Mercurial > hg > orthanc

annotate OrthancServer/Sources/ServerJobs/SplitStudyJob.cpp @ 4793:fc2ba1ce6538

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new configuration 'DicomThreadsCount'
author Alain Mazy <am@osimis.io>
date Thu, 30 Sep 2021 15:03:35 +0200
parents bad8935cd5f2
children 783f8a048035 94616af363ec
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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 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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34 #include "SplitStudyJob.h"
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35
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36 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h"
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37 #include "../../../OrthancFramework/Sources/Logging.h"
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38 #include "../../../OrthancFramework/Sources/SerializationToolbox.h"
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39 #include "../ServerContext.h"
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42 namespace Orthanc
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43 {
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44 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
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45 {
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46 if (allowedTags_.find(tag) == allowedTags_.end())
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47 {
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48 throw OrthancException(ErrorCode_ParameterOutOfRange,
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49 "Cannot modify the following tag while splitting a study "
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50 "(not in the patient/study modules): " +
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51 FromDcmtkBridge::GetTagName(tag, "") +
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52 " (" + tag.Format() + ")");
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53 }
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54 }
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56
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57 void SplitStudyJob::Setup()
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58 {
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59 SetPermissive(false);
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60
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61 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
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62 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
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63 allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
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64 allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
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65 }
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67
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68 bool SplitStudyJob::HandleInstance(const std::string& instance)
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69 {
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70 if (!HasTrailingStep())
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71 {
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72 throw OrthancException(ErrorCode_BadSequenceOfCalls,
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73 "AddTrailingStep() should have been called after AddSourceSeries()");
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74 }
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75
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76 /**
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77 * Retrieve the DICOM instance to be modified
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78 **/
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79
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80 std::unique_ptr<ParsedDicomFile> modified;
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81
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82 try
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83 {
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84 ServerContext::DicomCacheLocker locker(GetContext(), instance);
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85 modified.reset(locker.GetDicom().Clone(true));
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86 }
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87 catch (OrthancException&)
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88 {
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89 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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90 return false;
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91 }
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92
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93
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94 /**
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95 * Chose the target UIDs
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96 **/
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97
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98 assert(modified->GetHasher().HashStudy() == sourceStudy_);
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99
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100 std::string series = modified->GetHasher().HashSeries();
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101
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102 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series);
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103
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104 if (targetSeriesUid == seriesUidMap_.end())
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105 {
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106 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen
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107 }
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108
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109
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110 /**
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111 * Apply user-specified modifications
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112 **/
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113
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114 for (std::set<DicomTag>::const_iterator it = removals_.begin();
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115 it != removals_.end(); ++it)
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116 {
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117 modified->Remove(*it);
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118 }
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119
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120 for (Replacements::const_iterator it = replacements_.begin();
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121 it != replacements_.end(); ++it)
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122 {
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123 modified->ReplacePlainString(it->first, it->second);
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124 }
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125
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126
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127 /**
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128 * Store the new instance into Orthanc
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129 **/
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130
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131 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
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132 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second);
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133
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134 // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified
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135 modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
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136
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137 if (targetStudy_.empty())
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138 {
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139 targetStudy_ = modified->GetHasher().HashStudy();
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140 }
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141
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142 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified));
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143 toStore->SetOrigin(origin_);
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144
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145 std::string modifiedInstance;
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146 if (GetContext().Store(modifiedInstance, *toStore,
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147 StoreInstanceMode_Default) != StoreStatus_Success)
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148 {
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149 LOG(ERROR) << "Error while storing a modified instance " << instance;
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150 return false;
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151 }
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152
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153 return true;
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154 }
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155
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156
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157 SplitStudyJob::SplitStudyJob(ServerContext& context,
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158 const std::string& sourceStudy) :
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159 CleaningInstancesJob(context, false /* by default, remove source instances */),
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160 sourceStudy_(sourceStudy),
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161 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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162 {
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163 Setup();
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164
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165 ResourceType type;
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166
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167 if (!GetContext().GetIndex().LookupResourceType(type, sourceStudy) ||
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168 type != ResourceType_Study)
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169 {
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170 throw OrthancException(ErrorCode_UnknownResource,
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171 "Cannot split unknown study " + sourceStudy);
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172 }
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173 }
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174
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175
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176 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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177 {
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178 if (IsStarted())
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179 {
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180 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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181 }
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182 else
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183 {
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184 origin_ = origin;
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185 }
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186 }
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187
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188
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189 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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190 {
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191 SetOrigin(DicomInstanceOrigin::FromRest(call));
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192 }
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193
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194
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195 static void RegisterSeries(std::map<std::string, std::string>& target,
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196 const std::string& series)
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197 {
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198 // Generate a target SeriesInstanceUID for this series
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199 if (target.find(series) == target.end())
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200 {
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201 target[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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202 }
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203 }
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204
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205
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206 void SplitStudyJob::AddSourceSeries(const std::string& series)
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207 {
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208 std::string parent;
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209
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210 if (IsStarted())
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211 {
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212 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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213 }
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214 else if (!GetContext().GetIndex().LookupParent(parent, series, ResourceType_Study) ||
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215 parent != sourceStudy_)
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216 {
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217 throw OrthancException(ErrorCode_UnknownResource,
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218 "This series does not belong to the study to be split: " + series);
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219 }
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220 else
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221 {
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222 RegisterSeries(seriesUidMap_, series);
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223
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224 // Add all the instances of the series as to be processed
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225 std::list<std::string> instances;
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226 GetContext().GetIndex().GetChildren(instances, series);
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227
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228 for (std::list<std::string>::const_iterator
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229 it = instances.begin(); it != instances.end(); ++it)
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230 {
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231 AddInstance(*it);
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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
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237 void SplitStudyJob::AddSourceInstance(const std::string& instance)
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238 {
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239 std::string study, series;
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240
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241 if (IsStarted())
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242 {
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243 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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244 }
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245 else if (!GetContext().GetIndex().LookupParent(series, instance, ResourceType_Series) ||
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246 !GetContext().GetIndex().LookupParent(study, series, ResourceType_Study) ||
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247 study != sourceStudy_)
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248 {
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249 throw OrthancException(ErrorCode_UnknownResource,
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250 "This instance does not belong to the study to be split: " + instance);
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251 }
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252 else
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253 {
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254 RegisterSeries(seriesUidMap_, series);
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255 AddInstance(instance);
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256 }
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257 }
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258
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259
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260 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
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261 const std::string& series) const
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262 {
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263 SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
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264
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265 if (found == seriesUidMap_.end())
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266 {
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267 return false;
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268 }
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269 else
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270 {
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271 uid = found->second;
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272 return true;
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273 }
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274 }
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275
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276
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277 void SplitStudyJob::Remove(const DicomTag& tag)
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278 {
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279 if (IsStarted())
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280 {
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281 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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282 }
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283
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284 CheckAllowedTag(tag);
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285 removals_.insert(tag);
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286 }
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287
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288
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289 void SplitStudyJob::Replace(const DicomTag& tag,
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290 const std::string& value)
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291 {
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diff changeset
292 if (IsStarted())
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293 {
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294 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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295 }
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diff changeset
296
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297 CheckAllowedTag(tag);
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298 replacements_[tag] = value;
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299 }
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300
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diff changeset
301
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diff changeset
302 bool SplitStudyJob::LookupReplacement(std::string& value,
2da68edacab6 unit testing of SplitStudyJob
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303 const DicomTag& tag) const
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304 {
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305 Replacements::const_iterator found = replacements_.find(tag);
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306
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diff changeset
307 if (found == replacements_.end())
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diff changeset
308 {
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309 return false;
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310 }
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
311 else
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diff changeset
312 {
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diff changeset
313 value = found->second;
2da68edacab6 unit testing of SplitStudyJob
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314 return true;
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
315 }
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
316 }
2844
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317
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diff changeset
318
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diff changeset
319 void SplitStudyJob::GetPublicContent(Json::Value& value)
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diff changeset
320 {
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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diff changeset
321 CleaningInstancesJob::GetPublicContent(value);
2844
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diff changeset
322
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diff changeset
323 if (!targetStudy_.empty())
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diff changeset
324 {
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diff changeset
325 value["TargetStudy"] = targetStudy_;
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diff changeset
326 }
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diff changeset
327
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diff changeset
328 value["TargetStudyUID"] = targetStudyUid_;
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diff changeset
329 }
2845
218e2c864d1d serialization of SplitStudyJob
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diff changeset
330
218e2c864d1d serialization of SplitStudyJob
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diff changeset
331
218e2c864d1d serialization of SplitStudyJob
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diff changeset
332 static const char* SOURCE_STUDY = "SourceStudy";
218e2c864d1d serialization of SplitStudyJob
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diff changeset
333 static const char* TARGET_STUDY = "TargetStudy";
218e2c864d1d serialization of SplitStudyJob
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diff changeset
334 static const char* TARGET_STUDY_UID = "TargetStudyUID";
2846
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diff changeset
335 static const char* SERIES_UID_MAP = "SeriesUIDMap";
2845
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diff changeset
336 static const char* ORIGIN = "Origin";
218e2c864d1d serialization of SplitStudyJob
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diff changeset
337 static const char* REPLACEMENTS = "Replacements";
218e2c864d1d serialization of SplitStudyJob
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diff changeset
338 static const char* REMOVALS = "Removals";
218e2c864d1d serialization of SplitStudyJob
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diff changeset
339
218e2c864d1d serialization of SplitStudyJob
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diff changeset
340
218e2c864d1d serialization of SplitStudyJob
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diff changeset
341 SplitStudyJob::SplitStudyJob(ServerContext& context,
218e2c864d1d serialization of SplitStudyJob
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diff changeset
342 const Json::Value& serialized) :
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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diff changeset
343 CleaningInstancesJob(context, serialized,
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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diff changeset
344 false /* by default, remove source instances */) // (*)
2845
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diff changeset
345 {
218e2c864d1d serialization of SplitStudyJob
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diff changeset
346 if (!HasTrailingStep())
218e2c864d1d serialization of SplitStudyJob
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diff changeset
347 {
218e2c864d1d serialization of SplitStudyJob
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diff changeset
348 // Should have been set by (*)
218e2c864d1d serialization of SplitStudyJob
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diff changeset
349 throw OrthancException(ErrorCode_InternalError);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
350 }
218e2c864d1d serialization of SplitStudyJob
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diff changeset
351
218e2c864d1d serialization of SplitStudyJob
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diff changeset
352 Setup();
218e2c864d1d serialization of SplitStudyJob
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diff changeset
353
218e2c864d1d serialization of SplitStudyJob
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diff changeset
354 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
355 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
356 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
2846
d386abc18133 simplification in SplitStudyJob, fix possible memory leak
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diff changeset
357 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
2845
218e2c864d1d serialization of SplitStudyJob
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diff changeset
358 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
359 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
360 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
361 }
218e2c864d1d serialization of SplitStudyJob
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diff changeset
362
2844
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diff changeset
363
99863d6245b2 New URI: "/studies/.../split" to split a study
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diff changeset
364 bool SplitStudyJob::Serialize(Json::Value& target)
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parents:
diff changeset
365 {
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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diff changeset
366 if (!CleaningInstancesJob::Serialize(target))
2845
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diff changeset
367 {
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diff changeset
368 return false;
218e2c864d1d serialization of SplitStudyJob
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diff changeset
369 }
218e2c864d1d serialization of SplitStudyJob
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diff changeset
370 else
218e2c864d1d serialization of SplitStudyJob
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diff changeset
371 {
218e2c864d1d serialization of SplitStudyJob
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diff changeset
372 target[SOURCE_STUDY] = sourceStudy_;
218e2c864d1d serialization of SplitStudyJob
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diff changeset
373 target[TARGET_STUDY] = targetStudy_;
218e2c864d1d serialization of SplitStudyJob
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diff changeset
374 target[TARGET_STUDY_UID] = targetStudyUid_;
2846
d386abc18133 simplification in SplitStudyJob, fix possible memory leak
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diff changeset
375 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
2845
218e2c864d1d serialization of SplitStudyJob
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diff changeset
376 origin_.Serialize(target[ORIGIN]);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
377 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
378 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
218e2c864d1d serialization of SplitStudyJob
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diff changeset
379
218e2c864d1d serialization of SplitStudyJob
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diff changeset
380 return true;
218e2c864d1d serialization of SplitStudyJob
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2844
diff changeset
381 }
2844
99863d6245b2 New URI: "/studies/.../split" to split a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
382 }
99863d6245b2 New URI: "/studies/.../split" to split a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
383 }