Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerJobs/MergeStudyJob.cpp @ 5334:5b2a5cc64cb1
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 27 Jun 2023 15:12:39 +0200 |
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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) 2017-2023 Osimis S.A., Belgium |
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6 * Copyright (C) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
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7 * |
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8 * This program is free software: you can redistribute it and/or |
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9 * modify it under the terms of the GNU General Public License as |
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10 * published by the Free Software Foundation, either version 3 of the |
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11 * License, or (at your option) any later version. |
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12 * |
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13 * This program is distributed in the hope that it will be useful, but |
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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16 * General Public License for more details. |
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17 * |
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18 * You should have received a copy of the GNU General Public License |
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19 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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20 **/ |
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21 |
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22 |
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23 #include "MergeStudyJob.h" |
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24 |
4045 | 25 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" |
26 #include "../../../OrthancFramework/Sources/Logging.h" | |
27 #include "../../../OrthancFramework/Sources/SerializationToolbox.h" | |
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28 #include "../OrthancConfiguration.h" |
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29 #include "../ServerContext.h" |
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30 |
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31 |
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32 namespace Orthanc |
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33 { |
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34 static void RegisterSeries(std::map<std::string, std::string>& target, |
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35 const std::string& series) |
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36 { |
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37 // Generate a target SeriesInstanceUID for this series |
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38 if (target.find(series) == target.end()) |
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39 { |
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40 target[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series); |
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41 } |
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42 } |
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43 |
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44 |
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45 void MergeStudyJob::AddSourceSeriesInternal(const std::string& series) |
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46 { |
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47 RegisterSeries(seriesUidMap_, series); |
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48 |
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49 // Add all the instances of the series as to be processed |
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50 std::list<std::string> instances; |
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51 GetContext().GetIndex().GetChildren(instances, series); |
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52 |
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53 for (std::list<std::string>::const_iterator |
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54 it = instances.begin(); it != instances.end(); ++it) |
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55 { |
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56 AddInstance(*it); |
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57 } |
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58 } |
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59 |
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60 |
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61 void MergeStudyJob::AddSourceStudyInternal(const std::string& study) |
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62 { |
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63 if (study == targetStudy_) |
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64 { |
2955 | 65 throw OrthancException(ErrorCode_UnknownResource, |
66 "Cannot merge a study into the same study: " + study); | |
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67 } |
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68 else |
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69 { |
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70 std::list<std::string> series; |
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71 GetContext().GetIndex().GetChildren(series, study); |
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72 |
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73 for (std::list<std::string>::const_iterator |
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74 it = series.begin(); it != series.end(); ++it) |
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75 { |
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76 AddSourceSeriesInternal(*it); |
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77 } |
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78 } |
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79 } |
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80 |
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81 |
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82 bool MergeStudyJob::HandleInstance(const std::string& instance) |
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83 { |
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84 if (!HasTrailingStep()) |
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85 { |
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86 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
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87 "AddTrailingStep() should have been called after AddSourceXXX()"); |
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88 } |
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89 |
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90 /** |
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91 * Retrieve the DICOM instance to be modified |
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92 **/ |
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93 |
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94 std::unique_ptr<ParsedDicomFile> modified; |
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95 |
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96 try |
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97 { |
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98 ServerContext::DicomCacheLocker locker(GetContext(), instance); |
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99 modified.reset(locker.GetDicom().Clone(true)); |
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100 } |
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101 catch (OrthancException&) |
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102 { |
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103 LOG(WARNING) << "An instance was removed after the job was issued: " << instance; |
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104 return false; |
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105 } |
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106 |
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107 |
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108 /** |
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109 * Chose the target UIDs |
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110 **/ |
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111 |
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112 std::string series = modified->GetHasher().HashSeries(); |
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113 |
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114 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series); |
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115 |
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116 if (targetSeriesUid == seriesUidMap_.end()) |
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117 { |
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118 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen |
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119 } |
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120 |
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121 |
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122 /** |
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123 * Copy the tags from the "Patient Module Attributes" and "General |
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124 * Study Module Attributes" modules of the target study |
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125 **/ |
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126 |
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127 for (std::set<DicomTag>::const_iterator it = removals_.begin(); |
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128 it != removals_.end(); ++it) |
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129 { |
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130 modified->Remove(*it); |
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131 } |
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132 |
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133 for (Replacements::const_iterator it = replacements_.begin(); |
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134 it != replacements_.end(); ++it) |
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135 { |
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136 modified->ReplacePlainString(it->first, it->second); |
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137 } |
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138 |
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139 |
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140 /** |
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141 * Store the new instance into Orthanc |
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142 **/ |
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143 |
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144 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second); |
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145 |
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146 // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified |
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147 modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
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148 |
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149 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified)); |
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150 toStore->SetOrigin(origin_); |
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151 |
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152 std::string modifiedInstance; |
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153 ServerContext::StoreResult result = GetContext().Store(modifiedInstance, *toStore, StoreInstanceMode_Default); |
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154 if (result.GetStatus() != StoreStatus_Success) |
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155 { |
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156 LOG(ERROR) << "Error while storing a modified instance " << instance; |
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157 return false; |
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158 } |
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159 |
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160 return true; |
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161 } |
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162 |
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163 |
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164 MergeStudyJob::MergeStudyJob(ServerContext& context, |
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165 const std::string& targetStudy) : |
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166 CleaningInstancesJob(context, false /* by default, remove source instances */), |
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167 targetStudy_(targetStudy) |
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168 { |
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169 /** |
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170 * Check the validity of the input ID |
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171 **/ |
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172 |
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173 ResourceType type; |
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174 |
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175 if (!GetContext().GetIndex().LookupResourceType(type, targetStudy) || |
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176 type != ResourceType_Study) |
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177 { |
2955 | 178 throw OrthancException(ErrorCode_UnknownResource, |
179 "Cannot merge into an unknown study: " + targetStudy); | |
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180 } |
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181 |
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182 |
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183 /** |
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184 * Detect the tags to be removed/replaced by parsing one child |
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185 * instance of the study |
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186 **/ |
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187 |
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188 DicomTag::AddTagsForModule(removals_, DicomModule_Patient); |
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189 DicomTag::AddTagsForModule(removals_, DicomModule_Study); |
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190 |
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191 std::list<std::string> instances; |
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192 GetContext().GetIndex().GetChildInstances(instances, targetStudy); |
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193 |
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194 if (instances.empty()) |
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195 { |
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196 throw OrthancException(ErrorCode_UnknownResource); |
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197 } |
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198 |
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199 DicomMap dicom; |
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200 |
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201 { |
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202 ServerContext::DicomCacheLocker locker(GetContext(), instances.front()); |
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203 OrthancConfiguration::DefaultExtractDicomSummary(dicom, locker.GetDicom()); |
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204 } |
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205 |
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206 const std::set<DicomTag> moduleTags = removals_; |
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207 for (std::set<DicomTag>::const_iterator it = moduleTags.begin(); |
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208 it != moduleTags.end(); ++it) |
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209 { |
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210 const DicomValue* value = dicom.TestAndGetValue(*it); |
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211 std::string str; |
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212 |
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213 if (value != NULL && |
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214 value->CopyToString(str, false)) |
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215 { |
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216 removals_.erase(*it); |
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217 replacements_.insert(std::make_pair(*it, str)); |
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218 } |
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219 } |
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220 } |
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221 |
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222 |
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223 void MergeStudyJob::SetOrigin(const DicomInstanceOrigin& origin) |
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224 { |
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225 if (IsStarted()) |
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226 { |
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227 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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228 } |
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229 else |
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230 { |
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231 origin_ = origin; |
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232 } |
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233 } |
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234 |
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235 |
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236 void MergeStudyJob::SetOrigin(const RestApiCall& call) |
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237 { |
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238 SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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239 } |
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240 |
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241 |
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242 void MergeStudyJob::AddSource(const std::string& publicId) |
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243 { |
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244 ResourceType level; |
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245 |
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246 if (IsStarted()) |
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247 { |
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248 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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249 } |
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250 else if (!GetContext().GetIndex().LookupResourceType(level, publicId)) |
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251 { |
2955 | 252 throw OrthancException(ErrorCode_UnknownResource, |
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253 "Cannot find this resource: " + publicId); |
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254 } |
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255 else |
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256 { |
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257 switch (level) |
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258 { |
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259 case ResourceType_Study: |
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260 AddSourceStudyInternal(publicId); |
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261 break; |
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262 |
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263 case ResourceType_Series: |
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264 AddSourceSeries(publicId); |
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265 break; |
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266 |
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267 case ResourceType_Instance: |
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268 AddSourceInstance(publicId); |
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269 break; |
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270 |
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271 default: |
2955 | 272 throw OrthancException(ErrorCode_UnknownResource, |
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273 "This resource is neither a study, nor a series, nor an instance: " + |
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274 publicId + " is a " + std::string(EnumerationToString(level))); |
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275 } |
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276 } |
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277 } |
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278 |
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279 |
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280 void MergeStudyJob::AddSourceSeries(const std::string& series) |
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281 { |
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282 std::string parent; |
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283 |
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284 if (IsStarted()) |
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285 { |
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286 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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287 } |
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288 else if (!GetContext().GetIndex().LookupParent(parent, series, ResourceType_Study)) |
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289 { |
2955 | 290 throw OrthancException(ErrorCode_UnknownResource, |
291 "This resource is not a series: " + series); | |
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292 } |
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293 else if (parent == targetStudy_) |
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294 { |
2955 | 295 throw OrthancException(ErrorCode_UnknownResource, |
296 "Cannot merge series " + series + | |
297 " into its parent study " + targetStudy_); | |
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298 } |
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299 else |
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300 { |
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301 AddSourceSeriesInternal(series); |
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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 void MergeStudyJob::AddSourceStudy(const std::string& study) |
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307 { |
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308 ResourceType actualLevel; |
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309 |
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310 if (IsStarted()) |
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311 { |
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312 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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313 } |
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314 else if (!GetContext().GetIndex().LookupResourceType(actualLevel, study) || |
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315 actualLevel != ResourceType_Study) |
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316 { |
2955 | 317 throw OrthancException(ErrorCode_UnknownResource, |
318 "This resource is not a study: " + study); | |
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319 } |
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320 else |
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321 { |
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322 AddSourceStudyInternal(study); |
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323 } |
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324 } |
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325 |
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326 |
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327 void MergeStudyJob::AddSourceInstance(const std::string& instance) |
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328 { |
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329 std::string parentStudy, parentSeries; |
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330 |
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331 if (IsStarted()) |
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332 { |
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333 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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334 } |
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335 else if (!GetContext().GetIndex().LookupParent(parentSeries, instance, ResourceType_Series) || |
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336 !GetContext().GetIndex().LookupParent(parentStudy, parentSeries, ResourceType_Study)) |
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337 { |
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338 throw OrthancException(ErrorCode_UnknownResource, |
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339 "This resource is not an instance: " + instance); |
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340 } |
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341 else if (parentStudy == targetStudy_) |
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342 { |
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343 throw OrthancException(ErrorCode_UnknownResource, |
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344 "Cannot merge instance " + instance + |
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345 " into its parent study " + targetStudy_); |
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346 } |
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347 else |
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348 { |
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349 RegisterSeries(seriesUidMap_, parentSeries); |
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350 AddInstance(instance); |
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351 } |
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352 } |
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353 |
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354 |
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355 void MergeStudyJob::GetPublicContent(Json::Value& value) |
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356 { |
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357 CleaningInstancesJob::GetPublicContent(value); |
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358 value["TargetStudy"] = targetStudy_; |
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359 } |
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360 |
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361 |
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362 static const char* TARGET_STUDY = "TargetStudy"; |
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363 static const char* REPLACEMENTS = "Replacements"; |
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364 static const char* REMOVALS = "Removals"; |
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365 static const char* SERIES_UID_MAP = "SeriesUIDMap"; |
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366 static const char* ORIGIN = "Origin"; |
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367 |
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368 |
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369 MergeStudyJob::MergeStudyJob(ServerContext& context, |
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370 const Json::Value& serialized) : |
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371 CleaningInstancesJob(context, serialized, |
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372 false /* by default, remove source instances */) // (*) |
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373 { |
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374 if (!HasTrailingStep()) |
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375 { |
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376 // Should have been set by (*) |
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377 throw OrthancException(ErrorCode_InternalError); |
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378 } |
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379 |
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380 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY); |
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381 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS); |
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382 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS); |
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383 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP); |
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384 origin_ = DicomInstanceOrigin(serialized[ORIGIN]); |
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385 } |
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386 |
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387 |
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388 bool MergeStudyJob::Serialize(Json::Value& target) |
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389 { |
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390 if (!CleaningInstancesJob::Serialize(target)) |
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391 { |
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392 return false; |
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393 } |
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394 else |
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395 { |
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396 target[TARGET_STUDY] = targetStudy_; |
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397 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS); |
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398 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS); |
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399 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP); |
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400 origin_.Serialize(target[ORIGIN]); |
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401 |
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402 return true; |
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403 } |
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404 } |
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405 } |