annotate OrthancServer/Sources/ServerJobs/MergeStudyJob.cpp @ 4704:f0038043fb97 openssl-3.x

removed OpenSSL license exception, as OpenSSL 3.0 was relicensed under Apache 2.0
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 22 Jun 2021 07:37:20 +0200
parents 8f9090b137f1
children 783f8a048035
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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 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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22 #include "MergeStudyJob.h"
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23
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24 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h"
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25 #include "../../../OrthancFramework/Sources/Logging.h"
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26 #include "../../../OrthancFramework/Sources/SerializationToolbox.h"
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27 #include "../OrthancConfiguration.h"
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28 #include "../ServerContext.h"
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31 namespace Orthanc
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32 {
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33 void MergeStudyJob::AddSourceSeriesInternal(const std::string& series)
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34 {
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35 // Generate a target SeriesInstanceUID for this series
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36 seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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38 // Add all the instances of the series as to be processed
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39 std::list<std::string> instances;
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40 GetContext().GetIndex().GetChildren(instances, series);
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42 for (std::list<std::string>::const_iterator
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43 it = instances.begin(); it != instances.end(); ++it)
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44 {
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45 AddInstance(*it);
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46 }
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47 }
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50 void MergeStudyJob::AddSourceStudyInternal(const std::string& study)
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51 {
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52 if (study == targetStudy_)
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53 {
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54 throw OrthancException(ErrorCode_UnknownResource,
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55 "Cannot merge a study into the same study: " + study);
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56 }
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57 else
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58 {
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59 std::list<std::string> series;
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60 GetContext().GetIndex().GetChildren(series, study);
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61
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62 for (std::list<std::string>::const_iterator
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63 it = series.begin(); it != series.end(); ++it)
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64 {
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65 AddSourceSeriesInternal(*it);
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66 }
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67 }
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68 }
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69
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70
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71 bool MergeStudyJob::HandleInstance(const std::string& instance)
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72 {
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73 if (!HasTrailingStep())
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74 {
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75 throw OrthancException(ErrorCode_BadSequenceOfCalls,
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76 "AddTrailingStep() should have been called after AddSourceXXX()");
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77 }
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78
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79 /**
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80 * Retrieve the DICOM instance to be modified
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81 **/
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82
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83 std::unique_ptr<ParsedDicomFile> modified;
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84
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85 try
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86 {
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87 ServerContext::DicomCacheLocker locker(GetContext(), instance);
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88 modified.reset(locker.GetDicom().Clone(true));
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89 }
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90 catch (OrthancException&)
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91 {
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92 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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93 return false;
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94 }
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95
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96
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97 /**
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98 * Chose the target UIDs
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99 **/
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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 * Copy the tags from the "Patient Module Attributes" and "General
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113 * Study Module Attributes" modules of the target study
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114 **/
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115
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116 for (std::set<DicomTag>::const_iterator it = removals_.begin();
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117 it != removals_.end(); ++it)
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118 {
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119 modified->Remove(*it);
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120 }
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121
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122 for (Replacements::const_iterator it = replacements_.begin();
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123 it != replacements_.end(); ++it)
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124 {
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125 modified->ReplacePlainString(it->first, it->second);
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126 }
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127
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128
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129 /**
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130 * Store the new instance into Orthanc
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131 **/
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132
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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 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified));
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139 toStore->SetOrigin(origin_);
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140
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141 std::string modifiedInstance;
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142 if (GetContext().Store(modifiedInstance, *toStore,
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143 StoreInstanceMode_Default) != StoreStatus_Success)
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144 {
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145 LOG(ERROR) << "Error while storing a modified instance " << instance;
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146 return false;
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147 }
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148
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149 return true;
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150 }
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151
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152
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153 MergeStudyJob::MergeStudyJob(ServerContext& context,
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154 const std::string& targetStudy) :
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155 CleaningInstancesJob(context, false /* by default, remove source instances */),
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156 targetStudy_(targetStudy)
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157 {
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158 /**
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159 * Check the validity of the input ID
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160 **/
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161
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162 ResourceType type;
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163
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164 if (!GetContext().GetIndex().LookupResourceType(type, targetStudy) ||
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165 type != ResourceType_Study)
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166 {
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167 throw OrthancException(ErrorCode_UnknownResource,
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168 "Cannot merge into an unknown study: " + targetStudy);
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169 }
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170
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171
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172 /**
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173 * Detect the tags to be removed/replaced by parsing one child
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174 * instance of the study
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175 **/
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176
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177 DicomTag::AddTagsForModule(removals_, DicomModule_Patient);
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178 DicomTag::AddTagsForModule(removals_, DicomModule_Study);
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179
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180 std::list<std::string> instances;
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181 GetContext().GetIndex().GetChildInstances(instances, targetStudy);
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182
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183 if (instances.empty())
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184 {
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185 throw OrthancException(ErrorCode_UnknownResource);
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186 }
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187
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188 DicomMap dicom;
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189
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190 {
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191 ServerContext::DicomCacheLocker locker(GetContext(), instances.front());
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0ddc5297a8ab centralization of default parameters for JSON/DicomMap conversions from DCMTK
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192 OrthancConfiguration::DefaultExtractDicomSummary(dicom, locker.GetDicom());
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193 }
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194
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195 const std::set<DicomTag> moduleTags = removals_;
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196 for (std::set<DicomTag>::const_iterator it = moduleTags.begin();
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197 it != moduleTags.end(); ++it)
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198 {
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199 const DicomValue* value = dicom.TestAndGetValue(*it);
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200 std::string str;
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201
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202 if (value != NULL &&
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203 value->CopyToString(str, false))
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204 {
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205 removals_.erase(*it);
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diff changeset
206 replacements_.insert(std::make_pair(*it, str));
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diff changeset
207 }
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diff changeset
208 }
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diff changeset
209 }
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diff changeset
210
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parents:
diff changeset
211
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diff changeset
212 void MergeStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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213 {
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diff changeset
214 if (IsStarted())
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215 {
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216 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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217 }
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218 else
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219 {
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diff changeset
220 origin_ = origin;
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diff changeset
221 }
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diff changeset
222 }
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223
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224
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225 void MergeStudyJob::SetOrigin(const RestApiCall& call)
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226 {
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227 SetOrigin(DicomInstanceOrigin::FromRest(call));
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228 }
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229
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diff changeset
230
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diff changeset
231 void MergeStudyJob::AddSource(const std::string& studyOrSeries)
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232 {
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diff changeset
233 ResourceType level;
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234
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diff changeset
235 if (IsStarted())
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diff changeset
236 {
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diff changeset
237 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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238 }
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diff changeset
239 else if (!GetContext().GetIndex().LookupResourceType(level, studyOrSeries))
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240 {
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diff changeset
241 throw OrthancException(ErrorCode_UnknownResource,
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242 "Cannot find this resource: " + studyOrSeries);
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diff changeset
243 }
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diff changeset
244 else
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245 {
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parents:
diff changeset
246 switch (level)
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247 {
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parents:
diff changeset
248 case ResourceType_Study:
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diff changeset
249 AddSourceStudyInternal(studyOrSeries);
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diff changeset
250 break;
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
251
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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diff changeset
252 case ResourceType_Series:
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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diff changeset
253 AddSourceSeries(studyOrSeries);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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diff changeset
254 break;
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
255
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diff changeset
256 default:
2955
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257 throw OrthancException(ErrorCode_UnknownResource,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2860
diff changeset
258 "This resource is neither a study, nor a series: " +
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
259 studyOrSeries + " is a " +
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
260 std::string(EnumerationToString(level)));
2853
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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diff changeset
261 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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parents:
diff changeset
262 }
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parents:
diff changeset
263 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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parents:
diff changeset
264
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parents:
diff changeset
265
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diff changeset
266 void MergeStudyJob::AddSourceSeries(const std::string& series)
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diff changeset
267 {
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diff changeset
268 std::string parent;
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269
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diff changeset
270 if (IsStarted())
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271 {
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diff changeset
272 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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diff changeset
273 }
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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diff changeset
274 else if (!GetContext().GetIndex().LookupParent(parent, series, ResourceType_Study))
2853
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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diff changeset
275 {
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276 throw OrthancException(ErrorCode_UnknownResource,
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diff changeset
277 "This resource is not a series: " + series);
2853
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diff changeset
278 }
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diff changeset
279 else if (parent == targetStudy_)
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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diff changeset
280 {
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diff changeset
281 throw OrthancException(ErrorCode_UnknownResource,
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
282 "Cannot merge series " + series +
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
283 " into its parent study " + targetStudy_);
2853
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parents:
diff changeset
284 }
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parents:
diff changeset
285 else
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
286 {
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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diff changeset
287 AddSourceSeriesInternal(series);
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parents:
diff changeset
288 }
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parents:
diff changeset
289 }
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parents:
diff changeset
290
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parents:
diff changeset
291
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parents:
diff changeset
292 void MergeStudyJob::AddSourceStudy(const std::string& study)
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diff changeset
293 {
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parents:
diff changeset
294 ResourceType actualLevel;
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parents:
diff changeset
295
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diff changeset
296 if (IsStarted())
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parents:
diff changeset
297 {
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diff changeset
298 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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diff changeset
299 }
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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diff changeset
300 else if (!GetContext().GetIndex().LookupResourceType(actualLevel, study) ||
2853
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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parents:
diff changeset
301 actualLevel != ResourceType_Study)
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parents:
diff changeset
302 {
2955
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diff changeset
303 throw OrthancException(ErrorCode_UnknownResource,
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parents: 2860
diff changeset
304 "This resource is not a study: " + study);
2853
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
305 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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parents:
diff changeset
306 else
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
307 {
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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parents:
diff changeset
308 AddSourceStudyInternal(study);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
309 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
310 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
311
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
312
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
313 void MergeStudyJob::GetPublicContent(Json::Value& value)
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parents:
diff changeset
314 {
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
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parents: 3940
diff changeset
315 CleaningInstancesJob::GetPublicContent(value);
2853
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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parents:
diff changeset
316 value["TargetStudy"] = targetStudy_;
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parents:
diff changeset
317 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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parents:
diff changeset
318
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
319
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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parents:
diff changeset
320 static const char* TARGET_STUDY = "TargetStudy";
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
321 static const char* REPLACEMENTS = "Replacements";
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
322 static const char* REMOVALS = "Removals";
52b017d22a4f New URI: "/studies/.../merge" to merge a study
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parents:
diff changeset
323 static const char* SERIES_UID_MAP = "SeriesUIDMap";
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
324 static const char* ORIGIN = "Origin";
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
325
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
326
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
327 MergeStudyJob::MergeStudyJob(ServerContext& context,
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
328 const Json::Value& serialized) :
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3940
diff changeset
329 CleaningInstancesJob(context, serialized,
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3940
diff changeset
330 false /* by default, remove source instances */) // (*)
2853
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
331 {
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
332 if (!HasTrailingStep())
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
333 {
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
334 // Should have been set by (*)
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
335 throw OrthancException(ErrorCode_InternalError);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
336 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
337
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
338 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
339 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
340 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
341 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
342 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
343 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
344
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
345
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
346 bool MergeStudyJob::Serialize(Json::Value& target)
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
347 {
3941
771dbd9eb3bd class CleaningInstancesJob to share cleaning code by merge/split jobs
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3940
diff changeset
348 if (!CleaningInstancesJob::Serialize(target))
2853
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
349 {
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
350 return false;
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
351 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
352 else
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
353 {
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
354 target[TARGET_STUDY] = targetStudy_;
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
355 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
356 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
357 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
358 origin_.Serialize(target[ORIGIN]);
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
359
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
360 return true;
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
361 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
362 }
52b017d22a4f New URI: "/studies/.../merge" to merge a study
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
363 }