 |
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diff
changeset
|
928 // Find the parent resource (if it exists) |
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diff
changeset
|
929 if (type != ResourceType_Patient) |
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diff
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|
930 { |
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parents:
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diff
changeset
|
931 int64_t parentId; |
1247 | 932 if (!db_.LookupParent(parentId, id)) |
198
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diff
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|
933 { |
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diff
changeset
|
934 throw OrthancException(ErrorCode_InternalError); |
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|
935 } |
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diff
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|
936 |
1247 | 937 std::string parent = db_.GetPublicId(parentId); |
198
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938 |
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diff
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|
939 switch (type) |
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diff
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|
940 { |
269
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diff
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|
941 case ResourceType_Study: |
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diff
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|
942 result["ParentPatient"] = parent; |
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diff
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|
943 break; |
198
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|
944 |
269
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|
945 case ResourceType_Series: |
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diff
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|
946 result["ParentStudy"] = parent; |
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diff
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|
947 break; |
198
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|
948 |
269
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|
949 case ResourceType_Instance: |
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diff
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|
950 result["ParentSeries"] = parent; |
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diff
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|
951 break; |
198
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diff
changeset
|
952 |
269
f6fdf5abe751
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diff
changeset
|
953 default: |
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diff
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|
954 throw OrthancException(ErrorCode_InternalError); |
198
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diff
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|
955 } |
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diff
changeset
|
956 } |
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diff
changeset
|
957 |
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diff
changeset
|
958 // List the children resources |
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diff
changeset
|
959 std::list<std::string> children; |
1247 | 960 db_.GetChildrenPublicId(children, id); |
198
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
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diff
changeset
|
961 |
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diff
changeset
|
962 if (type != ResourceType_Instance) |
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diff
changeset
|
963 { |
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diff
changeset
|
964 Json::Value c = Json::arrayValue; |
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diff
changeset
|
965 |
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parents:
197
diff
changeset
|
966 for (std::list<std::string>::const_iterator |
656 | 967 it = children.begin(); it != children.end(); ++it) |
198
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diff
changeset
|
968 { |
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diff
changeset
|
969 c.append(*it); |
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parents:
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diff
changeset
|
970 } |
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parents:
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diff
changeset
|
971 |
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diff
changeset
|
972 switch (type) |
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197
diff
changeset
|
973 { |
269
f6fdf5abe751
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diff
changeset
|
974 case ResourceType_Patient: |
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diff
changeset
|
975 result["Studies"] = c; |
f6fdf5abe751
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268
diff
changeset
|
976 break; |
198
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
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diff
changeset
|
977 |
269
f6fdf5abe751
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268
diff
changeset
|
978 case ResourceType_Study: |
f6fdf5abe751
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diff
changeset
|
979 result["Series"] = c; |
f6fdf5abe751
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parents:
268
diff
changeset
|
980 break; |
198
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
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parents:
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diff
changeset
|
981 |
269
f6fdf5abe751
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diff
changeset
|
982 case ResourceType_Series: |
f6fdf5abe751
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parents:
268
diff
changeset
|
983 result["Instances"] = c; |
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
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268
diff
changeset
|
984 break; |
198
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
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diff
changeset
|
985 |
269
f6fdf5abe751
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268
diff
changeset
|
986 default: |
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268
diff
changeset
|
987 throw OrthancException(ErrorCode_InternalError); |
198
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
988 } |
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before refactoring of ServerIndex::GetXXX
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parents:
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diff
changeset
|
989 } |
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before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
990 |
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parents:
197
diff
changeset
|
991 // Set the resource type |
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
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parents:
197
diff
changeset
|
992 switch (type) |
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
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197
diff
changeset
|
993 { |
269
f6fdf5abe751
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parents:
268
diff
changeset
|
994 case ResourceType_Patient: |
f6fdf5abe751
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268
diff
changeset
|
995 result["Type"] = "Patient"; |
f6fdf5abe751
recycling up and running
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
996 break; |
198
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
997 |
269
f6fdf5abe751
recycling up and running
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
998 case ResourceType_Study: |
f6fdf5abe751
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parents:
268
diff
changeset
|
999 result["Type"] = "Study"; |
f6fdf5abe751
recycling up and running
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1000 break; |
199 | 1001 |
269
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1002 case ResourceType_Series: |
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
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268
diff
changeset
|
1003 { |
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1004 result["Type"] = "Series"; |
434
ccf3a0a43dac
EnumerationDictionary
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
433
diff
changeset
|
1005 result["Status"] = EnumerationToString(GetSeriesStatus(id)); |
198
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
1006 |
1238 | 1007 int64_t i; |
1237 | 1008 if (GetMetadataAsInteger(i, id, MetadataType_Series_ExpectedNumberOfInstances)) |
1238 | 1009 result["ExpectedNumberOfInstances"] = static_cast<int>(i); |
269
f6fdf5abe751
recycling up and running
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1010 else |
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1011 result["ExpectedNumberOfInstances"] = Json::nullValue; |
200
9c58b2b03cf0
refactoring of read operations
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
199
diff
changeset
|
1012 |
269
f6fdf5abe751
recycling up and running
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1013 break; |
200
9c58b2b03cf0
refactoring of read operations
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
199
diff
changeset
|
1014 } |
9c58b2b03cf0
refactoring of read operations
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
199
diff
changeset
|
1015 |
269
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1016 case ResourceType_Instance: |
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1017 { |
f6fdf5abe751
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268
diff
changeset
|
1018 result["Type"] = "Instance"; |
f6fdf5abe751
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268
diff
changeset
|
1019 |
f6fdf5abe751
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268
diff
changeset
|
1020 FileInfo attachment; |
1247 | 1021 if (!db_.LookupAttachment(attachment, id, FileContentType_Dicom)) |
269
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
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268
diff
changeset
|
1022 { |
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268
diff
changeset
|
1023 throw OrthancException(ErrorCode_InternalError); |
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1024 } |
200
9c58b2b03cf0
refactoring of read operations
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
199
diff
changeset
|
1025 |
269
f6fdf5abe751
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268
diff
changeset
|
1026 result["FileSize"] = static_cast<unsigned int>(attachment.GetUncompressedSize()); |
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1027 result["FileUuid"] = attachment.GetUuid(); |
200
9c58b2b03cf0
refactoring of read operations
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
199
diff
changeset
|
1028 |
1238 | 1029 int64_t i; |
1237 | 1030 if (GetMetadataAsInteger(i, id, MetadataType_Instance_IndexInSeries)) |
1238 | 1031 result["IndexInSeries"] = static_cast<int>(i); |
269
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
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268
diff
changeset
|
1032 else |
f6fdf5abe751
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
268
diff
changeset
|
1033 result["IndexInSeries"] = Json::nullValue; |
198
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
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197
diff
changeset
|
1034 |
269
f6fdf5abe751
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268
diff
changeset
|
1035 break; |
f6fdf5abe751
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parents:
268
diff
changeset
|
1036 } |
f6fdf5abe751
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268
diff
changeset
|
1037 |
f6fdf5abe751
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268
diff
changeset
|
1038 default: |
f6fdf5abe751
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268
diff
changeset
|
1039 throw OrthancException(ErrorCode_InternalError); |
198
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
1040 } |
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diff
changeset
|
1041 |
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diff
changeset
|
1042 // Record the remaining information |
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
197
diff
changeset
|
1043 result["ID"] = publicId; |
1668
de1413733c97
reconstructing main dicom tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1555
diff
changeset
|
1044 MainDicomTagsToJson(result, id, type); |
198
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
Sebastien Jodogne <s.jodogne@gmail.com>
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197
diff
changeset
|
1045 |
315 | 1046 std::string tmp; |
1047 | |
1247 | 1048 if (db_.LookupMetadata(tmp, id, MetadataType_AnonymizedFrom)) |
1236 | 1049 { |
315 | 1050 result["AnonymizedFrom"] = tmp; |
1236 | 1051 } |
315 | 1052 |
1247 | 1053 if (db_.LookupMetadata(tmp, id, MetadataType_ModifiedFrom)) |
1236 | 1054 { |
315 | 1055 result["ModifiedFrom"] = tmp; |
1236 | 1056 } |
315 | 1057 |
511
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
1058 if (type == ResourceType_Patient || |
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
1059 type == ResourceType_Study || |
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
1060 type == ResourceType_Series) |
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
1061 { |
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
1062 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
|
1063 |
1247 | 1064 if (db_.LookupMetadata(tmp, id, MetadataType_LastUpdate)) |
1236 | 1065 { |
1148
ac36589f699e
LastUpdate metadata is now always returned for patients, studies and series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1139
diff
changeset
|
1066 result["LastUpdate"] = tmp; |
1236 | 1067 } |
511
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
1068 } |
3b735fdf320b
monitoring of stable patients/studies/series
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
440
diff
changeset
|
1069 |
198
663cc6c46d0a
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parents:
197
diff
changeset
|
1070 return true; |
663cc6c46d0a
before refactoring of ServerIndex::GetXXX
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197
diff
changeset
|
1071 } |
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197
diff
changeset
|
1072 |
0 | 1073 |
232
5368bbe813cf
refactoring of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
231
diff
changeset
|
1074 bool ServerIndex::LookupAttachment(FileInfo& attachment, |
5368bbe813cf
refactoring of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
231
diff
changeset
|
1075 const std::string& instanceUuid, |
233 | 1076 FileContentType contentType) |
0 | 1077 { |
206
4453a010d0db
flush to disk thread
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
205
diff
changeset
|
1078 boost::mutex::scoped_lock lock(mutex_); |
0 | 1079 |
193
a1b9d1e1497b
failed attempt to compile with linux standard base
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
1080 int64_t id; |
a1b9d1e1497b
failed attempt to compile with linux standard base
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
1081 ResourceType type; |
1294 | 1082 if (!db_.LookupResource(id, type, instanceUuid)) |
192
c56dc32266e0
refactoring getfile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
191
diff
changeset
|
1083 { |
1113
ba5c0908600c
Refactoring of HttpOutput ("Content-Length" header is now always sent)
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
1102
diff
changeset
|
1084 throw OrthancException(ErrorCode_UnknownResource); |
192
c56dc32266e0
refactoring getfile
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
191
diff
changeset
|
1085 } |
193
a1b9d1e1497b
failed attempt to compile with linux standard base
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
192
diff
changeset
|
1086 |
1247 | 1087 if (db_.LookupAttachment(attachment, id, contentType)) |
232
5368bbe813cf
refactoring of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
231
diff
changeset
|
1088 { |
233 | 1089 assert(attachment.GetContentType() == contentType); |
232
5368bbe813cf
refactoring of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
231
diff
changeset
|
1090 return true; |
5368bbe813cf
refactoring of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
231
diff
changeset
|
1091 } |
5368bbe813cf
refactoring of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
231
diff
changeset
|
1092 else |
5368bbe813cf
refactoring of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
231
diff
changeset
|
1093 { |
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1094 return false; |
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1095 } |
192
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1096 } |
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1097 |
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1098 |
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1099 |
1354 | 1100 void ServerIndex::GetAllUuids(std::list<std::string>& target, |
190 | 1101 ResourceType resourceType) |
0 | 1102 { |
1357 | 1103 boost::mutex::scoped_lock lock(mutex_); |
1104 db_.GetAllPublicIds(target, resourceType); | |
0 | 1105 } |
1106 | |
1107 | |
1509
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1108 void ServerIndex::GetAllUuids(std::list<std::string>& target, |
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1109 ResourceType resourceType, |
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1110 size_t since, |
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1111 size_t limit) |
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1112 { |
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1113 if (limit == 0) |
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1114 { |
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1115 target.clear(); |
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1116 return; |
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1117 } |
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1118 |
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1119 boost::mutex::scoped_lock lock(mutex_); |
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1120 db_.GetAllPublicIds(target, resourceType, since, limit); |
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1121 } |
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1122 |
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1123 |
1244 | 1124 template <typename T> |
1125 static void FormatLog(Json::Value& target, | |
1126 const std::list<T>& log, | |
1127 const std::string& name, | |
1128 bool done, | |
1129 int64_t since) | |
1240 | 1130 { |
1131 Json::Value items = Json::arrayValue; | |
1244 | 1132 for (typename std::list<T>::const_iterator |
1304 | 1133 it = log.begin(); it != log.end(); ++it) |
1240 | 1134 { |
1135 Json::Value item; | |
1136 it->Format(item); | |
1137 items.append(item); | |
1138 } | |
1139 | |
1140 target = Json::objectValue; | |
1244 | 1141 target[name] = items; |
1240 | 1142 target["Done"] = done; |
1143 | |
1305 | 1144 int64_t last = (log.empty() ? since : log.back().GetSeq()); |
1240 | 1145 target["Last"] = static_cast<int>(last); |
1146 } | |
1147 | |
1148 | |
1247 | 1149 void ServerIndex::GetChanges(Json::Value& target, |
204 | 1150 int64_t since, |
0 | 1151 unsigned int maxResults) |
1152 { | |
1240 | 1153 std::list<ServerIndexChange> changes; |
1154 bool done; | |
1155 | |
1156 { | |
1157 boost::mutex::scoped_lock lock(mutex_); | |
1247 | 1158 db_.GetChanges(changes, done, since, maxResults); |
1240 | 1159 } |
1160 | |
1244 | 1161 FormatLog(target, changes, "Changes", done, since); |
237
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1162 } |
0 | 1163 |
1240 | 1164 |
1247 | 1165 void ServerIndex::GetLastChange(Json::Value& target) |
237
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1166 { |
1240 | 1167 std::list<ServerIndexChange> changes; |
1168 | |
1169 { | |
1170 boost::mutex::scoped_lock lock(mutex_); | |
1247 | 1171 db_.GetLastChange(changes); |
1240 | 1172 } |
1173 | |
1244 | 1174 FormatLog(target, changes, "Changes", true, 0); |
0 | 1175 } |
231 | 1176 |
1240 | 1177 |
231 | 1178 void ServerIndex::LogExportedResource(const std::string& publicId, |
1179 const std::string& remoteModality) | |
1180 { | |
1181 boost::mutex::scoped_lock lock(mutex_); | |
1310
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1182 Transaction transaction(*this); |
231 | 1183 |
1184 int64_t id; | |
1185 ResourceType type; | |
1294 | 1186 if (!db_.LookupResource(id, type, publicId)) |
231 | 1187 { |
1188 throw OrthancException(ErrorCode_InternalError); | |
1189 } | |
1190 | |
1191 std::string patientId; | |
1192 std::string studyInstanceUid; | |
1193 std::string seriesInstanceUid; | |
1194 std::string sopInstanceUid; | |
1195 | |
1196 int64_t currentId = id; | |
1197 ResourceType currentType = type; | |
1198 | |
1199 // Iteratively go up inside the patient/study/series/instance hierarchy | |
1200 bool done = false; | |
1201 while (!done) | |
1202 { | |
1203 DicomMap map; | |
1247 | 1204 db_.GetMainDicomTags(map, currentId); |
231 | 1205 |
1206 switch (currentType) | |
1207 { | |
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1208 case ResourceType_Patient: |
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1209 patientId = map.GetValue(DICOM_TAG_PATIENT_ID).GetContent(); |
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1210 done = true; |
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1211 break; |
231 | 1212 |
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1213 case ResourceType_Study: |
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1214 studyInstanceUid = map.GetValue(DICOM_TAG_STUDY_INSTANCE_UID).GetContent(); |
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1215 currentType = ResourceType_Patient; |
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1216 break; |
231 | 1217 |
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1218 case ResourceType_Series: |
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1219 seriesInstanceUid = map.GetValue(DICOM_TAG_SERIES_INSTANCE_UID).GetContent(); |
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1220 currentType = ResourceType_Study; |
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1221 break; |
231 | 1222 |
269
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1223 case ResourceType_Instance: |
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1224 sopInstanceUid = map.GetValue(DICOM_TAG_SOP_INSTANCE_UID).GetContent(); |
269
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1225 currentType = ResourceType_Series; |
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1226 break; |
231 | 1227 |
269
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1228 default: |
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1229 throw OrthancException(ErrorCode_InternalError); |
231 | 1230 } |
1231 | |
1232 // If we have not reached the Patient level, find the parent of | |
1233 // the current resource | |
1234 if (!done) | |
1235 { | |
1247 | 1236 bool ok = db_.LookupParent(currentId, currentId); |
375
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|
1237 assert(ok); |
231 | 1238 } |
1239 } | |
1240 | |
1246 | 1241 ExportedResource resource(-1, |
1242 type, | |
1243 publicId, | |
1244 remoteModality, | |
1245 Toolbox::GetNowIsoString(), | |
1246 patientId, | |
1247 studyInstanceUid, | |
1248 seriesInstanceUid, | |
1249 sopInstanceUid); | |
1310
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1250 |
1247 | 1251 db_.LogExportedResource(resource); |
1310
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|
1252 transaction.Commit(0); |
231 | 1253 } |
1254 | |
1255 | |
1247 | 1256 void ServerIndex::GetExportedResources(Json::Value& target, |
231 | 1257 int64_t since, |
1258 unsigned int maxResults) | |
1259 { | |
1244 | 1260 std::list<ExportedResource> exported; |
1261 bool done; | |
1262 | |
1263 { | |
1264 boost::mutex::scoped_lock lock(mutex_); | |
1247 | 1265 db_.GetExportedResources(exported, done, since, maxResults); |
1244 | 1266 } |
1267 | |
1268 FormatLog(target, exported, "Exports", done, since); | |
231 | 1269 } |
237
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1270 |
1244 | 1271 |
1247 | 1272 void ServerIndex::GetLastExportedResource(Json::Value& target) |
237
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1273 { |
1244 | 1274 std::list<ExportedResource> exported; |
1275 | |
1276 { | |
1277 boost::mutex::scoped_lock lock(mutex_); | |
1247 | 1278 db_.GetLastExportedResource(exported); |
1244 | 1279 } |
1280 | |
1281 FormatLog(target, exported, "Exports", true, 0); | |
237
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1282 } |
268
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1283 |
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1284 |
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1285 bool ServerIndex::IsRecyclingNeeded(uint64_t instanceSize) |
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1286 { |
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1287 if (maximumStorageSize_ != 0) |
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1288 { |
278
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|
1289 uint64_t currentSize = currentStorageSize_ - listener_->GetSizeOfFilesToRemove(); |
1247 | 1290 assert(db_.GetTotalCompressedSize() == currentSize); |
278
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1291 |
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1292 if (currentSize + instanceSize > maximumStorageSize_) |
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1293 { |
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1294 return true; |
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1295 } |
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1296 } |
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1297 |
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1298 if (maximumPatients_ != 0) |
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1299 { |
1247 | 1300 uint64_t patientCount = db_.GetResourceCount(ResourceType_Patient); |
269
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1301 if (patientCount > maximumPatients_) |
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1302 { |
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1303 return true; |
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1304 } |
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1305 } |
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1306 |
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1307 return false; |
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1308 } |
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1309 |
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1310 |
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1311 void ServerIndex::Recycle(uint64_t instanceSize, |
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1312 const std::string& newPatientId) |
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1313 { |
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1314 if (!IsRecyclingNeeded(instanceSize)) |
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1315 { |
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1316 return; |
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1317 } |
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1318 |
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1319 // Check whether other DICOM instances from this patient are |
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1320 // already stored |
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1321 int64_t patientToAvoid; |
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1322 ResourceType type; |
1294 | 1323 bool hasPatientToAvoid = db_.LookupResource(patientToAvoid, type, newPatientId); |
268
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1324 |
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1325 if (hasPatientToAvoid && type != ResourceType_Patient) |
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1326 { |
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1327 throw OrthancException(ErrorCode_InternalError); |
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1328 } |
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1329 |
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1330 // Iteratively select patient to remove until there is enough |
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1331 // space in the DICOM store |
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1332 int64_t patientToRecycle; |
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1333 while (true) |
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1334 { |
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1335 // If other instances of this patient are already in the store, |
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1336 // we must avoid to recycle them |
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1337 bool ok = hasPatientToAvoid ? |
1247 | 1338 db_.SelectPatientToRecycle(patientToRecycle, patientToAvoid) : |
1339 db_.SelectPatientToRecycle(patientToRecycle); | |
269
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1340 |
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1341 if (!ok) |
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1342 { |
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1343 throw OrthancException(ErrorCode_FullStorage); |
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1344 } |
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1345 |
1331
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1346 VLOG(1) << "Recycling one patient"; |
1247 | 1347 db_.DeleteResource(patientToRecycle); |
269
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1348 |
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1349 if (!IsRecyclingNeeded(instanceSize)) |
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1350 { |
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1351 // OK, we're done |
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1352 break; |
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1353 } |
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1354 } |
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1355 } |
269
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1356 |
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1357 void ServerIndex::SetMaximumPatientCount(unsigned int count) |
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1358 { |
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1359 boost::mutex::scoped_lock lock(mutex_); |
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1360 maximumPatients_ = count; |
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1361 |
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1362 if (count == 0) |
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1363 { |
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1364 LOG(WARNING) << "No limit on the number of stored patients"; |
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1365 } |
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1366 else |
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1367 { |
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1368 LOG(WARNING) << "At most " << count << " patients will be stored"; |
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1369 } |
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1370 |
269
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1371 StandaloneRecycling(); |
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1372 } |
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1373 |
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1374 void ServerIndex::SetMaximumStorageSize(uint64_t size) |
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1375 { |
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1376 boost::mutex::scoped_lock lock(mutex_); |
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1377 maximumStorageSize_ = size; |
270
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1378 |
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1379 if (size == 0) |
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1380 { |
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1381 LOG(WARNING) << "No limit on the size of the storage area"; |
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1382 } |
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1383 else |
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1384 { |
440
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|
1385 LOG(WARNING) << "At most " << (size / MEGA_BYTES) << "MB will be used for the storage area"; |
270
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1386 } |
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1387 |
269
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1388 StandaloneRecycling(); |
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1389 } |
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1390 |
272
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1391 void ServerIndex::StandaloneRecycling() |
269
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1392 { |
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1393 // WARNING: No mutex here, do not include this as a public method |
278
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1394 Transaction t(*this); |
269
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1395 Recycle(0, ""); |
278
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1396 t.Commit(0); |
269
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1397 } |
272
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1398 |
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1399 |
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1400 bool ServerIndex::IsProtectedPatient(const std::string& publicId) |
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1401 { |
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1402 boost::mutex::scoped_lock lock(mutex_); |
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1403 |
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1404 // Lookup for the requested resource |
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1405 int64_t id; |
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1406 ResourceType type; |
1294 | 1407 if (!db_.LookupResource(id, type, publicId) || |
272
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1408 type != ResourceType_Patient) |
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1409 { |
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1410 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1411 } |
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1412 |
1247 | 1413 return db_.IsProtectedPatient(id); |
272
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1414 } |
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1415 |
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1416 |
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1417 void ServerIndex::SetProtectedPatient(const std::string& publicId, |
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1418 bool isProtected) |
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1419 { |
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1420 boost::mutex::scoped_lock lock(mutex_); |
1310
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1421 Transaction transaction(*this); |
272
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1422 |
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1423 // Lookup for the requested resource |
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1424 int64_t id; |
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1425 ResourceType type; |
1294 | 1426 if (!db_.LookupResource(id, type, publicId) || |
272
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1427 type != ResourceType_Patient) |
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1428 { |
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1429 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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1430 } |
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1431 |
1247 | 1432 db_.SetProtectedPatient(id, isProtected); |
1310
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1433 transaction.Commit(0); |
272
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1434 |
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1435 if (isProtected) |
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1436 LOG(INFO) << "Patient " << publicId << " has been protected"; |
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1437 else |
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1438 LOG(INFO) << "Patient " << publicId << " has been unprotected"; |
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1439 } |
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1440 |
304 | 1441 |
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1442 void ServerIndex::GetChildren(std::list<std::string>& result, |
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1443 const std::string& publicId) |
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1444 { |
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1445 result.clear(); |
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1446 |
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1447 boost::mutex::scoped_lock lock(mutex_); |
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1448 |
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1449 ResourceType type; |
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1450 int64_t resource; |
1294 | 1451 if (!db_.LookupResource(resource, type, publicId)) |
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1452 { |
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1453 throw OrthancException(ErrorCode_UnknownResource); |
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1454 } |
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1455 |
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1456 if (type == ResourceType_Instance) |
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1457 { |
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1458 // An instance cannot have a child |
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1459 throw OrthancException(ErrorCode_BadParameterType); |
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1460 } |
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1461 |
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1462 std::list<int64_t> tmp; |
1247 | 1463 db_.GetChildrenInternalId(tmp, resource); |
714
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1464 |
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1465 for (std::list<int64_t>::const_iterator |
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1466 it = tmp.begin(); it != tmp.end(); ++it) |
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1467 { |
1247 | 1468 result.push_back(db_.GetPublicId(*it)); |
714
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1469 } |
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1470 } |
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1471 |
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1472 |
304 | 1473 void ServerIndex::GetChildInstances(std::list<std::string>& result, |
1474 const std::string& publicId) | |
1475 { | |
1476 result.clear(); | |
1477 | |
1478 boost::mutex::scoped_lock lock(mutex_); | |
1479 | |
1480 ResourceType type; | |
1481 int64_t top; | |
1294 | 1482 if (!db_.LookupResource(top, type, publicId)) |
304 | 1483 { |
1484 throw OrthancException(ErrorCode_UnknownResource); | |
1485 } | |
1486 | |
1487 if (type == ResourceType_Instance) | |
1488 { | |
1489 // The resource is already an instance: Do not go down the hierarchy | |
1490 result.push_back(publicId); | |
1491 return; | |
1492 } | |
1493 | |
1494 std::stack<int64_t> toExplore; | |
1495 toExplore.push(top); | |
1496 | |
1497 std::list<int64_t> tmp; | |
1498 | |
1499 while (!toExplore.empty()) | |
1500 { | |
1501 // Get the internal ID of the current resource | |
1502 int64_t resource = toExplore.top(); | |
1503 toExplore.pop(); | |
1504 | |
1247 | 1505 if (db_.GetResourceType(resource) == ResourceType_Instance) |
304 | 1506 { |
1247 | 1507 result.push_back(db_.GetPublicId(resource)); |
304 | 1508 } |
1509 else | |
1510 { | |
1511 // Tag all the children of this resource as to be explored | |
1247 | 1512 db_.GetChildrenInternalId(tmp, resource); |
304 | 1513 for (std::list<int64_t>::const_iterator |
656 | 1514 it = tmp.begin(); it != tmp.end(); ++it) |
304 | 1515 { |
1516 toExplore.push(*it); | |
1517 } | |
1518 } | |
1519 } | |
1520 } | |
1521 | |
306
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1522 |
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1523 void ServerIndex::SetMetadata(const std::string& publicId, |
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1524 MetadataType type, |
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1525 const std::string& value) |
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1526 { |
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1527 boost::mutex::scoped_lock lock(mutex_); |
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1528 |
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1529 ResourceType rtype; |
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1530 int64_t id; |
1294 | 1531 if (!db_.LookupResource(id, rtype, publicId)) |
306
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1532 { |
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1533 throw OrthancException(ErrorCode_UnknownResource); |
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1534 } |
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1535 |
1247 | 1536 db_.SetMetadata(id, type, value); |
306
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1537 } |
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1538 |
438 | 1539 |
1540 void ServerIndex::DeleteMetadata(const std::string& publicId, | |
1541 MetadataType type) | |
1542 { | |
1543 boost::mutex::scoped_lock lock(mutex_); | |
1544 | |
1545 ResourceType rtype; | |
1546 int64_t id; | |
1294 | 1547 if (!db_.LookupResource(id, rtype, publicId)) |
438 | 1548 { |
1549 throw OrthancException(ErrorCode_UnknownResource); | |
1550 } | |
1551 | |
1247 | 1552 db_.DeleteMetadata(id, type); |
438 | 1553 } |
1554 | |
1555 | |
306
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1556 bool ServerIndex::LookupMetadata(std::string& target, |
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1557 const std::string& publicId, |
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1558 MetadataType type) |
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1559 { |
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1560 boost::mutex::scoped_lock lock(mutex_); |
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1561 |
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1562 ResourceType rtype; |
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1563 int64_t id; |
1294 | 1564 if (!db_.LookupResource(id, rtype, publicId)) |
306
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1565 { |
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1566 throw OrthancException(ErrorCode_UnknownResource); |
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1567 } |
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1568 |
1247 | 1569 return db_.LookupMetadata(target, id, type); |
306
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1570 } |
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1571 |
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1572 |
739 | 1573 void ServerIndex::ListAvailableMetadata(std::list<MetadataType>& target, |
436
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1574 const std::string& publicId) |
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1575 { |
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1576 boost::mutex::scoped_lock lock(mutex_); |
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1577 |
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1578 ResourceType rtype; |
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1579 int64_t id; |
1294 | 1580 if (!db_.LookupResource(id, rtype, publicId)) |
436
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1581 { |
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1582 throw OrthancException(ErrorCode_UnknownResource); |
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1583 } |
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1584 |
1247 | 1585 db_.ListAvailableMetadata(target, id); |
436
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1586 } |
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1587 |
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1588 |
697
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1589 void ServerIndex::ListAvailableAttachments(std::list<FileContentType>& target, |
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1590 const std::string& publicId, |
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1591 ResourceType expectedType) |
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1592 { |
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1593 boost::mutex::scoped_lock lock(mutex_); |
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1594 |
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1595 ResourceType type; |
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1596 int64_t id; |
1294 | 1597 if (!db_.LookupResource(id, type, publicId) || |
697
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1598 expectedType != type) |
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1599 { |
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1600 throw OrthancException(ErrorCode_UnknownResource); |
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1601 } |
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1602 |
1247 | 1603 db_.ListAvailableAttachments(target, id); |
697
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1604 } |
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1605 |
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1606 |
306
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1607 bool ServerIndex::LookupParent(std::string& target, |
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1608 const std::string& publicId) |
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1609 { |
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1610 boost::mutex::scoped_lock lock(mutex_); |
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1611 |
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1612 ResourceType type; |
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1613 int64_t id; |
1294 | 1614 if (!db_.LookupResource(id, type, publicId)) |
306
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1615 { |
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1616 throw OrthancException(ErrorCode_UnknownResource); |
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1617 } |
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1618 |
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1619 int64_t parentId; |
1247 | 1620 if (db_.LookupParent(parentId, id)) |
306
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1621 { |
1247 | 1622 target = db_.GetPublicId(parentId); |
306
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1623 return true; |
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1624 } |
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1625 else |
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1626 { |
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1627 return false; |
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1628 } |
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1629 } |
310 | 1630 |
1631 | |
1632 uint64_t ServerIndex::IncrementGlobalSequence(GlobalProperty sequence) | |
1633 { | |
1634 boost::mutex::scoped_lock lock(mutex_); | |
1310
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1635 Transaction transaction(*this); |
311 | 1636 |
1237 | 1637 uint64_t seq = IncrementGlobalSequenceInternal(sequence); |
1310
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1638 transaction.Commit(0); |
311 | 1639 |
1640 return seq; | |
310 | 1641 } |
315 | 1642 |
1643 | |
1644 | |
1645 void ServerIndex::LogChange(ChangeType changeType, | |
1646 const std::string& publicId) | |
1647 { | |
1648 boost::mutex::scoped_lock lock(mutex_); | |
1310
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1649 Transaction transaction(*this); |
315 | 1650 |
1651 int64_t id; | |
1652 ResourceType type; | |
1294 | 1653 if (!db_.LookupResource(id, type, publicId)) |
315 | 1654 { |
1655 throw OrthancException(ErrorCode_UnknownResource); | |
1656 } | |
1657 | |
1237 | 1658 LogChange(id, changeType, type, publicId); |
1310
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1659 transaction.Commit(0); |
315 | 1660 } |
413
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1661 |
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1662 |
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1663 void ServerIndex::DeleteChanges() |
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1664 { |
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1665 boost::mutex::scoped_lock lock(mutex_); |
1286 | 1666 db_.ClearChanges(); |
413
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1667 } |
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1668 |
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|
1669 void ServerIndex::DeleteExportedResources() |
47d63c941902
clearing /exports and /changes
Sebastien Jodogne <s.jodogne@gmail.com>
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399
diff
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|
1670 { |
47d63c941902
clearing /exports and /changes
Sebastien Jodogne <s.jodogne@gmail.com>
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399
diff
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|
1671 boost::mutex::scoped_lock lock(mutex_); |
1286 | 1672 db_.ClearExportedResources(); |
413
47d63c941902
clearing /exports and /changes
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diff
changeset
|
1673 } |
440
23e5b35e3c5c
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diff
changeset
|
1674 |
23e5b35e3c5c
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diff
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|
1675 |
646 | 1676 void ServerIndex::GetStatisticsInternal(/* out */ uint64_t& compressedSize, |
1677 /* out */ uint64_t& uncompressedSize, | |
1678 /* out */ unsigned int& countStudies, | |
1679 /* out */ unsigned int& countSeries, | |
1680 /* out */ unsigned int& countInstances, | |
1681 /* in */ int64_t id, | |
1682 /* in */ ResourceType type) | |
440
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diff
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|
1683 { |
646 | 1684 std::stack<int64_t> toExplore; |
1685 toExplore.push(id); | |
440
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diff
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|
1686 |
646 | 1687 countInstances = 0; |
1688 countSeries = 0; | |
1689 countStudies = 0; | |
1690 compressedSize = 0; | |
1691 uncompressedSize = 0; | |
440
23e5b35e3c5c
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diff
changeset
|
1692 |
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diff
changeset
|
1693 while (!toExplore.empty()) |
23e5b35e3c5c
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diff
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|
1694 { |
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diff
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|
1695 // Get the internal ID of the current resource |
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diff
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|
1696 int64_t resource = toExplore.top(); |
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diff
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|
1697 toExplore.pop(); |
23e5b35e3c5c
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diff
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|
1698 |
1247 | 1699 ResourceType thisType = db_.GetResourceType(resource); |
440
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diff
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|
1700 |
702
7592a48e97e4
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diff
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|
1701 std::list<FileContentType> f; |
1247 | 1702 db_.ListAvailableAttachments(f, resource); |
702
7592a48e97e4
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diff
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|
1703 |
7592a48e97e4
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diff
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|
1704 for (std::list<FileContentType>::const_iterator |
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diff
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|
1705 it = f.begin(); it != f.end(); ++it) |
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diff
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|
1706 { |
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diff
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|
1707 FileInfo attachment; |
1247 | 1708 if (db_.LookupAttachment(attachment, resource, *it)) |
702
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diff
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|
1709 { |
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diff
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|
1710 compressedSize += attachment.GetCompressedSize(); |
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diff
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|
1711 uncompressedSize += attachment.GetUncompressedSize(); |
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diff
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|
1712 } |
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diff
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|
1713 } |
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diff
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|
1714 |
440
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diff
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|
1715 if (thisType == ResourceType_Instance) |
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diff
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|
1716 { |
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diff
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|
1717 countInstances++; |
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|
1718 } |
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diff
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|
1719 else |
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diff
changeset
|
1720 { |
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diff
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|
1721 switch (thisType) |
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diff
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|
1722 { |
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diff
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|
1723 case ResourceType_Study: |
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1724 countStudies++; |
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diff
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|
1725 break; |
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diff
changeset
|
1726 |
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diff
changeset
|
1727 case ResourceType_Series: |
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diff
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|
1728 countSeries++; |
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diff
changeset
|
1729 break; |
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diff
changeset
|
1730 |
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diff
changeset
|
1731 default: |
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diff
changeset
|
1732 break; |
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diff
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|
1733 } |
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|
1734 |
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|
1735 // Tag all the children of this resource as to be explored |
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diff
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|
1736 std::list<int64_t> tmp; |
1247 | 1737 db_.GetChildrenInternalId(tmp, resource); |
440
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diff
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|
1738 for (std::list<int64_t>::const_iterator |
656 | 1739 it = tmp.begin(); it != tmp.end(); ++it) |
440
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diff
changeset
|
1740 { |
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diff
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|
1741 toExplore.push(*it); |
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diff
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|
1742 } |
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diff
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|
1743 } |
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diff
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|
1744 } |
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diff
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|
1745 |
646 | 1746 if (countStudies == 0) |
1747 { | |
1748 countStudies = 1; | |
1749 } | |
1750 | |
1751 if (countSeries == 0) | |
1752 { | |
1753 countSeries = 1; | |
1754 } | |
1755 } | |
1756 | |
1757 | |
1758 | |
1759 void ServerIndex::GetStatistics(Json::Value& target, | |
1760 const std::string& publicId) | |
1761 { | |
1762 boost::mutex::scoped_lock lock(mutex_); | |
1763 | |
1764 ResourceType type; | |
1765 int64_t top; | |
1294 | 1766 if (!db_.LookupResource(top, type, publicId)) |
646 | 1767 { |
1768 throw OrthancException(ErrorCode_UnknownResource); | |
1769 } | |
1770 | |
1771 uint64_t uncompressedSize; | |
1772 uint64_t compressedSize; | |
1773 unsigned int countStudies; | |
1774 unsigned int countSeries; | |
1775 unsigned int countInstances; | |
1776 GetStatisticsInternal(compressedSize, uncompressedSize, countStudies, | |
1777 countSeries, countInstances, top, type); | |
1778 | |
440
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diff
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|
1779 target = Json::objectValue; |
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|
1780 target["DiskSize"] = boost::lexical_cast<std::string>(compressedSize); |
1310
61ce8147f30d
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1306
diff
changeset
|
1781 target["DiskSizeMB"] = static_cast<unsigned int>(compressedSize / MEGA_BYTES); |
440
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diff
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|
1782 target["UncompressedSize"] = boost::lexical_cast<std::string>(uncompressedSize); |
1310
61ce8147f30d
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diff
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|
1783 target["UncompressedSizeMB"] = static_cast<unsigned int>(uncompressedSize / MEGA_BYTES); |
440
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diff
changeset
|
1784 |
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diff
changeset
|
1785 switch (type) |
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diff
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|
1786 { |
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diff
changeset
|
1787 // Do NOT add "break" below this point! |
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diff
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|
1788 case ResourceType_Patient: |
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|
1789 target["CountStudies"] = countStudies; |
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diff
changeset
|
1790 |
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diff
changeset
|
1791 case ResourceType_Study: |
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|
1792 target["CountSeries"] = countSeries; |
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diff
changeset
|
1793 |
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diff
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|
1794 case ResourceType_Series: |
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|
1795 target["CountInstances"] = countInstances; |
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diff
changeset
|
1796 |
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diff
changeset
|
1797 case ResourceType_Instance: |
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|
1798 default: |
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diff
changeset
|
1799 break; |
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diff
changeset
|
1800 } |
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diff
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|
1801 } |
511
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1802 |
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|
1803 |
646 | 1804 void ServerIndex::GetStatistics(/* out */ uint64_t& compressedSize, |
1805 /* out */ uint64_t& uncompressedSize, | |
1806 /* out */ unsigned int& countStudies, | |
1807 /* out */ unsigned int& countSeries, | |
1808 /* out */ unsigned int& countInstances, | |
1809 const std::string& publicId) | |
1810 { | |
1811 boost::mutex::scoped_lock lock(mutex_); | |
1812 | |
1813 ResourceType type; | |
1814 int64_t top; | |
1294 | 1815 if (!db_.LookupResource(top, type, publicId)) |
646 | 1816 { |
1817 throw OrthancException(ErrorCode_UnknownResource); | |
1818 } | |
1819 | |
1820 GetStatisticsInternal(compressedSize, uncompressedSize, countStudies, | |
1821 countSeries, countInstances, top, type); | |
1822 } | |
1823 | |
1824 | |
511
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1825 void ServerIndex::UnstableResourcesMonitorThread(ServerIndex* that) |
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|
1826 { |
810
401a9633e492
configuration into a namespace
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diff
changeset
|
1827 int stableAge = Configuration::GetGlobalIntegerParameter("StableAge", 60); |
511
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1828 if (stableAge <= 0) |
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1829 { |
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|
1830 stableAge = 60; |
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1831 } |
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changeset
|
1832 |
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changeset
|
1833 LOG(INFO) << "Starting the monitor for stable resources (stable age = " << stableAge << ")"; |
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1834 |
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changeset
|
1835 while (!that->done_) |
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|
1836 { |
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changeset
|
1837 // Check for stable resources each second |
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|
1838 boost::this_thread::sleep(boost::posix_time::seconds(1)); |
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1839 |
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changeset
|
1840 boost::mutex::scoped_lock lock(that->mutex_); |
513 | 1841 |
511
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|
1842 while (!that->unstableResources_.IsEmpty() && |
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1843 that->unstableResources_.GetOldestPayload().GetAge() > static_cast<unsigned int>(stableAge)) |
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1844 { |
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1845 // This DICOM resource has not received any new instance for |
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1846 // some time. It can be considered as stable. |
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1847 |
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1848 UnstableResourcePayload payload; |
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1849 int64_t id = that->unstableResources_.RemoveOldest(payload); |
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1850 |
513 | 1851 // Ensure that the resource is still existing before logging the change |
1247 | 1852 if (that->db_.IsExistingResource(id)) |
511
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1853 { |
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1854 switch (payload.GetResourceType()) |
513 | 1855 { |
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1856 case ResourceType_Patient: |
1237 | 1857 that->LogChange(id, ChangeType_StablePatient, ResourceType_Patient, payload.GetPublicId()); |
513 | 1858 break; |
511
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1859 |
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1860 case ResourceType_Study: |
1237 | 1861 that->LogChange(id, ChangeType_StableStudy, ResourceType_Study, payload.GetPublicId()); |
513 | 1862 break; |
511
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1863 |
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1864 case ResourceType_Series: |
1237 | 1865 that->LogChange(id, ChangeType_StableSeries, ResourceType_Series, payload.GetPublicId()); |
513 | 1866 break; |
1867 | |
1868 default: | |
1869 throw OrthancException(ErrorCode_InternalError); | |
1870 } | |
1871 | |
1872 //LOG(INFO) << "Stable resource: " << EnumerationToString(payload.type_) << " " << id; | |
511
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1873 } |
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1874 } |
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1875 } |
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1876 |
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1877 LOG(INFO) << "Closing the monitor thread for stable resources"; |
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1878 } |
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1879 |
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1880 |
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1881 void ServerIndex::MarkAsUnstable(int64_t id, |
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1882 Orthanc::ResourceType type, |
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1883 const std::string& publicId) |
511
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1884 { |
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1885 // WARNING: Before calling this method, "mutex_" must be locked. |
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1886 |
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1887 assert(type == Orthanc::ResourceType_Patient || |
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1888 type == Orthanc::ResourceType_Study || |
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1889 type == Orthanc::ResourceType_Series); |
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1890 |
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1891 UnstableResourcePayload payload(type, publicId); |
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1892 unstableResources_.AddOrMakeMostRecent(id, payload); |
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1893 //LOG(INFO) << "Unstable resource: " << EnumerationToString(type) << " " << id; |
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1894 |
1237 | 1895 LogChange(id, ChangeType_NewChildInstance, type, publicId); |
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1896 } |
521 | 1897 |
1898 | |
1899 | |
1728
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1900 void ServerIndex::LookupIdentifierExact(std::list<std::string>& result, |
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1901 ResourceType level, |
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1902 const DicomTag& tag, |
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1903 const std::string& value) |
615 | 1904 { |
1727 | 1905 assert((level == ResourceType_Patient && tag == DICOM_TAG_PATIENT_ID) || |
1906 (level == ResourceType_Study && tag == DICOM_TAG_STUDY_INSTANCE_UID) || | |
1907 (level == ResourceType_Study && tag == DICOM_TAG_ACCESSION_NUMBER) || | |
1908 (level == ResourceType_Series && tag == DICOM_TAG_SERIES_INSTANCE_UID) || | |
1909 (level == ResourceType_Instance && tag == DICOM_TAG_SOP_INSTANCE_UID)); | |
1725 | 1910 |
615 | 1911 result.clear(); |
1912 | |
1913 boost::mutex::scoped_lock lock(mutex_); | |
1914 | |
1746 | 1915 LookupIdentifierQuery query(level); |
1916 query.AddConstraint(tag, IdentifierConstraintType_Equal, value); | |
1917 query.Apply(result, db_); | |
615 | 1918 } |
1919 | |
1920 | |
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1921 StoreStatus ServerIndex::AddAttachment(const FileInfo& attachment, |
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1922 const std::string& publicId) |
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1923 { |
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1924 boost::mutex::scoped_lock lock(mutex_); |
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1925 |
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1926 Transaction t(*this); |
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1927 |
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1928 ResourceType resourceType; |
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1929 int64_t resourceId; |
1294 | 1930 if (!db_.LookupResource(resourceId, resourceType, publicId)) |
699
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1931 { |
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1932 return StoreStatus_Failure; // Inexistent resource |
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1933 } |
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1934 |
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1935 // Remove possible previous attachment |
1247 | 1936 db_.DeleteAttachment(resourceId, attachment.GetContentType()); |
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1937 |
704
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1938 // Locate the patient of the target resource |
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1939 int64_t patientId = resourceId; |
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1940 for (;;) |
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1941 { |
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1942 int64_t parent; |
1247 | 1943 if (db_.LookupParent(parent, patientId)) |
704
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1944 { |
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1945 // We have not reached the patient level yet |
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1946 patientId = parent; |
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1947 } |
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1948 else |
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1949 { |
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1950 // We have reached the patient level |
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1951 break; |
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1952 } |
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1953 } |
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1954 |
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1955 // Possibly apply the recycling mechanism while preserving this patient |
1247 | 1956 assert(db_.GetResourceType(patientId) == ResourceType_Patient); |
1957 Recycle(attachment.GetCompressedSize(), db_.GetPublicId(patientId)); | |
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1958 |
1247 | 1959 db_.AddAttachment(resourceId, attachment); |
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1960 |
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1961 t.Commit(attachment.GetCompressedSize()); |
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1962 |
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1963 return StoreStatus_Success; |
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1964 } |
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1965 |
702
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1966 |
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1967 void ServerIndex::DeleteAttachment(const std::string& publicId, |
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1968 FileContentType type) |
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1969 { |
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1970 boost::mutex::scoped_lock lock(mutex_); |
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1971 Transaction t(*this); |
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1972 |
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1973 ResourceType rtype; |
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1974 int64_t id; |
1294 | 1975 if (!db_.LookupResource(id, rtype, publicId)) |
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1976 { |
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1977 throw OrthancException(ErrorCode_UnknownResource); |
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1978 } |
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1979 |
1247 | 1980 db_.DeleteAttachment(id, type); |
702
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1981 |
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1982 t.Commit(0); |
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1983 } |
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1984 |
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1985 |
1002
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1986 bool ServerIndex::GetMetadata(Json::Value& target, |
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1987 const std::string& publicId) |
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1988 { |
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1989 boost::mutex::scoped_lock lock(mutex_); |
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1990 |
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1991 target = Json::objectValue; |
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1992 |
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1993 ResourceType type; |
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1994 int64_t id; |
1294 | 1995 if (!db_.LookupResource(id, type, publicId)) |
1002
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1996 { |
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1997 return false; |
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1998 } |
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1999 |
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2000 std::list<MetadataType> metadata; |
1247 | 2001 db_.ListAvailableMetadata(metadata, id); |
1002
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2002 |
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2003 for (std::list<MetadataType>::const_iterator |
1304 | 2004 it = metadata.begin(); it != metadata.end(); ++it) |
1002
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2005 { |
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2006 std::string key = EnumerationToString(*it); |
1238 | 2007 |
2008 std::string value; | |
1247 | 2009 if (!db_.LookupMetadata(value, id, *it)) |
1238 | 2010 { |
2011 value.clear(); | |
2012 } | |
2013 | |
1002
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2014 target[key] = value; |
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2015 } |
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2016 |
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2017 return true; |
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2018 } |
1218
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2019 |
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2020 |
1249
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2021 void ServerIndex::SetGlobalProperty(GlobalProperty property, |
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2022 const std::string& value) |
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2023 { |
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2024 boost::mutex::scoped_lock lock(mutex_); |
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2025 db_.SetGlobalProperty(property, value); |
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2026 } |
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2027 |
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2028 |
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2029 std::string ServerIndex::GetGlobalProperty(GlobalProperty property, |
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2030 const std::string& defaultValue) |
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2031 { |
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2032 boost::mutex::scoped_lock lock(mutex_); |
1239 | 2033 |
2034 std::string value; | |
1247 | 2035 if (db_.LookupGlobalProperty(value, property)) |
1239 | 2036 { |
2037 return value; | |
2038 } | |
2039 else | |
2040 { | |
2041 return defaultValue; | |
2042 } | |
1218
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2043 } |
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2044 |
1352 | 2045 |
2046 bool ServerIndex::GetMainDicomTags(DicomMap& result, | |
2047 const std::string& publicId, | |
1677
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2048 ResourceType expectedType, |
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2049 ResourceType levelOfInterest) |
1352 | 2050 { |
1677
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2051 // Yes, the following test could be shortened, but we wish to make it as clear as possible |
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2052 if (!(expectedType == ResourceType_Patient && levelOfInterest == ResourceType_Patient) && |
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2053 !(expectedType == ResourceType_Study && levelOfInterest == ResourceType_Patient) && |
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2054 !(expectedType == ResourceType_Study && levelOfInterest == ResourceType_Study) && |
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2055 !(expectedType == ResourceType_Series && levelOfInterest == ResourceType_Series) && |
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2056 !(expectedType == ResourceType_Instance && levelOfInterest == ResourceType_Instance)) |
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2057 { |
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2058 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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2059 } |
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2060 |
1352 | 2061 result.Clear(); |
2062 | |
2063 boost::mutex::scoped_lock lock(mutex_); | |
2064 | |
2065 // Lookup for the requested resource | |
2066 int64_t id; | |
2067 ResourceType type; | |
2068 if (!db_.LookupResource(id, type, publicId) || | |
2069 type != expectedType) | |
2070 { | |
2071 return false; | |
2072 } | |
1677
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2073 |
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2074 if (type == ResourceType_Study) |
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2075 { |
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2076 DicomMap tmp; |
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2077 db_.GetMainDicomTags(tmp, id); |
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2078 |
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2079 switch (levelOfInterest) |
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2080 { |
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2081 case ResourceType_Patient: |
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2082 tmp.ExtractPatientInformation(result); |
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2083 return true; |
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2084 |
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2085 case ResourceType_Study: |
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2086 tmp.ExtractStudyInformation(result); |
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2087 return true; |
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2088 |
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2089 default: |
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2090 throw OrthancException(ErrorCode_InternalError); |
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2091 } |
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2092 } |
1352 | 2093 else |
2094 { | |
2095 db_.GetMainDicomTags(result, id); | |
2096 return true; | |
2097 } | |
2098 } | |
1555
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2099 |
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2100 |
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2101 bool ServerIndex::LookupResourceType(ResourceType& type, |
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2102 const std::string& publicId) |
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2103 { |
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2104 boost::mutex::scoped_lock lock(mutex_); |
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2105 |
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2106 int64_t id; |
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2107 return db_.LookupResource(id, type, publicId); |
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2108 } |
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2109 |
1668
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2110 |
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2111 unsigned int ServerIndex::GetDatabaseVersion() |
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2112 { |
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2113 boost::mutex::scoped_lock lock(mutex_); |
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2114 return db_.GetDatabaseVersion(); |
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2115 } |
1750
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2116 |
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2117 |
1753 | 2118 void ServerIndex::FindCandidates(std::vector<std::string>& resources, |
2119 std::vector<std::string>& instances, | |
1757
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2120 const ::Orthanc::LookupResource& lookup) |
1750
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2121 { |
1753 | 2122 boost::mutex::scoped_lock lock(mutex_); |
2123 | |
2124 std::list<int64_t> tmp; | |
2125 lookup.FindCandidates(tmp, db_); | |
2126 | |
2127 resources.resize(tmp.size()); | |
2128 instances.resize(tmp.size()); | |
2129 | |
2130 size_t pos = 0; | |
2131 for (std::list<int64_t>::const_iterator | |
2132 it = tmp.begin(); it != tmp.end(); ++it, pos++) | |
2133 { | |
1754 | 2134 assert(db_.GetResourceType(*it) == lookup.GetLevel()); |
2135 | |
1753 | 2136 int64_t instance; |
2137 if (!Toolbox::FindOneChildInstance(instance, db_, *it, lookup.GetLevel())) | |
2138 { | |
2139 throw OrthancException(ErrorCode_InternalError); | |
2140 } | |
2141 | |
2142 resources[pos] = db_.GetPublicId(*it); | |
2143 instances[pos] = db_.GetPublicId(instance); | |
2144 } | |
1750
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2145 } |
0 | 2146 } |