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annotate OrthancServer/Sources/ServerJobs/SplitStudyJob.cpp @ 4831:7053502fbf97

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added copyright UCLouvain
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 25 Nov 2021 19:01:11 +0100
parents 94616af363ec
children 2e71a08eea15 43e613a7756b
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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) 2017-2021 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2021 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 * In addition, as a special exception, the copyright holders of this
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14 * program give permission to link the code of its release with the
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15 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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16 * that use the same license as the "OpenSSL" library), and distribute
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17 * the linked executables. You must obey the GNU General Public License
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18 * in all respects for all of the code used other than "OpenSSL". If you
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19 * modify file(s) with this exception, you may extend this exception to
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20 * your version of the file(s), but you are not obligated to do so. If
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21 * you do not wish to do so, delete this exception statement from your
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22 * version. If you delete this exception statement from all source files
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23 * in the program, then also delete it here.
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24 *
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25 * This program is distributed in the hope that it will be useful, but
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26 * WITHOUT ANY WARRANTY; without even the implied warranty of
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27 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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28 * General Public License for more details.
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29 *
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30 * You should have received a copy of the GNU General Public License
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31 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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32 **/
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33
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35 #include "SplitStudyJob.h"
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36
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37 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h"
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38 #include "../../../OrthancFramework/Sources/Logging.h"
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39 #include "../../../OrthancFramework/Sources/SerializationToolbox.h"
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40 #include "../ServerContext.h"
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41
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42
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43 namespace Orthanc
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44 {
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45 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
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46 {
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47 if (allowedTags_.find(tag) == allowedTags_.end())
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48 {
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49 throw OrthancException(ErrorCode_ParameterOutOfRange,
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50 "Cannot modify the following tag while splitting a study "
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51 "(not in the patient/study modules): " +
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52 FromDcmtkBridge::GetTagName(tag, "") +
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53 " (" + tag.Format() + ")");
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54 }
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55 }
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56
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57
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58 void SplitStudyJob::Setup()
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59 {
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60 SetPermissive(false);
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61
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62 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
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63 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
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64 allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
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65 allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
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66 }
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67
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68
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69 bool SplitStudyJob::HandleInstance(const std::string& instance)
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70 {
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71 if (!HasTrailingStep())
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72 {
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73 throw OrthancException(ErrorCode_BadSequenceOfCalls,
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74 "AddTrailingStep() should have been called after AddSourceSeries()");
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75 }
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76
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77 /**
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78 * Retrieve the DICOM instance to be modified
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79 **/
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80
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81 std::unique_ptr<ParsedDicomFile> modified;
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82
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83 try
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84 {
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85 ServerContext::DicomCacheLocker locker(GetContext(), instance);
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86 modified.reset(locker.GetDicom().Clone(true));
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87 }
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88 catch (OrthancException&)
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89 {
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90 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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91 return false;
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92 }
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93
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94
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95 /**
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96 * Chose the target UIDs
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97 **/
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98
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99 assert(modified->GetHasher().HashStudy() == sourceStudy_);
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100
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101 std::string series = modified->GetHasher().HashSeries();
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102
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103 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series);
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104
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105 if (targetSeriesUid == seriesUidMap_.end())
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106 {
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107 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen
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108 }
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109
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110
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111 /**
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112 * Apply user-specified modifications
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113 **/
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114
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115 for (std::set<DicomTag>::const_iterator it = removals_.begin();
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116 it != removals_.end(); ++it)
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117 {
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118 modified->Remove(*it);
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119 }
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120
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121 for (Replacements::const_iterator it = replacements_.begin();
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122 it != replacements_.end(); ++it)
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123 {
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124 modified->ReplacePlainString(it->first, it->second);
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125 }
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126
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127
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128 /**
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129 * Store the new instance into Orthanc
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130 **/
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131
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132 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
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133 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second);
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134
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135 // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified
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136 modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
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137
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138 if (targetStudy_.empty())
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139 {
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140 targetStudy_ = modified->GetHasher().HashStudy();
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141 }
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142
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143 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified));
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144 toStore->SetOrigin(origin_);
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145
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146 std::string modifiedInstance;
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147 ServerContext::StoreResult result = GetContext().Store(modifiedInstance, *toStore, StoreInstanceMode_Default);
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148 if (result.GetStatus() != StoreStatus_Success)
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149 {
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150 LOG(ERROR) << "Error while storing a modified instance " << instance;
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151 return false;
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152 }
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153
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154 return true;
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155 }
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156
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157
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158 SplitStudyJob::SplitStudyJob(ServerContext& context,
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159 const std::string& sourceStudy) :
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160 CleaningInstancesJob(context, false /* by default, remove source instances */),
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161 sourceStudy_(sourceStudy),
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162 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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163 {
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164 Setup();
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165
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166 ResourceType type;
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167
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168 if (!GetContext().GetIndex().LookupResourceType(type, sourceStudy) ||
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169 type != ResourceType_Study)
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170 {
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171 throw OrthancException(ErrorCode_UnknownResource,
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172 "Cannot split unknown study " + sourceStudy);
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173 }
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174 }
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175
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176
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177 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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178 {
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179 if (IsStarted())
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180 {
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181 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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182 }
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183 else
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184 {
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185 origin_ = origin;
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186 }
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187 }
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188
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189
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190 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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191 {
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192 SetOrigin(DicomInstanceOrigin::FromRest(call));
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193 }
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194
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195
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196 static void RegisterSeries(std::map<std::string, std::string>& target,
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197 const std::string& series)
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198 {
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199 // Generate a target SeriesInstanceUID for this series
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200 if (target.find(series) == target.end())
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201 {
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202 target[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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203 }
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204 }
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205
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206
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207 void SplitStudyJob::AddSourceSeries(const std::string& series)
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208 {
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209 std::string parent;
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210
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211 if (IsStarted())
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212 {
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213 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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214 }
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215 else if (!GetContext().GetIndex().LookupParent(parent, series, ResourceType_Study) ||
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216 parent != sourceStudy_)
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217 {
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218 throw OrthancException(ErrorCode_UnknownResource,
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219 "This series does not belong to the study to be split: " + series);
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220 }
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221 else
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222 {
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223 RegisterSeries(seriesUidMap_, series);
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224
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225 // Add all the instances of the series as to be processed
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226 std::list<std::string> instances;
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227 GetContext().GetIndex().GetChildren(instances, series);
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228
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229 for (std::list<std::string>::const_iterator
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230 it = instances.begin(); it != instances.end(); ++it)
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231 {
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232 AddInstance(*it);
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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
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238 void SplitStudyJob::AddSourceInstance(const std::string& instance)
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239 {
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240 std::string study, series;
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241
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242 if (IsStarted())
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243 {
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244 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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245 }
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246 else if (!GetContext().GetIndex().LookupParent(series, instance, ResourceType_Series) ||
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247 !GetContext().GetIndex().LookupParent(study, series, ResourceType_Study) ||
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248 study != sourceStudy_)
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249 {
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250 throw OrthancException(ErrorCode_UnknownResource,
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251 "This instance does not belong to the study to be split: " + instance);
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252 }
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253 else
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254 {
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255 RegisterSeries(seriesUidMap_, series);
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256 AddInstance(instance);
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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 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
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262 const std::string& series) const
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263 {
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264 SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
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265
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266 if (found == seriesUidMap_.end())
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267 {
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268 return false;
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269 }
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270 else
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271 {
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272 uid = found->second;
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273 return true;
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274 }
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275 }
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276
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277
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278 void SplitStudyJob::Remove(const DicomTag& tag)
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279 {
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280 if (IsStarted())
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281 {
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282 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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283 }
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284
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285 CheckAllowedTag(tag);
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286 removals_.insert(tag);
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287 }
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288
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289
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290 void SplitStudyJob::Replace(const DicomTag& tag,
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291 const std::string& value)
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292 {
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293 if (IsStarted())
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294 {
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295 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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296 }
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297
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298 CheckAllowedTag(tag);
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299 replacements_[tag] = value;
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300 }
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301
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diff changeset
302
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diff changeset
303 bool SplitStudyJob::LookupReplacement(std::string& value,
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304 const DicomTag& tag) const
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305 {
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306 Replacements::const_iterator found = replacements_.find(tag);
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307
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diff changeset
308 if (found == replacements_.end())
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309 {
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310 return false;
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diff changeset
311 }
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diff changeset
312 else
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diff changeset
313 {
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diff changeset
314 value = found->second;
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diff changeset
315 return true;
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diff changeset
316 }
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diff changeset
317 }
2844
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318
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diff changeset
319
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diff changeset
320 void SplitStudyJob::GetPublicContent(Json::Value& value)
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321 {
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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322 CleaningInstancesJob::GetPublicContent(value);
2844
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diff changeset
323
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diff changeset
324 if (!targetStudy_.empty())
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diff changeset
325 {
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diff changeset
326 value["TargetStudy"] = targetStudy_;
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327 }
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diff changeset
328
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diff changeset
329 value["TargetStudyUID"] = targetStudyUid_;
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diff changeset
330 }
2845
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diff changeset
331
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diff changeset
332
218e2c864d1d serialization of SplitStudyJob
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diff changeset
333 static const char* SOURCE_STUDY = "SourceStudy";
218e2c864d1d serialization of SplitStudyJob
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diff changeset
334 static const char* TARGET_STUDY = "TargetStudy";
218e2c864d1d serialization of SplitStudyJob
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diff changeset
335 static const char* TARGET_STUDY_UID = "TargetStudyUID";
2846
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diff changeset
336 static const char* SERIES_UID_MAP = "SeriesUIDMap";
2845
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diff changeset
337 static const char* ORIGIN = "Origin";
218e2c864d1d serialization of SplitStudyJob
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diff changeset
338 static const char* REPLACEMENTS = "Replacements";
218e2c864d1d serialization of SplitStudyJob
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diff changeset
339 static const char* REMOVALS = "Removals";
218e2c864d1d serialization of SplitStudyJob
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diff changeset
340
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diff changeset
341
218e2c864d1d serialization of SplitStudyJob
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diff changeset
342 SplitStudyJob::SplitStudyJob(ServerContext& context,
218e2c864d1d serialization of SplitStudyJob
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diff changeset
343 const Json::Value& serialized) :
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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diff changeset
344 CleaningInstancesJob(context, serialized,
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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diff changeset
345 false /* by default, remove source instances */) // (*)
2845
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diff changeset
346 {
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diff changeset
347 if (!HasTrailingStep())
218e2c864d1d serialization of SplitStudyJob
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diff changeset
348 {
218e2c864d1d serialization of SplitStudyJob
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diff changeset
349 // Should have been set by (*)
218e2c864d1d serialization of SplitStudyJob
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diff changeset
350 throw OrthancException(ErrorCode_InternalError);
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diff changeset
351 }
218e2c864d1d serialization of SplitStudyJob
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diff changeset
352
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diff changeset
353 Setup();
218e2c864d1d serialization of SplitStudyJob
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diff changeset
354
218e2c864d1d serialization of SplitStudyJob
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diff changeset
355 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
356 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
357 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
2846
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diff changeset
358 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
2845
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diff changeset
359 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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diff changeset
360 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
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diff changeset
361 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
362 }
218e2c864d1d serialization of SplitStudyJob
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diff changeset
363
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diff changeset
364
99863d6245b2 New URI: "/studies/.../split" to split a study
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diff changeset
365 bool SplitStudyJob::Serialize(Json::Value& target)
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diff changeset
366 {
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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diff changeset
367 if (!CleaningInstancesJob::Serialize(target))
2845
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diff changeset
368 {
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diff changeset
369 return false;
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diff changeset
370 }
218e2c864d1d serialization of SplitStudyJob
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diff changeset
371 else
218e2c864d1d serialization of SplitStudyJob
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diff changeset
372 {
218e2c864d1d serialization of SplitStudyJob
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diff changeset
373 target[SOURCE_STUDY] = sourceStudy_;
218e2c864d1d serialization of SplitStudyJob
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diff changeset
374 target[TARGET_STUDY] = targetStudy_;
218e2c864d1d serialization of SplitStudyJob
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diff changeset
375 target[TARGET_STUDY_UID] = targetStudyUid_;
2846
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diff changeset
376 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
2845
218e2c864d1d serialization of SplitStudyJob
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diff changeset
377 origin_.Serialize(target[ORIGIN]);
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diff changeset
378 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
379 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
380
218e2c864d1d serialization of SplitStudyJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2844
diff changeset
381 return true;
218e2c864d1d serialization of SplitStudyJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2844
diff changeset
382 }
2844
99863d6245b2 New URI: "/studies/.../split" to split a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
383 }
99863d6245b2 New URI: "/studies/.../split" to split a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
384 }