Mercurial > hg > orthanc
annotate OrthancServer/ServerContext.cpp @ 2129:0c09d1af22f3
"/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Mon, 07 Nov 2016 17:44:10 +0100 |
parents | 9329ba17a069 |
children | ddc75c6c712d |
rev | line source |
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224 | 1 /** |
2 * Orthanc - A Lightweight, RESTful DICOM Store | |
1900 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
224 | 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. | |
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. | |
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" |
224 | 34 #include "ServerContext.h" |
35 | |
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36 #include "../Core/FileStorage/StorageAccessor.h" |
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37 #include "../Core/HttpServer/FilesystemHttpSender.h" |
1525 | 38 #include "../Core/HttpServer/HttpStreamTranscoder.h" |
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39 #include "../Core/Logging.h" |
795 | 40 #include "FromDcmtkBridge.h" |
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41 #include "ServerToolbox.h" |
771 | 42 #include "OrthancInitialization.h" |
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43 |
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44 #include <EmbeddedResources.h> |
794 | 45 #include <dcmtk/dcmdata/dcfilefo.h> |
224 | 46 |
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47 |
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48 #include "Scheduler/CallSystemCommand.h" |
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49 #include "Scheduler/DeleteInstanceCommand.h" |
1008 | 50 #include "Scheduler/ModifyInstanceCommand.h" |
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51 #include "Scheduler/StoreScuCommand.h" |
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52 #include "Scheduler/StorePeerCommand.h" |
1010 | 53 #include "OrthancRestApi/OrthancRestApi.h" |
1133 | 54 #include "../Plugins/Engine/OrthancPlugins.h" |
2122 | 55 #include "Search/LookupResource.h" |
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56 |
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57 |
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58 #define ENABLE_DICOM_CACHE 1 |
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59 |
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60 static const size_t DICOM_CACHE_SIZE = 2; |
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61 |
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62 /** |
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63 * IMPORTANT: We make the assumption that the same instance of |
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64 * FileStorage can be accessed from multiple threads. This seems OK |
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65 * since the filesystem implements the required locking mechanisms, |
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66 * but maybe a read-writer lock on the "FileStorage" could be |
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67 * useful. Conversely, "ServerIndex" already implements mutex-based |
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68 * locking. |
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69 **/ |
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70 |
224 | 71 namespace Orthanc |
72 { | |
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73 void ServerContext::ChangeThread(ServerContext* that) |
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74 { |
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75 while (!that->done_) |
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76 { |
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77 std::auto_ptr<IDynamicObject> obj(that->pendingChanges_.Dequeue(100)); |
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78 |
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79 if (obj.get() != NULL) |
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80 { |
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81 const ServerIndexChange& change = dynamic_cast<const ServerIndexChange&>(*obj.get()); |
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82 |
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83 boost::recursive_mutex::scoped_lock lock(that->listenersMutex_); |
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84 for (ServerListeners::iterator it = that->listeners_.begin(); |
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85 it != that->listeners_.end(); ++it) |
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86 { |
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87 try |
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88 { |
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89 it->GetListener().SignalChange(change); |
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90 } |
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91 catch (OrthancException& e) |
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92 { |
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93 LOG(ERROR) << "Error in the " << it->GetDescription() |
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94 << " callback while signaling a change: " << e.What(); |
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95 } |
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96 } |
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97 } |
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98 } |
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99 } |
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100 |
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101 |
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102 ServerContext::ServerContext(IDatabaseWrapper& database, |
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103 IStorageArea& area) : |
1247 | 104 index_(*this, database), |
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105 area_(area), |
656 | 106 compressionEnabled_(false), |
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107 storeMD5_(true), |
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108 provider_(*this), |
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109 dicomCache_(provider_, DICOM_CACHE_SIZE), |
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110 scheduler_(Configuration::GetGlobalUnsignedIntegerParameter("LimitJobs", 10)), |
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111 lua_(*this), |
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112 #if ORTHANC_PLUGINS_ENABLED == 1 |
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113 plugins_(NULL), |
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114 #endif |
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115 done_(false), |
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116 queryRetrieveArchive_(Configuration::GetGlobalUnsignedIntegerParameter("QueryRetrieveSize", 10)), |
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117 defaultLocalAet_(Configuration::GetGlobalStringParameter("DicomAet", "ORTHANC")) |
224 | 118 { |
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119 uint64_t s = Configuration::GetGlobalUnsignedIntegerParameter("DicomAssociationCloseDelay", 5); // In seconds |
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120 scu_.SetMillisecondsBeforeClose(s * 1000); // Milliseconds are expected here |
774 | 121 |
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122 listeners_.push_back(ServerListener(lua_, "Lua")); |
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123 |
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124 changeThread_ = boost::thread(ChangeThread, this); |
224 | 125 } |
126 | |
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127 |
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128 |
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129 ServerContext::~ServerContext() |
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130 { |
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131 if (!done_) |
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132 { |
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133 LOG(ERROR) << "INTERNAL ERROR: ServerContext::Stop() should be invoked manually to avoid mess in the destruction order!"; |
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134 Stop(); |
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135 } |
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136 } |
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137 |
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138 |
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139 void ServerContext::Stop() |
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140 { |
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141 if (!done_) |
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142 { |
1459 | 143 { |
144 boost::recursive_mutex::scoped_lock lock(listenersMutex_); | |
145 listeners_.clear(); | |
146 } | |
147 | |
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148 done_ = true; |
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149 |
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150 if (changeThread_.joinable()) |
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151 { |
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152 changeThread_.join(); |
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153 } |
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154 |
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155 scu_.Finalize(); |
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156 |
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157 // Do not change the order below! |
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158 scheduler_.Stop(); |
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159 index_.Stop(); |
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160 } |
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161 } |
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162 |
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163 |
236 | 164 void ServerContext::SetCompressionEnabled(bool enabled) |
165 { | |
166 if (enabled) | |
167 LOG(WARNING) << "Disk compression is enabled"; | |
168 else | |
169 LOG(WARNING) << "Disk compression is disabled"; | |
170 | |
171 compressionEnabled_ = enabled; | |
172 } | |
173 | |
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174 |
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175 void ServerContext::RemoveFile(const std::string& fileUuid, |
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176 FileContentType type) |
227
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177 { |
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178 area_.Remove(fileUuid, type); |
227
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179 } |
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180 |
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181 |
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182 StoreStatus ServerContext::Store(std::string& resultPublicId, |
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183 DicomInstanceToStore& dicom) |
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184 { |
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185 try |
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186 { |
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187 StorageAccessor accessor(area_); |
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188 |
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189 DicomInstanceHasher hasher(dicom.GetSummary()); |
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190 resultPublicId = hasher.HashInstance(); |
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191 |
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192 Json::Value simplifiedTags; |
2120 | 193 ServerToolbox::SimplifyTags(simplifiedTags, dicom.GetJson(), DicomToJsonFormat_Human); |
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194 |
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195 // Test if the instance must be filtered out |
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196 bool accepted = true; |
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197 |
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198 { |
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199 boost::recursive_mutex::scoped_lock lock(listenersMutex_); |
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200 |
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201 for (ServerListeners::iterator it = listeners_.begin(); it != listeners_.end(); ++it) |
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202 { |
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203 try |
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204 { |
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205 if (!it->GetListener().FilterIncomingInstance(dicom, simplifiedTags)) |
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206 { |
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207 accepted = false; |
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208 break; |
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209 } |
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210 } |
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211 catch (OrthancException& e) |
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212 { |
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213 LOG(ERROR) << "Error in the " << it->GetDescription() |
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214 << " callback while receiving an instance: " << e.What(); |
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215 throw; |
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216 } |
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217 } |
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218 } |
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219 |
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220 if (!accepted) |
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221 { |
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222 LOG(INFO) << "An incoming instance has been discarded by the filter"; |
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223 return StoreStatus_FilteredOut; |
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224 } |
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225 |
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226 // TODO Should we use "gzip" instead? |
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227 CompressionType compression = (compressionEnabled_ ? CompressionType_ZlibWithSize : CompressionType_None); |
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228 |
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229 FileInfo dicomInfo = accessor.Write(dicom.GetBufferData(), dicom.GetBufferSize(), |
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230 FileContentType_Dicom, compression, storeMD5_); |
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231 FileInfo jsonInfo = accessor.Write(dicom.GetJson().toStyledString(), |
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232 FileContentType_DicomAsJson, compression, storeMD5_); |
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233 |
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234 ServerIndex::Attachments attachments; |
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235 attachments.push_back(dicomInfo); |
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236 attachments.push_back(jsonInfo); |
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237 |
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238 typedef std::map<MetadataType, std::string> InstanceMetadata; |
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239 InstanceMetadata instanceMetadata; |
1822 | 240 StoreStatus status = index_.Store(instanceMetadata, dicom, attachments); |
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241 |
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242 // Only keep the metadata for the "instance" level |
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243 dicom.GetMetadata().clear(); |
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244 |
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245 for (InstanceMetadata::const_iterator it = instanceMetadata.begin(); |
1304 | 246 it != instanceMetadata.end(); ++it) |
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247 { |
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248 dicom.GetMetadata().insert(std::make_pair(std::make_pair(ResourceType_Instance, it->first), |
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249 it->second)); |
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250 } |
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251 |
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252 if (status != StoreStatus_Success) |
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253 { |
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254 accessor.Remove(dicomInfo); |
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255 accessor.Remove(jsonInfo); |
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256 } |
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257 |
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258 switch (status) |
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259 { |
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260 case StoreStatus_Success: |
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261 LOG(INFO) << "New instance stored"; |
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262 break; |
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263 |
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264 case StoreStatus_AlreadyStored: |
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265 LOG(INFO) << "Already stored"; |
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266 break; |
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267 |
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268 case StoreStatus_Failure: |
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269 LOG(ERROR) << "Store failure"; |
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270 break; |
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271 |
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272 default: |
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273 // This should never happen |
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274 break; |
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275 } |
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276 |
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277 if (status == StoreStatus_Success || |
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278 status == StoreStatus_AlreadyStored) |
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279 { |
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280 boost::recursive_mutex::scoped_lock lock(listenersMutex_); |
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281 |
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282 for (ServerListeners::iterator it = listeners_.begin(); it != listeners_.end(); ++it) |
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283 { |
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284 try |
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285 { |
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286 it->GetListener().SignalStoredInstance(resultPublicId, dicom, simplifiedTags); |
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287 } |
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288 catch (OrthancException& e) |
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289 { |
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290 LOG(ERROR) << "Error in the " << it->GetDescription() |
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291 << " callback while receiving an instance: " << e.What(); |
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292 } |
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293 } |
1004
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DicomInstanceToStore
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294 } |
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295 |
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296 return status; |
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297 } |
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298 catch (OrthancException& e) |
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299 { |
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300 if (e.GetErrorCode() == ErrorCode_InexistentTag) |
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301 { |
2120 | 302 ServerToolbox::LogMissingRequiredTag(dicom.GetSummary()); |
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303 } |
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304 |
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305 throw; |
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306 } |
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307 } |
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308 |
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309 |
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310 void ServerContext::AnswerAttachment(RestApiOutput& output, |
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311 const std::string& resourceId, |
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312 FileContentType content) |
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313 { |
232
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314 FileInfo attachment; |
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315 if (!index_.LookupAttachment(attachment, resourceId, content)) |
232
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316 { |
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317 throw OrthancException(ErrorCode_UnknownResource); |
236 | 318 } |
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319 |
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320 StorageAccessor accessor(area_); |
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321 accessor.AnswerFile(output, attachment, GetFileContentMime(content)); |
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322 } |
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323 |
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324 |
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325 void ServerContext::ChangeAttachmentCompression(const std::string& resourceId, |
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326 FileContentType attachmentType, |
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327 CompressionType compression) |
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328 { |
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329 LOG(INFO) << "Changing compression type for attachment " |
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330 << EnumerationToString(attachmentType) |
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331 << " of resource " << resourceId << " to " |
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332 << compression; |
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333 |
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334 FileInfo attachment; |
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335 if (!index_.LookupAttachment(attachment, resourceId, attachmentType)) |
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336 { |
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337 throw OrthancException(ErrorCode_UnknownResource); |
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338 } |
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339 |
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340 if (attachment.GetCompressionType() == compression) |
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341 { |
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342 // Nothing to do |
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343 return; |
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344 } |
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345 |
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346 std::string content; |
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347 |
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348 StorageAccessor accessor(area_); |
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349 accessor.Read(content, attachment); |
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350 |
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351 FileInfo modified = accessor.Write(content.empty() ? NULL : content.c_str(), |
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352 content.size(), attachmentType, compression, storeMD5_); |
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353 |
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354 try |
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355 { |
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356 StoreStatus status = index_.AddAttachment(modified, resourceId); |
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357 if (status != StoreStatus_Success) |
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358 { |
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359 accessor.Remove(modified); |
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360 throw OrthancException(ErrorCode_Database); |
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361 } |
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362 } |
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363 catch (OrthancException&) |
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364 { |
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365 accessor.Remove(modified); |
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366 throw; |
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367 } |
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368 } |
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369 |
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370 |
2127 | 371 void ServerContext::ReadDicomAsJson(std::string& result, |
372 const std::string& instancePublicId) | |
373 { | |
2128
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374 FileInfo attachment; |
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375 if (index_.LookupAttachment(attachment, instancePublicId, FileContentType_DicomAsJson)) |
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376 { |
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377 ReadAttachment(result, attachment); |
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378 return; |
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379 } |
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380 |
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381 // The "DICOM as JSON" summary is not available from the Orthanc |
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382 // store (most probably deleted), reconstruct it from the DICOM file |
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|
383 std::string dicom; |
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diff
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|
384 ReadDicom(dicom, instancePublicId); |
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|
385 |
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|
386 LOG(INFO) << "Reconstructing the missing DICOM-as-JSON summary for instance: " << instancePublicId; |
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387 |
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|
388 ParsedDicomFile parsed(dicom); |
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389 |
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|
390 Json::Value summary; |
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391 parsed.DatasetToJson(summary); |
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392 |
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393 result = summary.toStyledString(); |
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394 |
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395 if (!AddAttachment(instancePublicId, FileContentType_DicomAsJson, result.c_str(), result.size())) |
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396 { |
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397 LOG(WARNING) << "Cannot associate the DICOM-as-JSON summary to instance: " << instancePublicId; |
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398 throw OrthancException(ErrorCode_InternalError); |
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399 } |
2127 | 400 } |
401 | |
402 | |
2124 | 403 void ServerContext::ReadDicomAsJson(Json::Value& result, |
404 const std::string& instancePublicId) | |
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405 { |
2127 | 406 std::string tmp; |
407 ReadDicomAsJson(tmp, instancePublicId); | |
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408 |
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409 Json::Reader reader; |
2127 | 410 if (!reader.parse(tmp, result)) |
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411 { |
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412 throw OrthancException(ErrorCode_CorruptedFile); |
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413 } |
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414 } |
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415 |
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416 |
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417 void ServerContext::ReadAttachment(std::string& result, |
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418 const std::string& instancePublicId, |
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419 FileContentType content, |
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420 bool uncompressIfNeeded) |
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421 { |
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422 FileInfo attachment; |
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423 if (!index_.LookupAttachment(attachment, instancePublicId, content)) |
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424 { |
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425 LOG(WARNING) << "Unable to read attachment " << EnumerationToString(content) << " of instance " << instancePublicId; |
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426 throw OrthancException(ErrorCode_InternalError); |
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427 } |
1550 | 428 |
429 if (uncompressIfNeeded) | |
430 { | |
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431 ReadAttachment(result, attachment); |
1550 | 432 } |
433 else | |
434 { | |
435 // Do not interpret the content of the storage area, return the | |
436 // raw data | |
437 area_.Read(result, attachment.GetUuid(), content); | |
438 } | |
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439 } |
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440 |
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441 |
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442 void ServerContext::ReadAttachment(std::string& result, |
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443 const FileInfo& attachment) |
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444 { |
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445 // This will decompress the attachment |
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446 StorageAccessor accessor(area_); |
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447 accessor.Read(result, attachment); |
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448 } |
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449 |
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450 |
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451 IDynamicObject* ServerContext::DicomCacheProvider::Provide(const std::string& instancePublicId) |
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452 { |
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453 std::string content; |
2124 | 454 context_.ReadDicom(content, instancePublicId); |
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455 return new ParsedDicomFile(content); |
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456 } |
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457 |
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458 |
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459 ServerContext::DicomCacheLocker::DicomCacheLocker(ServerContext& that, |
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460 const std::string& instancePublicId) : |
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461 that_(that), |
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462 lock_(that_.dicomCacheMutex_) |
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463 { |
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464 #if ENABLE_DICOM_CACHE == 0 |
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465 static std::auto_ptr<IDynamicObject> p; |
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466 p.reset(provider_.Provide(instancePublicId)); |
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467 dicom_ = dynamic_cast<ParsedDicomFile*>(p.get()); |
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468 #else |
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469 dicom_ = &dynamic_cast<ParsedDicomFile&>(that_.dicomCache_.Access(instancePublicId)); |
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470 #endif |
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471 } |
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472 |
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473 |
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474 ServerContext::DicomCacheLocker::~DicomCacheLocker() |
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475 { |
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476 } |
304 | 477 |
478 | |
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479 void ServerContext::SetStoreMD5ForAttachments(bool storeMD5) |
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480 { |
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481 LOG(INFO) << "Storing MD5 for attachments: " << (storeMD5 ? "yes" : "no"); |
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482 storeMD5_ = storeMD5; |
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483 } |
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484 |
699
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485 |
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486 bool ServerContext::AddAttachment(const std::string& resourceId, |
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487 FileContentType attachmentType, |
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488 const void* data, |
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489 size_t size) |
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490 { |
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491 LOG(INFO) << "Adding attachment " << EnumerationToString(attachmentType) << " to resource " << resourceId; |
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492 |
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493 // TODO Should we use "gzip" instead? |
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494 CompressionType compression = (compressionEnabled_ ? CompressionType_ZlibWithSize : CompressionType_None); |
699
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495 |
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496 StorageAccessor accessor(area_); |
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497 FileInfo attachment = accessor.Write(data, size, attachmentType, compression, storeMD5_); |
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498 |
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499 StoreStatus status = index_.AddAttachment(attachment, resourceId); |
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500 if (status != StoreStatus_Success) |
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501 { |
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502 accessor.Remove(attachment); |
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503 return false; |
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504 } |
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505 else |
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506 { |
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507 return true; |
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508 } |
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509 } |
1145
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510 |
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511 |
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512 bool ServerContext::DeleteResource(Json::Value& target, |
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513 const std::string& uuid, |
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514 ResourceType expectedType) |
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515 { |
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516 return index_.DeleteResource(target, uuid, expectedType); |
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517 } |
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518 |
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519 |
1198 | 520 void ServerContext::SignalChange(const ServerIndexChange& change) |
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521 { |
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522 pendingChanges_.Enqueue(change.Clone()); |
1189
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523 } |
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524 |
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525 |
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526 #if ORTHANC_PLUGINS_ENABLED == 1 |
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527 void ServerContext::SetPlugins(OrthancPlugins& plugins) |
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528 { |
1459 | 529 boost::recursive_mutex::scoped_lock lock(listenersMutex_); |
530 | |
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531 plugins_ = &plugins; |
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532 |
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533 // TODO REFACTOR THIS |
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534 listeners_.clear(); |
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535 listeners_.push_back(ServerListener(lua_, "Lua")); |
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536 listeners_.push_back(ServerListener(plugins, "plugin")); |
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537 } |
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538 |
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539 |
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540 void ServerContext::ResetPlugins() |
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541 { |
1459 | 542 boost::recursive_mutex::scoped_lock lock(listenersMutex_); |
543 | |
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544 plugins_ = NULL; |
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545 |
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546 // TODO REFACTOR THIS |
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547 listeners_.clear(); |
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548 listeners_.push_back(ServerListener(lua_, "Lua")); |
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549 } |
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550 |
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551 |
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552 const OrthancPlugins& ServerContext::GetPlugins() const |
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553 { |
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554 if (HasPlugins()) |
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555 { |
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556 return *plugins_; |
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557 } |
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558 else |
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559 { |
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560 throw OrthancException(ErrorCode_InternalError); |
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561 } |
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562 } |
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563 |
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564 OrthancPlugins& ServerContext::GetPlugins() |
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565 { |
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566 if (HasPlugins()) |
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567 { |
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568 return *plugins_; |
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569 } |
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570 else |
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571 { |
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572 throw OrthancException(ErrorCode_InternalError); |
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573 } |
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574 } |
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575 |
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576 #endif |
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577 |
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578 |
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579 bool ServerContext::HasPlugins() const |
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580 { |
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581 #if ORTHANC_PLUGINS_ENABLED == 1 |
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582 return (plugins_ != NULL); |
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583 #else |
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584 return false; |
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585 #endif |
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586 } |
1757
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587 |
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588 |
1758 | 589 bool ServerContext::Apply(std::list<std::string>& result, |
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590 const ::Orthanc::LookupResource& lookup, |
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591 size_t maxResults) |
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592 { |
1758 | 593 result.clear(); |
594 | |
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595 std::vector<std::string> resources, instances; |
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596 GetIndex().FindCandidates(resources, instances, lookup); |
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597 |
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598 assert(resources.size() == instances.size()); |
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599 |
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600 for (size_t i = 0; i < instances.size(); i++) |
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601 { |
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602 Json::Value dicom; |
2124 | 603 ReadDicomAsJson(dicom, instances[i]); |
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604 |
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605 if (lookup.IsMatch(dicom)) |
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606 { |
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607 if (maxResults != 0 && |
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608 result.size() >= maxResults) |
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609 { |
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610 return false; // too many results |
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611 } |
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612 else |
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613 { |
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614 result.push_back(resources[i]); |
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615 } |
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616 } |
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617 } |
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618 |
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619 return true; // finished |
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620 } |
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621 |
224 | 622 } |