Mercurial > hg > orthanc

annotate OrthancServer/ServerJobs/ResourceModificationJob.cpp @ 3941:771dbd9eb3bd transcoding

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class CleaningInstancesJob to share cleaning code by merge/split jobs
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 18 May 2020 18:20:19 +0200
parents 54dbebbcc032
children 5b882ad2ffd0
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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 namespace Orthanc
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42 {
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43 class ResourceModificationJob::Output : public boost::noncopyable
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44 {
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45 private:
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46 ResourceType level_;
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47 bool isFirst_;
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48 std::string id_;
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49 std::string patientId_;
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50
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51 public:
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52 Output(ResourceType level) :
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53 level_(level),
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54 isFirst_(true)
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55 {
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56 if (level_ != ResourceType_Patient &&
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57 level_ != ResourceType_Study &&
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58 level_ != ResourceType_Series)
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59 {
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60 throw OrthancException(ErrorCode_ParameterOutOfRange);
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61 }
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62 }
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63
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64 ResourceType GetLevel() const
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65 {
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66 return level_;
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67 }
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68
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69
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70 void Update(DicomInstanceHasher& hasher)
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71 {
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72 if (isFirst_)
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73 {
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74 switch (level_)
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75 {
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76 case ResourceType_Series:
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77 id_ = hasher.HashSeries();
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78 break;
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79
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80 case ResourceType_Study:
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81 id_ = hasher.HashStudy();
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82 break;
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83
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84 case ResourceType_Patient:
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85 id_ = hasher.HashPatient();
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86 break;
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87
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88 default:
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89 throw OrthancException(ErrorCode_InternalError);
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90 }
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91
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92 patientId_ = hasher.HashPatient();
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93 isFirst_ = false;
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94 }
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95 }
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96
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97
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98 bool Format(Json::Value& target)
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99 {
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100 if (isFirst_)
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101 {
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102 return false;
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103 }
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104 else
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105 {
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106 target = Json::objectValue;
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107 target["Type"] = EnumerationToString(level_);
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108 target["ID"] = id_;
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109 target["Path"] = GetBasePath(level_, id_);
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110 target["PatientID"] = patientId_;
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111 return true;
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112 }
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113 }
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114
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115
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116 bool GetIdentifier(std::string& id)
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117 {
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118 if (isFirst_)
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119 {
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120 return false;
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121 }
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122 else
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123 {
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124 id = id_;
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125 return true;
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126 }
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127 }
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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 bool ResourceModificationJob::HandleInstance(const std::string& instance)
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134 {
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135 if (modification_.get() == NULL ||
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136 output_.get() == NULL)
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137 {
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138 throw OrthancException(ErrorCode_BadSequenceOfCalls,
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139 "No modification was provided for this job");
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140 }
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141
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142
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143 LOG(INFO) << "Modifying instance in a job: " << instance;
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144
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145
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146 /**
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147 * Retrieve the original instance from the DICOM cache.
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148 **/
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149
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150 std::unique_ptr<DicomInstanceHasher> originalHasher;
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151 std::unique_ptr<ParsedDicomFile> modified;
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152
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153 try
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154 {
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155 ServerContext::DicomCacheLocker locker(context_, instance);
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156 ParsedDicomFile& original = locker.GetDicom();
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157
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158 originalHasher.reset(new DicomInstanceHasher(original.GetHasher()));
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159 modified.reset(original.Clone(true));
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160 }
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161 catch (OrthancException& e)
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162 {
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163 LOG(WARNING) << "An error occurred while executing a Modification job on instance " << instance << ": " << e.GetDetails();
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164 return false;
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165 }
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166
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167
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168 /**
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169 * Compute the resulting DICOM instance.
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170 **/
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171
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172 modification_->Apply(*modified);
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173
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174 DicomInstanceToStore toStore;
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175 toStore.SetOrigin(origin_);
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176 toStore.SetParsedDicomFile(*modified);
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177
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178
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179 /**
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180 * Prepare the metadata information to associate with the
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181 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom).
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182 **/
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183
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184 DicomInstanceHasher modifiedHasher = modified->GetHasher();
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185
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186 MetadataType metadataType = (isAnonymization_ ?
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187 MetadataType_AnonymizedFrom :
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188 MetadataType_ModifiedFrom);
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189
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190 if (originalHasher->HashSeries() != modifiedHasher.HashSeries())
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191 {
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192 toStore.AddMetadata(ResourceType_Series, metadataType, originalHasher->HashSeries());
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193 }
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194
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195 if (originalHasher->HashStudy() != modifiedHasher.HashStudy())
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196 {
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197 toStore.AddMetadata(ResourceType_Study, metadataType, originalHasher->HashStudy());
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198 }
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199
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200 if (originalHasher->HashPatient() != modifiedHasher.HashPatient())
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201 {
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202 toStore.AddMetadata(ResourceType_Patient, metadataType, originalHasher->HashPatient());
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203 }
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204
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205 assert(instance == originalHasher->HashInstance());
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206 toStore.AddMetadata(ResourceType_Instance, metadataType, instance);
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207
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208
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209 /**
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210 * Store the resulting DICOM instance into the Orthanc store.
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211 **/
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212
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213 std::string modifiedInstance;
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214 if (context_.Store(modifiedInstance, toStore,
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215 StoreInstanceMode_Default) != StoreStatus_Success)
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216 {
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217 throw OrthancException(ErrorCode_CannotStoreInstance,
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218 "Error while storing a modified instance " + instance);
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219 }
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220
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221 /**
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222 * The assertion below will fail if automated transcoding to a
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223 * lossy transfer syntax is enabled in the Orthanc core, and if
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224 * the source instance is not in this transfer syntax.
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225 **/
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226 // assert(modifiedInstance == modifiedHasher.HashInstance());
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227
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228 output_->Update(modifiedHasher);
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229
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230 return true;
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231 }
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232
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233
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234 bool ResourceModificationJob::HandleTrailingStep()
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235 {
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236 throw OrthancException(ErrorCode_InternalError);
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237 }
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238
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239
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240 void ResourceModificationJob::SetModification(DicomModification* modification,
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241 ResourceType level,
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242 bool isAnonymization)
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243 {
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244 if (modification == NULL)
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245 {
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246 throw OrthancException(ErrorCode_NullPointer);
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247 }
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248 else if (IsStarted())
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249 {
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250 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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251 }
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252 else
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253 {
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254 modification_.reset(modification);
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255 output_.reset(new Output(level));
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256 isAnonymization_ = isAnonymization;
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257 }
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258 }
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259
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260
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261 void ResourceModificationJob::SetOrigin(const DicomInstanceOrigin& origin)
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262 {
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263 if (IsStarted())
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264 {
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265 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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266 }
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267 else
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268 {
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269 origin_ = origin;
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270 }
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271 }
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272
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273
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274 void ResourceModificationJob::SetOrigin(const RestApiCall& call)
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275 {
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276 SetOrigin(DicomInstanceOrigin::FromRest(call));
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277 }
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278
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279
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280 const DicomModification& ResourceModificationJob::GetModification() const
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281 {
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282 if (modification_.get() == NULL)
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283 {
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284 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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285 }
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286 else
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287 {
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288 return *modification_;
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289 }
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290 }
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291
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292
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293 void ResourceModificationJob::GetPublicContent(Json::Value& value)
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294 {
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295 SetOfInstancesJob::GetPublicContent(value);
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296
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297 value["IsAnonymization"] = isAnonymization_;
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298
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299 if (output_.get() != NULL)
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300 {
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301 output_->Format(value);
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302 }
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303 }
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304
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305
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306 static const char* MODIFICATION = "Modification";
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307 static const char* ORIGIN = "Origin";
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308 static const char* IS_ANONYMIZATION = "IsAnonymization";
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309
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310
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311 ResourceModificationJob::ResourceModificationJob(ServerContext& context,
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312 const Json::Value& serialized) :
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313 SetOfInstancesJob(serialized),
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314 context_(context)
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315 {
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316 isAnonymization_ = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION);
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317 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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318 modification_.reset(new DicomModification(serialized[MODIFICATION]));
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319 }
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320
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321 bool ResourceModificationJob::Serialize(Json::Value& value)
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322 {
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323 if (!SetOfInstancesJob::Serialize(value))
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324 {
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325 return false;
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326 }
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327 else
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328 {
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329 value[IS_ANONYMIZATION] = isAnonymization_;
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330 origin_.Serialize(value[ORIGIN]);
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331
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332 Json::Value tmp;
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333 modification_->Serialize(tmp);
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334 value[MODIFICATION] = tmp;
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335
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336 return true;
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337 }
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338 }
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339 }