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annotate OrthancServer/ServerJobs/SplitStudyJob.cpp @ 2912:ab03dae59d6e

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 31 Oct 2018 14:14:16 +0100
parents 8b00e4cb4a6b
children bbfd95a0c429
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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) 2017-2018 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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32
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34 #include "SplitStudyJob.h"
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35
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36 #include "../../Core/DicomParsing/FromDcmtkBridge.h"
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37 #include "../../Core/Logging.h"
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38 #include "../../Core/SerializationToolbox.h"
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39
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40 namespace Orthanc
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41 {
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42 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
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43 {
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44 if (allowedTags_.find(tag) == allowedTags_.end())
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45 {
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46 LOG(ERROR) << "Cannot modify the following tag while splitting a study "
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47 << "(not in the patient/study modules): "
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48 << FromDcmtkBridge::GetTagName(tag, "") << " (" << tag.Format() << ")";
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49 throw OrthancException(ErrorCode_ParameterOutOfRange);
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50 }
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51 }
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52
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53
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54 void SplitStudyJob::Setup()
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55 {
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56 SetPermissive(false);
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57
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58 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
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59 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
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60 allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
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61 allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
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62 }
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63
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64
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65 bool SplitStudyJob::HandleInstance(const std::string& instance)
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66 {
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67 /**
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68 * Retrieve the DICOM instance to be modified
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69 **/
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70
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71 std::auto_ptr<ParsedDicomFile> modified;
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72
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73 try
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74 {
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75 ServerContext::DicomCacheLocker locker(context_, instance);
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76 modified.reset(locker.GetDicom().Clone(true));
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77 }
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78 catch (OrthancException&)
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79 {
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80 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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81 return false;
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82 }
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83
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84
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85 /**
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86 * Chose the target UIDs
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87 **/
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88
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89 assert(modified->GetHasher().HashStudy() == sourceStudy_);
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90
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91 std::string series = modified->GetHasher().HashSeries();
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92
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93 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series);
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94
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95 if (targetSeriesUid == seriesUidMap_.end())
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96 {
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97 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen
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98 }
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99
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100
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101 /**
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102 * Apply user-specified modifications
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103 **/
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104
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105 for (std::set<DicomTag>::const_iterator it = removals_.begin();
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106 it != removals_.end(); ++it)
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107 {
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108 modified->Remove(*it);
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109 }
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110
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111 for (Replacements::const_iterator it = replacements_.begin();
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112 it != replacements_.end(); ++it)
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113 {
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114 modified->ReplacePlainString(it->first, it->second);
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115 }
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117
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118 /**
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119 * Store the new instance into Orthanc
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120 **/
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121
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122 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
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123 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second);
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124
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125 if (targetStudy_.empty())
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126 {
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127 targetStudy_ = modified->GetHasher().HashStudy();
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128 }
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129
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130 DicomInstanceToStore toStore;
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131 toStore.SetOrigin(origin_);
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132 toStore.SetParsedDicomFile(*modified);
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133
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134 std::string modifiedInstance;
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135 if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success)
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136 {
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137 LOG(ERROR) << "Error while storing a modified instance " << instance;
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138 return false;
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139 }
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140
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141 return true;
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142 }
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143
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144
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145 bool SplitStudyJob::HandleTrailingStep()
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146 {
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147 if (!keepSource_)
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148 {
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149 const size_t n = GetInstancesCount();
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150
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151 for (size_t i = 0; i < n; i++)
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152 {
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153 Json::Value tmp;
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154 context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance);
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155 }
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156 }
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157
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158 return true;
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159 }
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160
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161
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162 SplitStudyJob::SplitStudyJob(ServerContext& context,
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163 const std::string& sourceStudy) :
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164 context_(context),
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165 keepSource_(false),
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166 sourceStudy_(sourceStudy),
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167 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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168 {
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169 Setup();
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170
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171 ResourceType type;
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172
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173 if (!context_.GetIndex().LookupResourceType(type, sourceStudy) ||
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174 type != ResourceType_Study)
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175 {
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176 LOG(ERROR) << "Cannot split unknown study: " << sourceStudy;
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177 throw OrthancException(ErrorCode_UnknownResource);
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178 }
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179 }
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180
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181
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182 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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183 {
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184 if (IsStarted())
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185 {
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186 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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187 }
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188 else
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189 {
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190 origin_ = origin;
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191 }
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192 }
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193
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194
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195 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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196 {
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197 SetOrigin(DicomInstanceOrigin::FromRest(call));
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198 }
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199
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200
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201 void SplitStudyJob::AddSourceSeries(const std::string& series)
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202 {
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203 std::string parent;
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204
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205 if (IsStarted())
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206 {
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207 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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208 }
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209 else if (!context_.GetIndex().LookupParent(parent, series, ResourceType_Study) ||
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210 parent != sourceStudy_)
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211 {
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212 LOG(ERROR) << "This series does not belong to the study to be split: " << series;
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213 throw OrthancException(ErrorCode_UnknownResource);
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214 }
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215 else
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216 {
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217 // Generate a target SeriesInstanceUID for this series
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218 seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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219
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220 // Add all the instances of the series as to be processed
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221 std::list<std::string> instances;
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222 context_.GetIndex().GetChildren(instances, series);
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223
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224 for (std::list<std::string>::const_iterator
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225 it = instances.begin(); it != instances.end(); ++it)
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226 {
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227 AddInstance(*it);
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228 }
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229 }
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230 }
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231
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232
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233 void SplitStudyJob::SetKeepSource(bool keep)
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234 {
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235 if (IsStarted())
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236 {
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237 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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238 }
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239
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240 keepSource_ = keep;
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241 }
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242
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243
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244 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
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245 const std::string& series) const
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246 {
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247 SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
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248
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249 if (found == seriesUidMap_.end())
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250 {
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251 return false;
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252 }
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253 else
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254 {
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255 uid = found->second;
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256 return true;
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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 void SplitStudyJob::Remove(const DicomTag& tag)
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262 {
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263 if (IsStarted())
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264 {
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265 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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266 }
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267
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268 CheckAllowedTag(tag);
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269 removals_.insert(tag);
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270 }
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271
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272
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273 void SplitStudyJob::Replace(const DicomTag& tag,
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274 const std::string& value)
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275 {
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276 if (IsStarted())
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277 {
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278 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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279 }
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280
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281 CheckAllowedTag(tag);
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282 replacements_[tag] = value;
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283 }
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284
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285
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286 bool SplitStudyJob::LookupReplacement(std::string& value,
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287 const DicomTag& tag) const
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288 {
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289 Replacements::const_iterator found = replacements_.find(tag);
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290
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291 if (found == replacements_.end())
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292 {
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293 return false;
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294 }
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295 else
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296 {
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297 value = found->second;
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298 return true;
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299 }
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300 }
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301
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302
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303 void SplitStudyJob::GetPublicContent(Json::Value& value)
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304 {
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305 SetOfInstancesJob::GetPublicContent(value);
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306
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307 if (!targetStudy_.empty())
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308 {
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309 value["TargetStudy"] = targetStudy_;
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310 }
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311
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312 value["TargetStudyUID"] = targetStudyUid_;
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313 }
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314
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315
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316 static const char* KEEP_SOURCE = "KeepSource";
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317 static const char* SOURCE_STUDY = "SourceStudy";
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318 static const char* TARGET_STUDY = "TargetStudy";
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319 static const char* TARGET_STUDY_UID = "TargetStudyUID";
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320 static const char* SERIES_UID_MAP = "SeriesUIDMap";
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321 static const char* ORIGIN = "Origin";
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322 static const char* REPLACEMENTS = "Replacements";
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323 static const char* REMOVALS = "Removals";
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324
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325
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326 SplitStudyJob::SplitStudyJob(ServerContext& context,
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327 const Json::Value& serialized) :
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328 SetOfInstancesJob(serialized), // (*)
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329 context_(context)
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330 {
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331 if (!HasTrailingStep())
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332 {
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333 // Should have been set by (*)
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334 throw OrthancException(ErrorCode_InternalError);
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335 }
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336
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337 Setup();
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338
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339 keepSource_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SOURCE);
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340 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
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341 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
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342 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
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343 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
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344 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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345 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
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346 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
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347 }
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348
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349
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350 bool SplitStudyJob::Serialize(Json::Value& target)
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351 {
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352 if (!SetOfInstancesJob::Serialize(target))
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353 {
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354 return false;
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355 }
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356 else
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357 {
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358 target[KEEP_SOURCE] = keepSource_;
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359 target[SOURCE_STUDY] = sourceStudy_;
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360 target[TARGET_STUDY] = targetStudy_;
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361 target[TARGET_STUDY_UID] = targetStudyUid_;
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362 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
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diff changeset
363 origin_.Serialize(target[ORIGIN]);
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364 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
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365 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
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diff changeset
366
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367 return true;
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368 }
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369 }
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370 }