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annotate OrthancServer/ServerContext.cpp @ 1006:649d47854314 lua-scripting

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proper handling of metadata in Store
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 08 Jul 2014 15:11:00 +0200
parents 84b6d7bca6db
children 871c49c9b11d
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege,
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4 * Belgium
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5 *
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6 * This program is free software: you can redistribute it and/or
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7 * modify it under the terms of the GNU General Public License as
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8 * published by the Free Software Foundation, either version 3 of the
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9 * License, or (at your option) any later version.
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10 *
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11 * In addition, as a special exception, the copyright holders of this
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12 * program give permission to link the code of its release with the
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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14 * that use the same license as the "OpenSSL" library), and distribute
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15 * the linked executables. You must obey the GNU General Public License
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16 * in all respects for all of the code used other than "OpenSSL". If you
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17 * modify file(s) with this exception, you may extend this exception to
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18 * your version of the file(s), but you are not obligated to do so. If
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19 * you do not wish to do so, delete this exception statement from your
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20 * version. If you delete this exception statement from all source files
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21 * in the program, then also delete it here.
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22 *
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23 * This program is distributed in the hope that it will be useful, but
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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26 * General Public License for more details.
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27 *
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28 * You should have received a copy of the GNU General Public License
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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30 **/
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31
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32
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33 #include "PrecompiledHeadersServer.h"
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34 #include "ServerContext.h"
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35
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36 #include "../Core/HttpServer/FilesystemHttpSender.h"
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37 #include "../Core/Lua/LuaFunctionCall.h"
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38 #include "FromDcmtkBridge.h"
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39 #include "ServerToolbox.h"
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40 #include "OrthancInitialization.h"
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41
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42 #include <glog/logging.h>
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43 #include <EmbeddedResources.h>
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44 #include <dcmtk/dcmdata/dcfilefo.h>
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45
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46
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47 #include "Scheduler/DeleteInstanceCommand.h"
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48 #include "Scheduler/StoreScuCommand.h"
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49
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51
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52 #define ENABLE_DICOM_CACHE 1
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53
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54 static const char* RECEIVED_INSTANCE_FILTER = "ReceivedInstanceFilter";
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55 static const char* ON_STORED_INSTANCE = "OnStoredInstance";
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56
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57 static const size_t DICOM_CACHE_SIZE = 2;
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58
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59 /**
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60 * IMPORTANT: We make the assumption that the same instance of
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61 * FileStorage can be accessed from multiple threads. This seems OK
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62 * since the filesystem implements the required locking mechanisms,
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63 * but maybe a read-writer lock on the "FileStorage" could be
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64 * useful. Conversely, "ServerIndex" already implements mutex-based
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65 * locking.
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66 **/
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67
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68 namespace Orthanc
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69 {
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70 ServerContext::ServerContext(const boost::filesystem::path& storagePath,
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71 const boost::filesystem::path& indexPath) :
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72 storage_(storagePath.string()),
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73 index_(*this, indexPath.string()),
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74 accessor_(storage_),
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75 compressionEnabled_(false),
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76 provider_(*this),
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77 dicomCache_(provider_, DICOM_CACHE_SIZE),
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78 scheduler_(Configuration::GetGlobalIntegerParameter("LimitJobs", 10))
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79 {
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80 scu_.SetLocalApplicationEntityTitle(Configuration::GetGlobalStringParameter("DicomAet", "ORTHANC"));
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81 //scu_.SetMillisecondsBeforeClose(1); // The connection is always released
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82
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83 lua_.Execute(Orthanc::EmbeddedResources::LUA_TOOLBOX);
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84 }
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85
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86 void ServerContext::SetCompressionEnabled(bool enabled)
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87 {
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88 if (enabled)
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89 LOG(WARNING) << "Disk compression is enabled";
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90 else
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91 LOG(WARNING) << "Disk compression is disabled";
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92
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93 compressionEnabled_ = enabled;
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94 }
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95
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96 void ServerContext::RemoveFile(const std::string& fileUuid)
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97 {
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98 storage_.Remove(fileUuid);
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99 }
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101
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102 bool ServerContext::ApplyReceivedInstanceFilter(const Json::Value& simplified,
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103 const std::string& remoteAet)
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104 {
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105 LuaContextLocker locker(*this);
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106
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107 if (locker.GetLua().IsExistingFunction(RECEIVED_INSTANCE_FILTER))
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108 {
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109 LuaFunctionCall call(locker.GetLua(), RECEIVED_INSTANCE_FILTER);
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110 call.PushJson(simplified);
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111 call.PushString(remoteAet);
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112
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113 if (!call.ExecutePredicate())
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114 {
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115 return false;
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116 }
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117 }
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118
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119 return true;
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120 }
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121
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122
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123 void ServerContext::ApplyOnStoredInstance(const std::string& instanceId,
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124 const Json::Value& simplifiedDicom,
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125 const Json::Value& metadata)
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126 {
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127 LuaContextLocker locker(*this);
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128
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129 if (locker.GetLua().IsExistingFunction(ON_STORED_INSTANCE))
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130 {
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131 LuaFunctionCall call(locker.GetLua(), ON_STORED_INSTANCE);
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132 call.PushString(instanceId);
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133 call.PushJson(simplifiedDicom);
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134 call.PushJson(metadata);
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135
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136 Json::Value result;
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137 call.ExecuteToJson(result);
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138
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139 printf("TODO\n");
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140 std::cout << result;
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141 }
1001
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142
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143 #if 0
1001
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144 {
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145 // Autorouting test
f3929718ea7e autorouting primitives
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146 RemoteModalityParameters p = Configuration::GetModalityUsingSymbolicName("sample");
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147
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148 ServerJob job;
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149 ServerCommandInstance& a = job.AddCommand(new StoreScuCommand(*this, p));
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150 a.AddInput(instanceId);
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diff changeset
151
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152 /*ServerCommandInstance& b = job.AddCommand(new DeleteInstanceCommand(*this));
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153 a.ConnectNext(b);*/
1001
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diff changeset
154
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155 job.SetDescription("Autorouting test");
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156 scheduler_.Submit(job);
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157 }
1002
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diff changeset
158 #endif
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159 }
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160
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diff changeset
161
1004
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diff changeset
162 StoreStatus ServerContext::Store(std::string& resultPublicId,
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163 DicomInstanceToStore& dicom)
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164 {
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165 try
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166 {
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167 DicomInstanceHasher hasher(dicom.GetSummary());
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168 resultPublicId = hasher.HashInstance();
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diff changeset
169
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170 Json::Value simplified;
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diff changeset
171 SimplifyTags(simplified, dicom.GetJson());
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172
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173 // Test if the instance must be filtered out
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diff changeset
174 if (!ApplyReceivedInstanceFilter(simplified, dicom.GetRemoteAet()))
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diff changeset
175 {
a226e0959d8b DicomInstanceToStore
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diff changeset
176 LOG(INFO) << "An incoming instance has been discarded by the filter";
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diff changeset
177 return StoreStatus_FilteredOut;
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diff changeset
178 }
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diff changeset
179
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diff changeset
180 if (compressionEnabled_)
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diff changeset
181 {
a226e0959d8b DicomInstanceToStore
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diff changeset
182 accessor_.SetCompressionForNextOperations(CompressionType_Zlib);
a226e0959d8b DicomInstanceToStore
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183 }
a226e0959d8b DicomInstanceToStore
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diff changeset
184 else
a226e0959d8b DicomInstanceToStore
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diff changeset
185 {
a226e0959d8b DicomInstanceToStore
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diff changeset
186 accessor_.SetCompressionForNextOperations(CompressionType_None);
a226e0959d8b DicomInstanceToStore
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diff changeset
187 }
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diff changeset
188
a226e0959d8b DicomInstanceToStore
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diff changeset
189 FileInfo dicomInfo = accessor_.Write(dicom.GetBufferData(), dicom.GetBufferSize(), FileContentType_Dicom);
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parents: 1002
diff changeset
190 FileInfo jsonInfo = accessor_.Write(dicom.GetJson().toStyledString(), FileContentType_DicomAsJson);
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diff changeset
191
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diff changeset
192 ServerIndex::Attachments attachments;
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diff changeset
193 attachments.push_back(dicomInfo);
a226e0959d8b DicomInstanceToStore
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diff changeset
194 attachments.push_back(jsonInfo);
a226e0959d8b DicomInstanceToStore
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diff changeset
195
1006
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diff changeset
196 std::map<MetadataType, std::string> instanceMetadata;
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diff changeset
197 StoreStatus status = index_.Store(instanceMetadata, dicom.GetSummary(), attachments,
649d47854314 proper handling of metadata in Store
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diff changeset
198 dicom.GetRemoteAet(), dicom.GetMetadata());
1004
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diff changeset
199
a226e0959d8b DicomInstanceToStore
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diff changeset
200 if (status != StoreStatus_Success)
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
201 {
a226e0959d8b DicomInstanceToStore
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diff changeset
202 storage_.Remove(dicomInfo.GetUuid());
a226e0959d8b DicomInstanceToStore
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diff changeset
203 storage_.Remove(jsonInfo.GetUuid());
a226e0959d8b DicomInstanceToStore
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diff changeset
204 }
a226e0959d8b DicomInstanceToStore
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diff changeset
205
a226e0959d8b DicomInstanceToStore
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diff changeset
206 switch (status)
a226e0959d8b DicomInstanceToStore
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diff changeset
207 {
a226e0959d8b DicomInstanceToStore
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diff changeset
208 case StoreStatus_Success:
a226e0959d8b DicomInstanceToStore
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diff changeset
209 LOG(INFO) << "New instance stored";
a226e0959d8b DicomInstanceToStore
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diff changeset
210 break;
a226e0959d8b DicomInstanceToStore
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diff changeset
211
a226e0959d8b DicomInstanceToStore
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diff changeset
212 case StoreStatus_AlreadyStored:
a226e0959d8b DicomInstanceToStore
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diff changeset
213 LOG(INFO) << "Already stored";
a226e0959d8b DicomInstanceToStore
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diff changeset
214 break;
a226e0959d8b DicomInstanceToStore
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diff changeset
215
a226e0959d8b DicomInstanceToStore
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diff changeset
216 case StoreStatus_Failure:
a226e0959d8b DicomInstanceToStore
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diff changeset
217 LOG(ERROR) << "Store failure";
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
218 break;
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
219
a226e0959d8b DicomInstanceToStore
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diff changeset
220 default:
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
221 // This should never happen
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
222 break;
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
223 }
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
224
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
225 if (status == StoreStatus_Success ||
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
226 status == StoreStatus_AlreadyStored)
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
227 {
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
228 try
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
229 {
1006
649d47854314 proper handling of metadata in Store
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
230 #if 1
1004
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
231 Json::Value metadata = Json::objectValue;
1006
649d47854314 proper handling of metadata in Store
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parents: 1005
diff changeset
232 for (std::map<MetadataType, std::string>::const_iterator
649d47854314 proper handling of metadata in Store
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diff changeset
233 it = instanceMetadata.begin();
649d47854314 proper handling of metadata in Store
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1005
diff changeset
234 it != instanceMetadata.end(); ++it)
1004
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
235 {
1006
649d47854314 proper handling of metadata in Store
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
236 metadata[EnumerationToString(it->first)] = it->second;
1004
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
237 }
1006
649d47854314 proper handling of metadata in Store
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1005
diff changeset
238 #else
649d47854314 proper handling of metadata in Store
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diff changeset
239 Json::Value metadata;
649d47854314 proper handling of metadata in Store
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1005
diff changeset
240 index_.GetMetadata(metadata, resultPublicId);
649d47854314 proper handling of metadata in Store
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1005
diff changeset
241 #endif
649d47854314 proper handling of metadata in Store
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diff changeset
242
649d47854314 proper handling of metadata in Store
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
243 std::cout << metadata;
1004
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
244
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
245 ApplyOnStoredInstance(resultPublicId, simplified, metadata);
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
246 }
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
247 catch (OrthancException&)
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
248 {
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
249 LOG(ERROR) << "Error when dealing with OnStoredInstance";
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
250 }
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
251 }
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
252
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
253 return status;
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
254 }
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
255 catch (OrthancException& e)
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
256 {
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
257 if (e.GetErrorCode() == ErrorCode_InexistentTag)
a226e0959d8b DicomInstanceToStore
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parents: 1002
diff changeset
258 {
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
259 LogMissingRequiredTag(dicom.GetSummary());
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
260 }
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
261
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
262 throw;
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
263 }
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
264 }
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
265
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
266
a226e0959d8b DicomInstanceToStore
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1002
diff changeset
267
697
dd1ce9a2844c access to attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 696
diff changeset
268 void ServerContext::AnswerDicomFile(RestApiOutput& output,
dd1ce9a2844c access to attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 696
diff changeset
269 const std::string& instancePublicId,
dd1ce9a2844c access to attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 696
diff changeset
270 FileContentType content)
226
8a26a8e85edf refactoring to read files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 224
diff changeset
271 {
232
5368bbe813cf refactoring of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 227
diff changeset
272 FileInfo attachment;
236
6d9be2b470b4 compression
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 233
diff changeset
273 if (!index_.LookupAttachment(attachment, instancePublicId, content))
232
5368bbe813cf refactoring of attachments
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 227
diff changeset
274 {
236
6d9be2b470b4 compression
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 233
diff changeset
275 throw OrthancException(ErrorCode_InternalError);
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276 }
226
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277
236
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278 accessor_.SetCompressionForNextOperations(attachment.GetCompressionType());
320
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279
236
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280 std::auto_ptr<HttpFileSender> sender(accessor_.ConstructHttpFileSender(attachment.GetUuid()));
320
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281 sender->SetContentType("application/dicom");
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282 sender->SetDownloadFilename(instancePublicId + ".dcm");
236
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283 output.AnswerFile(*sender);
226
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284 }
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285
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286
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287 void ServerContext::ReadJson(Json::Value& result,
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288 const std::string& instancePublicId)
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289 {
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290 std::string s;
697
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291 ReadFile(s, instancePublicId, FileContentType_DicomAsJson);
226
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292
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293 Json::Reader reader;
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294 if (!reader.parse(s, result))
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295 {
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296 throw OrthancException("Corrupted JSON file");
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297 }
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298 }
227
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299
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300
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301 void ServerContext::ReadFile(std::string& result,
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302 const std::string& instancePublicId,
697
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303 FileContentType content,
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304 bool uncompressIfNeeded)
227
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305 {
232
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306 FileInfo attachment;
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307 if (!index_.LookupAttachment(attachment, instancePublicId, content))
227
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308 {
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309 throw OrthancException(ErrorCode_InternalError);
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310 }
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311
697
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312 if (uncompressIfNeeded)
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313 {
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314 accessor_.SetCompressionForNextOperations(attachment.GetCompressionType());
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315 }
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316 else
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317 {
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318 accessor_.SetCompressionForNextOperations(CompressionType_None);
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319 }
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320
232
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321 accessor_.Read(result, attachment.GetUuid());
227
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322 }
285
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323
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324
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diff changeset
325 IDynamicObject* ServerContext::DicomCacheProvider::Provide(const std::string& instancePublicId)
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326 {
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327 std::string content;
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diff changeset
328 context_.ReadFile(content, instancePublicId, FileContentType_Dicom);
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329 return new ParsedDicomFile(content);
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330 }
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diff changeset
331
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diff changeset
332
778
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diff changeset
333 ServerContext::DicomCacheLocker::DicomCacheLocker(ServerContext& that,
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334 const std::string& instancePublicId) :
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335 that_(that)
285
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diff changeset
336 {
291
4d7469f72a0b embedding of dicom dictionaries
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diff changeset
337 #if ENABLE_DICOM_CACHE == 0
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diff changeset
338 static std::auto_ptr<IDynamicObject> p;
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diff changeset
339 p.reset(provider_.Provide(instancePublicId));
778
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340 dicom_ = dynamic_cast<ParsedDicomFile*>(p.get());
291
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diff changeset
341 #else
778
aebf0071020e refactoring of the mutex for the dicom cache
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diff changeset
342 that_.dicomCacheMutex_.lock();
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343 dicom_ = &dynamic_cast<ParsedDicomFile&>(that_.dicomCache_.Access(instancePublicId));
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diff changeset
344 #endif
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345 }
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diff changeset
346
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diff changeset
347
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diff changeset
348 ServerContext::DicomCacheLocker::~DicomCacheLocker()
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349 {
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diff changeset
350 #if ENABLE_DICOM_CACHE == 0
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351 #else
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diff changeset
352 that_.dicomCacheMutex_.unlock();
291
4d7469f72a0b embedding of dicom dictionaries
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diff changeset
353 #endif
285
4031f73fe0e4 access to the raw dicom tags
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diff changeset
354 }
304
4eea080e6e7a refactoring
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diff changeset
355
4eea080e6e7a refactoring
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diff changeset
356
695
c59bc408fb10 parameter to disable the computation of the MD5
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diff changeset
357 void ServerContext::SetStoreMD5ForAttachments(bool storeMD5)
c59bc408fb10 parameter to disable the computation of the MD5
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diff changeset
358 {
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diff changeset
359 LOG(INFO) << "Storing MD5 for attachments: " << (storeMD5 ? "yes" : "no");
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diff changeset
360 accessor_.SetStoreMD5(storeMD5);
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diff changeset
361 }
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diff changeset
362
699
2929e17f8447 add attachments to resources
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diff changeset
363
2929e17f8447 add attachments to resources
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diff changeset
364 bool ServerContext::AddAttachment(const std::string& resourceId,
2929e17f8447 add attachments to resources
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diff changeset
365 FileContentType attachmentType,
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diff changeset
366 const void* data,
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diff changeset
367 size_t size)
2929e17f8447 add attachments to resources
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diff changeset
368 {
2929e17f8447 add attachments to resources
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diff changeset
369 LOG(INFO) << "Adding attachment " << EnumerationToString(attachmentType) << " to resource " << resourceId;
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diff changeset
370
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diff changeset
371 if (compressionEnabled_)
2929e17f8447 add attachments to resources
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diff changeset
372 {
2929e17f8447 add attachments to resources
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diff changeset
373 accessor_.SetCompressionForNextOperations(CompressionType_Zlib);
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diff changeset
374 }
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diff changeset
375 else
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diff changeset
376 {
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diff changeset
377 accessor_.SetCompressionForNextOperations(CompressionType_None);
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diff changeset
378 }
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diff changeset
379
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diff changeset
380 FileInfo info = accessor_.Write(data, size, attachmentType);
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diff changeset
381 StoreStatus status = index_.AddAttachment(info, resourceId);
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diff changeset
382
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diff changeset
383 if (status != StoreStatus_Success)
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diff changeset
384 {
2929e17f8447 add attachments to resources
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diff changeset
385 storage_.Remove(info.GetUuid());
2929e17f8447 add attachments to resources
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diff changeset
386 return false;
2929e17f8447 add attachments to resources
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diff changeset
387 }
2929e17f8447 add attachments to resources
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diff changeset
388 else
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diff changeset
389 {
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diff changeset
390 return true;
2929e17f8447 add attachments to resources
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diff changeset
391 }
2929e17f8447 add attachments to resources
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diff changeset
392 }
224
4eb0c7ce86c9 refactoring for store
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parents:
diff changeset
393 }