Mercurial > hg > orthanc

annotate OrthancServer/ServerJobs/ResourceModificationJob.cpp @ 3943:b26d25d3c1c7 transcoding

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"/{patients|studies|series}/.../modify": New option "Transcode"
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 18 May 2020 21:37:31 +0200
parents 5b882ad2ffd0
children 0b3256c3ee14
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2020 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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32
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33
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34 #include "../PrecompiledHeadersServer.h"
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35 #include "ResourceModificationJob.h"
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36
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37 #include "../../Core/Logging.h"
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38 #include "../../Core/SerializationToolbox.h"
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39 #include "../ServerContext.h"
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40
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41 #include <dcmtk/dcmdata/dcfilefo.h>
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42
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43 namespace Orthanc
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44 {
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45 class ResourceModificationJob::Output : public boost::noncopyable
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46 {
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47 private:
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48 ResourceType level_;
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49 bool isFirst_;
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50 std::string id_;
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51 std::string patientId_;
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52
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53 public:
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54 Output(ResourceType level) :
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55 level_(level),
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56 isFirst_(true)
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57 {
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58 if (level_ != ResourceType_Patient &&
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59 level_ != ResourceType_Study &&
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60 level_ != ResourceType_Series)
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61 {
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62 throw OrthancException(ErrorCode_ParameterOutOfRange);
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63 }
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64 }
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65
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66 ResourceType GetLevel() const
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67 {
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68 return level_;
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69 }
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70
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71
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72 void Update(DicomInstanceHasher& hasher)
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73 {
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74 if (isFirst_)
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75 {
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76 switch (level_)
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77 {
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78 case ResourceType_Series:
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79 id_ = hasher.HashSeries();
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80 break;
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81
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82 case ResourceType_Study:
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83 id_ = hasher.HashStudy();
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84 break;
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85
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86 case ResourceType_Patient:
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87 id_ = hasher.HashPatient();
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88 break;
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89
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90 default:
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91 throw OrthancException(ErrorCode_InternalError);
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92 }
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93
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94 patientId_ = hasher.HashPatient();
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95 isFirst_ = false;
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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 bool Format(Json::Value& target)
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101 {
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102 if (isFirst_)
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103 {
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104 return false;
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105 }
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106 else
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107 {
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108 target = Json::objectValue;
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109 target["Type"] = EnumerationToString(level_);
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110 target["ID"] = id_;
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111 target["Path"] = GetBasePath(level_, id_);
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112 target["PatientID"] = patientId_;
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113 return true;
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114 }
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115 }
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116
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117
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118 bool GetIdentifier(std::string& id)
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119 {
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120 if (isFirst_)
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121 {
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122 return false;
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123 }
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124 else
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125 {
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126 id = id_;
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127 return true;
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128 }
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129 }
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130 };
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131
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132
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133
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134
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135 bool ResourceModificationJob::HandleInstance(const std::string& instance)
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136 {
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137 if (modification_.get() == NULL ||
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138 output_.get() == NULL)
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139 {
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140 throw OrthancException(ErrorCode_BadSequenceOfCalls,
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141 "No modification was provided for this job");
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142 }
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143
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144
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145 LOG(INFO) << "Modifying instance in a job: " << instance;
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146
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147
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148 /**
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149 * Retrieve the original instance from the DICOM cache.
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150 **/
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151
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152 std::unique_ptr<DicomInstanceHasher> originalHasher;
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153 std::unique_ptr<ParsedDicomFile> modified;
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154
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155 try
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156 {
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157 ServerContext::DicomCacheLocker locker(GetContext(), instance);
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158 ParsedDicomFile& original = locker.GetDicom();
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159
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160 originalHasher.reset(new DicomInstanceHasher(original.GetHasher()));
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161 modified.reset(original.Clone(true));
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162 }
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163 catch (OrthancException& e)
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164 {
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165 LOG(WARNING) << "An error occurred while executing a Modification job on instance " << instance << ": " << e.GetDetails();
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166 return false;
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167 }
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168
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169
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170 /**
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171 * Compute the resulting DICOM instance.
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172 **/
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173
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174 modification_->Apply(*modified);
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175
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176 if (transcode_)
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177 {
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178 std::set<DicomTransferSyntax> syntaxes;
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179 syntaxes.insert(transferSyntax_);
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180
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181 std::string s;
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182 modified->SaveToMemoryBuffer(s); // TODO - AVOID THIS SERIALIZATION IF NO PLUGIN
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183
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184 std::unique_ptr<IDicomTranscoder::TranscodedDicom> transcoded;
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185 transcoded.reset(GetContext().TranscodeToParsed(modified->GetDcmtkObject(), s.empty() ? NULL : s.c_str(), s.size(), syntaxes, true));
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186 if (transcoded.get() == NULL)
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187 {
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188 LOG(WARNING) << "Cannot transcode instance, keeping original transfer syntax: " << instance;
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189 }
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190 else
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191 {
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192 modified.reset(ParsedDicomFile::AcquireDcmtkObject(transcoded->ReleaseDicom()));
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193 }
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194 }
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195
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196 DicomInstanceToStore toStore;
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197 toStore.SetOrigin(origin_);
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198 toStore.SetParsedDicomFile(*modified);
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199
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200
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201 /**
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202 * Prepare the metadata information to associate with the
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203 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom).
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204 **/
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205
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206 DicomInstanceHasher modifiedHasher = modified->GetHasher();
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207
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208 MetadataType metadataType = (isAnonymization_ ?
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209 MetadataType_AnonymizedFrom :
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210 MetadataType_ModifiedFrom);
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211
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212 if (originalHasher->HashSeries() != modifiedHasher.HashSeries())
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213 {
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214 toStore.AddMetadata(ResourceType_Series, metadataType, originalHasher->HashSeries());
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215 }
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216
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diff changeset
217 if (originalHasher->HashStudy() != modifiedHasher.HashStudy())
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218 {
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219 toStore.AddMetadata(ResourceType_Study, metadataType, originalHasher->HashStudy());
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220 }
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221
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222 if (originalHasher->HashPatient() != modifiedHasher.HashPatient())
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223 {
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diff changeset
224 toStore.AddMetadata(ResourceType_Patient, metadataType, originalHasher->HashPatient());
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225 }
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226
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diff changeset
227 assert(instance == originalHasher->HashInstance());
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228 toStore.AddMetadata(ResourceType_Instance, metadataType, instance);
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229
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230
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231 /**
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232 * Store the resulting DICOM instance into the Orthanc store.
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233 **/
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234
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235 std::string modifiedInstance;
3942
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diff changeset
236 if (GetContext().Store(modifiedInstance, toStore,
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diff changeset
237 StoreInstanceMode_Default) != StoreStatus_Success)
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238 {
2955
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239 throw OrthancException(ErrorCode_CannotStoreInstance,
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240 "Error while storing a modified instance " + instance);
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241 }
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242
3938
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parents: 3814
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243 /**
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244 * The assertion below will fail if automated transcoding to a
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245 * lossy transfer syntax is enabled in the Orthanc core, and if
Sebastien Jodogne <s.jodogne@gmail.com>
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246 * the source instance is not in this transfer syntax.
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247 **/
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248 // assert(modifiedInstance == modifiedHasher.HashInstance());
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249
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250 output_->Update(modifiedHasher);
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251
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252 return true;
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253 }
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254
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255
3943
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diff changeset
256 ResourceModificationJob::ResourceModificationJob(ServerContext& context) :
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diff changeset
257 CleaningInstancesJob(context, true /* by default, keep source */),
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diff changeset
258 modification_(new DicomModification),
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diff changeset
259 isAnonymization_(false),
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diff changeset
260 transcode_(false)
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diff changeset
261 {
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diff changeset
262 }
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diff changeset
263
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diff changeset
264
2642
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diff changeset
265 void ResourceModificationJob::SetModification(DicomModification* modification,
2868
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diff changeset
266 ResourceType level,
2642
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diff changeset
267 bool isAnonymization)
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parents:
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268 {
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diff changeset
269 if (modification == NULL)
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diff changeset
270 {
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271 throw OrthancException(ErrorCode_NullPointer);
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272 }
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273 else if (IsStarted())
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parents:
diff changeset
274 {
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275 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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parents:
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276 }
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diff changeset
277 else
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parents:
diff changeset
278 {
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diff changeset
279 modification_.reset(modification);
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diff changeset
280 output_.reset(new Output(level));
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281 isAnonymization_ = isAnonymization;
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282 }
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283 }
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284
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285
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286 void ResourceModificationJob::SetOrigin(const DicomInstanceOrigin& origin)
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287 {
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288 if (IsStarted())
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289 {
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290 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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291 }
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292 else
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293 {
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294 origin_ = origin;
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295 }
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296 }
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297
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298
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299 void ResourceModificationJob::SetOrigin(const RestApiCall& call)
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300 {
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301 SetOrigin(DicomInstanceOrigin::FromRest(call));
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302 }
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303
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304
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305 const DicomModification& ResourceModificationJob::GetModification() const
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306 {
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307 if (modification_.get() == NULL)
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308 {
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309 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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310 }
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311 else
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312 {
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313 return *modification_;
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314 }
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315 }
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316
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317
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318 DicomTransferSyntax ResourceModificationJob::GetTransferSyntax() const
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319 {
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320 if (transcode_)
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321 {
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322 return transferSyntax_;
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323 }
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324 else
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325 {
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326 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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327 }
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328 }
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329
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330
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331 void ResourceModificationJob::SetTranscode(DicomTransferSyntax syntax)
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332 {
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diff changeset
333 if (IsStarted())
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diff changeset
334 {
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335 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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336 }
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diff changeset
337 else
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338 {
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339 transcode_ = true;
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340 transferSyntax_ = syntax;
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341 }
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342 }
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343
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344
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345 void ResourceModificationJob::SetTranscode(const std::string& transferSyntaxUid)
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346 {
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347 DicomTransferSyntax s;
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348 if (LookupTransferSyntax(s, transferSyntaxUid))
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349 {
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diff changeset
350 SetTranscode(s);
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351 }
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352 else
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diff changeset
353 {
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diff changeset
354 throw OrthancException(ErrorCode_BadFileFormat,
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diff changeset
355 "Unknown transfer syntax UID: " + transferSyntaxUid);
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diff changeset
356 }
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diff changeset
357 }
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diff changeset
358
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diff changeset
359
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diff changeset
360 void ResourceModificationJob::ClearTranscode()
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diff changeset
361 {
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diff changeset
362 if (IsStarted())
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diff changeset
363 {
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diff changeset
364 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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diff changeset
365 }
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diff changeset
366 else
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diff changeset
367 {
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diff changeset
368 transcode_ = false;
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diff changeset
369 }
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diff changeset
370 }
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diff changeset
371
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diff changeset
372
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diff changeset
373 void ResourceModificationJob::GetPublicContent(Json::Value& value)
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374 {
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diff changeset
375 CleaningInstancesJob::GetPublicContent(value);
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diff changeset
376
ccc470091ea6 reorganization
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diff changeset
377 value["IsAnonymization"] = isAnonymization_;
2868
abce036683cd sharing code within OrthancRestAnonymizeModify
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diff changeset
378
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diff changeset
379 if (output_.get() != NULL)
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diff changeset
380 {
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diff changeset
381 output_->Format(value);
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diff changeset
382 }
3943
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diff changeset
383
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diff changeset
384 if (transcode_)
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diff changeset
385 {
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diff changeset
386 value["Transcode"] = GetTransferSyntaxUid(transferSyntax_);
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diff changeset
387 }
2642
ccc470091ea6 reorganization
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parents:
diff changeset
388 }
ccc470091ea6 reorganization
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parents:
diff changeset
389
2664
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diff changeset
390
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff changeset
391 static const char* MODIFICATION = "Modification";
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff changeset
392 static const char* ORIGIN = "Origin";
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff changeset
393 static const char* IS_ANONYMIZATION = "IsAnonymization";
3943
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Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
394 static const char* TRANSCODE = "Transcode";
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff changeset
395
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
396
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
397 ResourceModificationJob::ResourceModificationJob(ServerContext& context,
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff changeset
398 const Json::Value& serialized) :
3942
5b882ad2ffd0 "/{patients|studies|series}/.../modify": New option "KeepSource"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3938
diff changeset
399 CleaningInstancesJob(context, serialized, true /* by default, keep source */)
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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diff changeset
400 {
3943
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diff changeset
401 assert(serialized.type() == Json::objectValue);
b26d25d3c1c7 "/{patients|studies|series}/.../modify": New option "Transcode"
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parents: 3942
diff changeset
402
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
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parents: 2663
diff changeset
403 isAnonymization_ = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
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404 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
405 modification_.reset(new DicomModification(serialized[MODIFICATION]));
3943
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
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406
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
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407 if (serialized.isMember(TRANSCODE))
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
408 {
b26d25d3c1c7 "/{patients|studies|series}/.../modify": New option "Transcode"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
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409 SetTranscode(SerializationToolbox::ReadString(serialized, TRANSCODE));
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
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410 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
411 else
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
412 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
413 transcode_ = false;
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parents: 3942
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414 }
2664
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
415 }
2642
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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416
2663
228e2783ce83 some jobs might not be serializable
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2648
diff changeset
417 bool ResourceModificationJob::Serialize(Json::Value& value)
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418 {
3942
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3938
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419 if (!CleaningInstancesJob::Serialize(value))
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
420 {
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
421 return false;
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
422 }
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
423 else
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
424 {
3943
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
425 assert(value.type() == Json::objectValue);
b26d25d3c1c7 "/{patients|studies|series}/.../modify": New option "Transcode"
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parents: 3942
diff changeset
426
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
427 value[IS_ANONYMIZATION] = isAnonymization_;
3943
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
428
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
429 if (transcode_)
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
430 {
b26d25d3c1c7 "/{patients|studies|series}/.../modify": New option "Transcode"
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3942
diff changeset
431 value[TRANSCODE] = GetTransferSyntaxUid(transferSyntax_);
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parents: 3942
diff changeset
432 }
b26d25d3c1c7 "/{patients|studies|series}/.../modify": New option "Transcode"
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parents: 3942
diff changeset
433
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
434 origin_.Serialize(value[ORIGIN]);
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
435
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
436 Json::Value tmp;
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
437 modification_->Serialize(tmp);
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
438 value[MODIFICATION] = tmp;
2642
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
439
2664
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
440 return true;
a21b244efb37 serialization of DicomModalityStoreJob, OrthancPeerStoreJob and ResourceModificationJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2663
diff changeset
441 }
2642
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
442 }
ccc470091ea6 reorganization
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
443 }