Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerJobs/MergeStudyJob.cpp @ 5640:f7adfb22e20e
updated copyright, as Orthanc Team now replaces Osimis
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 30 May 2024 21:19:57 +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) 2024-2024 Orthanc Team SRL, Belgium |
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium |
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8 * |
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9 * This program is free software: you can redistribute it and/or |
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10 * modify it under the terms of the GNU General Public License as |
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11 * published by the Free Software Foundation, either version 3 of the |
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12 * License, or (at your option) any later version. |
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13 * |
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14 * This program is distributed in the hope that it will be useful, but |
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15 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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17 * General Public License for more details. |
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18 * |
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19 * You should have received a copy of the GNU General Public License |
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20 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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21 **/ |
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22 |
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23 |
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24 #include "MergeStudyJob.h" |
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25 |
4045 | 26 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h" |
27 #include "../../../OrthancFramework/Sources/Logging.h" | |
28 #include "../../../OrthancFramework/Sources/SerializationToolbox.h" | |
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29 #include "../OrthancConfiguration.h" |
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30 #include "../ServerContext.h" |
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31 |
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32 |
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33 namespace Orthanc |
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34 { |
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35 static void RegisterSeries(std::map<std::string, std::string>& target, |
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36 const std::string& series) |
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37 { |
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38 // Generate a target SeriesInstanceUID for this series |
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39 if (target.find(series) == target.end()) |
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40 { |
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41 target[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series); |
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42 } |
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43 } |
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44 |
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45 |
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46 void MergeStudyJob::AddSourceSeriesInternal(const std::string& series) |
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47 { |
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48 RegisterSeries(seriesUidMap_, series); |
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49 |
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50 // Add all the instances of the series as to be processed |
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51 std::list<std::string> instances; |
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52 GetContext().GetIndex().GetChildren(instances, series); |
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53 |
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54 for (std::list<std::string>::const_iterator |
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55 it = instances.begin(); it != instances.end(); ++it) |
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56 { |
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57 AddInstance(*it); |
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58 } |
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59 } |
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60 |
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61 |
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62 void MergeStudyJob::AddSourceStudyInternal(const std::string& study) |
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63 { |
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64 if (study == targetStudy_) |
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65 { |
2955 | 66 throw OrthancException(ErrorCode_UnknownResource, |
67 "Cannot merge a study into the same study: " + study); | |
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68 } |
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69 else |
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70 { |
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71 std::list<std::string> series; |
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72 GetContext().GetIndex().GetChildren(series, study); |
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73 |
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74 for (std::list<std::string>::const_iterator |
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75 it = series.begin(); it != series.end(); ++it) |
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76 { |
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77 AddSourceSeriesInternal(*it); |
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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 |
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83 bool MergeStudyJob::HandleInstance(const std::string& instance) |
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84 { |
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85 if (!HasTrailingStep()) |
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86 { |
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87 throw OrthancException(ErrorCode_BadSequenceOfCalls, |
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88 "AddTrailingStep() should have been called after AddSourceXXX()"); |
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89 } |
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90 |
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91 /** |
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92 * Retrieve the DICOM instance to be modified |
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93 **/ |
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94 |
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95 std::unique_ptr<ParsedDicomFile> modified; |
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96 |
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97 try |
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98 { |
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99 ServerContext::DicomCacheLocker locker(GetContext(), instance); |
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100 modified.reset(locker.GetDicom().Clone(true)); |
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101 } |
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102 catch (OrthancException&) |
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103 { |
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104 LOG(WARNING) << "An instance was removed after the job was issued: " << instance; |
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105 return false; |
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106 } |
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107 |
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108 |
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109 /** |
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110 * Chose the target UIDs |
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111 **/ |
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112 |
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113 std::string series = modified->GetHasher().HashSeries(); |
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114 |
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115 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series); |
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116 |
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117 if (targetSeriesUid == seriesUidMap_.end()) |
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118 { |
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119 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen |
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120 } |
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121 |
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122 |
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123 /** |
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124 * Copy the tags from the "Patient Module Attributes" and "General |
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125 * Study Module Attributes" modules of the target study |
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126 **/ |
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127 |
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128 for (std::set<DicomTag>::const_iterator it = removals_.begin(); |
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129 it != removals_.end(); ++it) |
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130 { |
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131 modified->Remove(*it); |
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132 } |
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133 |
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134 for (Replacements::const_iterator it = replacements_.begin(); |
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135 it != replacements_.end(); ++it) |
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136 { |
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137 modified->ReplacePlainString(it->first, it->second); |
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138 } |
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139 |
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140 |
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141 /** |
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142 * Store the new instance into Orthanc |
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143 **/ |
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144 |
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145 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second); |
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146 |
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147 // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified |
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148 modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
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149 |
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150 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified)); |
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151 toStore->SetOrigin(origin_); |
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152 |
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153 std::string modifiedInstance; |
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154 ServerContext::StoreResult result = GetContext().Store(modifiedInstance, *toStore, StoreInstanceMode_Default); |
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155 if (result.GetStatus() != StoreStatus_Success) |
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156 { |
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157 LOG(ERROR) << "Error while storing a modified instance " << instance; |
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158 return false; |
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159 } |
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160 |
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161 return true; |
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162 } |
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163 |
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164 |
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165 MergeStudyJob::MergeStudyJob(ServerContext& context, |
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166 const std::string& targetStudy) : |
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167 CleaningInstancesJob(context, false /* by default, remove source instances */), |
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168 targetStudy_(targetStudy) |
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169 { |
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170 /** |
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171 * Check the validity of the input ID |
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172 **/ |
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173 |
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174 ResourceType type; |
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175 |
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176 if (!GetContext().GetIndex().LookupResourceType(type, targetStudy) || |
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177 type != ResourceType_Study) |
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178 { |
2955 | 179 throw OrthancException(ErrorCode_UnknownResource, |
180 "Cannot merge into an unknown study: " + targetStudy); | |
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181 } |
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182 |
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183 |
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184 /** |
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185 * Detect the tags to be removed/replaced by parsing one child |
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186 * instance of the study |
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187 **/ |
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188 |
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189 DicomTag::AddTagsForModule(removals_, DicomModule_Patient); |
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190 DicomTag::AddTagsForModule(removals_, DicomModule_Study); |
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191 |
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192 std::list<std::string> instances; |
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193 GetContext().GetIndex().GetChildInstances(instances, targetStudy); |
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194 |
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195 if (instances.empty()) |
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196 { |
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197 throw OrthancException(ErrorCode_UnknownResource); |
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198 } |
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199 |
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200 DicomMap dicom; |
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201 |
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202 { |
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203 ServerContext::DicomCacheLocker locker(GetContext(), instances.front()); |
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204 OrthancConfiguration::DefaultExtractDicomSummary(dicom, locker.GetDicom()); |
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205 } |
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206 |
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207 const std::set<DicomTag> moduleTags = removals_; |
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208 for (std::set<DicomTag>::const_iterator it = moduleTags.begin(); |
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209 it != moduleTags.end(); ++it) |
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210 { |
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211 const DicomValue* value = dicom.TestAndGetValue(*it); |
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212 std::string str; |
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213 |
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214 if (value != NULL && |
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215 value->CopyToString(str, false)) |
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216 { |
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217 removals_.erase(*it); |
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218 replacements_.insert(std::make_pair(*it, str)); |
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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 |
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224 void MergeStudyJob::SetOrigin(const DicomInstanceOrigin& origin) |
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225 { |
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226 if (IsStarted()) |
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227 { |
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228 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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229 } |
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230 else |
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231 { |
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232 origin_ = origin; |
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233 } |
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234 } |
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235 |
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236 |
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237 void MergeStudyJob::SetOrigin(const RestApiCall& call) |
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238 { |
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239 SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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240 } |
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241 |
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242 |
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243 void MergeStudyJob::AddSource(const std::string& publicId) |
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244 { |
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245 ResourceType level; |
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246 |
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247 if (IsStarted()) |
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248 { |
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249 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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250 } |
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251 else if (!GetContext().GetIndex().LookupResourceType(level, publicId)) |
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252 { |
2955 | 253 throw OrthancException(ErrorCode_UnknownResource, |
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254 "Cannot find this resource: " + publicId); |
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255 } |
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256 else |
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257 { |
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258 switch (level) |
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259 { |
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260 case ResourceType_Study: |
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261 AddSourceStudyInternal(publicId); |
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262 break; |
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263 |
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264 case ResourceType_Series: |
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265 AddSourceSeries(publicId); |
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266 break; |
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267 |
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268 case ResourceType_Instance: |
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269 AddSourceInstance(publicId); |
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270 break; |
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271 |
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272 default: |
2955 | 273 throw OrthancException(ErrorCode_UnknownResource, |
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274 "This resource is neither a study, nor a series, nor an instance: " + |
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275 publicId + " is a " + std::string(EnumerationToString(level))); |
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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 |
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281 void MergeStudyJob::AddSourceSeries(const std::string& series) |
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282 { |
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283 std::string parent; |
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284 |
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285 if (IsStarted()) |
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286 { |
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287 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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288 } |
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289 else if (!GetContext().GetIndex().LookupParent(parent, series, ResourceType_Study)) |
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290 { |
2955 | 291 throw OrthancException(ErrorCode_UnknownResource, |
292 "This resource is not a series: " + series); | |
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293 } |
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294 else if (parent == targetStudy_) |
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295 { |
2955 | 296 throw OrthancException(ErrorCode_UnknownResource, |
297 "Cannot merge series " + series + | |
298 " into its parent study " + targetStudy_); | |
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299 } |
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300 else |
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301 { |
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302 AddSourceSeriesInternal(series); |
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303 } |
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304 } |
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305 |
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306 |
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307 void MergeStudyJob::AddSourceStudy(const std::string& study) |
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308 { |
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309 ResourceType actualLevel; |
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310 |
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311 if (IsStarted()) |
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312 { |
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313 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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314 } |
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315 else if (!GetContext().GetIndex().LookupResourceType(actualLevel, study) || |
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316 actualLevel != ResourceType_Study) |
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317 { |
2955 | 318 throw OrthancException(ErrorCode_UnknownResource, |
319 "This resource is not a study: " + study); | |
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320 } |
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321 else |
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322 { |
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323 AddSourceStudyInternal(study); |
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324 } |
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325 } |
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326 |
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327 |
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328 void MergeStudyJob::AddSourceInstance(const std::string& instance) |
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329 { |
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330 std::string parentStudy, parentSeries; |
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331 |
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332 if (IsStarted()) |
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333 { |
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334 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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335 } |
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336 else if (!GetContext().GetIndex().LookupParent(parentSeries, instance, ResourceType_Series) || |
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337 !GetContext().GetIndex().LookupParent(parentStudy, parentSeries, ResourceType_Study)) |
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338 { |
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339 throw OrthancException(ErrorCode_UnknownResource, |
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340 "This resource is not an instance: " + instance); |
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341 } |
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342 else if (parentStudy == targetStudy_) |
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343 { |
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344 throw OrthancException(ErrorCode_UnknownResource, |
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345 "Cannot merge instance " + instance + |
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346 " into its parent study " + targetStudy_); |
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347 } |
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348 else |
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349 { |
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350 RegisterSeries(seriesUidMap_, parentSeries); |
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351 AddInstance(instance); |
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352 } |
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353 } |
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354 |
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355 |
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356 void MergeStudyJob::GetPublicContent(Json::Value& value) |
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357 { |
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358 CleaningInstancesJob::GetPublicContent(value); |
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359 value["TargetStudy"] = targetStudy_; |
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360 } |
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361 |
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362 |
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363 static const char* TARGET_STUDY = "TargetStudy"; |
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364 static const char* REPLACEMENTS = "Replacements"; |
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365 static const char* REMOVALS = "Removals"; |
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366 static const char* SERIES_UID_MAP = "SeriesUIDMap"; |
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367 static const char* ORIGIN = "Origin"; |
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368 |
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369 |
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370 MergeStudyJob::MergeStudyJob(ServerContext& context, |
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371 const Json::Value& serialized) : |
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372 CleaningInstancesJob(context, serialized, |
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373 false /* by default, remove source instances */) // (*) |
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374 { |
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375 if (!HasTrailingStep()) |
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376 { |
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377 // Should have been set by (*) |
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378 throw OrthancException(ErrorCode_InternalError); |
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379 } |
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380 |
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381 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY); |
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382 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS); |
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383 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS); |
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384 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP); |
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385 origin_ = DicomInstanceOrigin(serialized[ORIGIN]); |
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386 } |
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387 |
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388 |
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389 bool MergeStudyJob::Serialize(Json::Value& target) |
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390 { |
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391 if (!CleaningInstancesJob::Serialize(target)) |
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392 { |
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393 return false; |
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394 } |
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395 else |
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396 { |
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397 target[TARGET_STUDY] = targetStudy_; |
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398 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS); |
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399 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS); |
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400 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP); |
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401 origin_.Serialize(target[ORIGIN]); |
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402 |
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403 return true; |
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404 } |
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405 } |
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406 } |