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annotate OrthancServer/Sources/ServerJobs/SplitStudyJob.cpp @ 4443:fd958175c5b9

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ImageProcessing::ConvertJpegYCbCrToRgb()
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 12 Jan 2021 13:07:15 +0100
parents d9473bd5ed43
children 8f9090b137f1
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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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32
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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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41
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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 DicomInstanceToStore toStore;
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143 toStore.SetOrigin(origin_);
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144 toStore.SetParsedDicomFile(*modified);
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145
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146 std::string modifiedInstance;
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147 if (GetContext().Store(modifiedInstance, toStore,
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148 StoreInstanceMode_Default) != StoreStatus_Success)
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149 {
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150 LOG(ERROR) << "Error while storing a modified instance " << instance;
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151 return false;
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152 }
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153
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154 return true;
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155 }
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156
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157
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158 SplitStudyJob::SplitStudyJob(ServerContext& context,
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159 const std::string& sourceStudy) :
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160 CleaningInstancesJob(context, false /* by default, remove source instances */),
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161 sourceStudy_(sourceStudy),
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162 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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163 {
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164 Setup();
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165
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166 ResourceType type;
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167
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168 if (!GetContext().GetIndex().LookupResourceType(type, sourceStudy) ||
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169 type != ResourceType_Study)
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170 {
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171 throw OrthancException(ErrorCode_UnknownResource,
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172 "Cannot split unknown study " + sourceStudy);
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173 }
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174 }
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175
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176
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177 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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178 {
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179 if (IsStarted())
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180 {
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181 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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182 }
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183 else
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184 {
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185 origin_ = origin;
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186 }
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187 }
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188
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189
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190 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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191 {
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192 SetOrigin(DicomInstanceOrigin::FromRest(call));
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193 }
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194
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195
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196 void SplitStudyJob::AddSourceSeries(const std::string& series)
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197 {
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198 std::string parent;
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199
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200 if (IsStarted())
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201 {
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202 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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203 }
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204 else if (!GetContext().GetIndex().LookupParent(parent, series, ResourceType_Study) ||
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205 parent != sourceStudy_)
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206 {
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207 throw OrthancException(ErrorCode_UnknownResource,
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208 "This series does not belong to the study to be split: " + series);
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209 }
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210 else
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diff changeset
211 {
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212 // Generate a target SeriesInstanceUID for this series
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213 seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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diff changeset
214
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215 // Add all the instances of the series as to be processed
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216 std::list<std::string> instances;
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217 GetContext().GetIndex().GetChildren(instances, series);
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218
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diff changeset
219 for (std::list<std::string>::const_iterator
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220 it = instances.begin(); it != instances.end(); ++it)
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221 {
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diff changeset
222 AddInstance(*it);
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223 }
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diff changeset
224 }
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225 }
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diff changeset
226
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diff changeset
227
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diff changeset
228 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
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diff changeset
229 const std::string& series) const
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230 {
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
231 SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
232
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
233 if (found == seriesUidMap_.end())
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
234 {
2da68edacab6 unit testing of SplitStudyJob
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235 return false;
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
236 }
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
237 else
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
238 {
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
239 uid = found->second;
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240 return true;
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241 }
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242 }
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diff changeset
243
2da68edacab6 unit testing of SplitStudyJob
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diff changeset
244
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245 void SplitStudyJob::Remove(const DicomTag& tag)
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246 {
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diff changeset
247 if (IsStarted())
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diff changeset
248 {
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249 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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250 }
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251
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252 CheckAllowedTag(tag);
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diff changeset
253 removals_.insert(tag);
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254 }
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255
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256
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257 void SplitStudyJob::Replace(const DicomTag& tag,
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258 const std::string& value)
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259 {
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260 if (IsStarted())
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261 {
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262 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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263 }
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264
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265 CheckAllowedTag(tag);
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266 replacements_[tag] = value;
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267 }
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268
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269
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270 bool SplitStudyJob::LookupReplacement(std::string& value,
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271 const DicomTag& tag) const
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272 {
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273 Replacements::const_iterator found = replacements_.find(tag);
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274
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275 if (found == replacements_.end())
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276 {
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277 return false;
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278 }
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279 else
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280 {
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281 value = found->second;
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282 return true;
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283 }
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284 }
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285
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286
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287 void SplitStudyJob::GetPublicContent(Json::Value& value)
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288 {
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289 CleaningInstancesJob::GetPublicContent(value);
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290
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291 if (!targetStudy_.empty())
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292 {
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293 value["TargetStudy"] = targetStudy_;
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294 }
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295
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296 value["TargetStudyUID"] = targetStudyUid_;
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297 }
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298
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299
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300 static const char* SOURCE_STUDY = "SourceStudy";
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301 static const char* TARGET_STUDY = "TargetStudy";
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302 static const char* TARGET_STUDY_UID = "TargetStudyUID";
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303 static const char* SERIES_UID_MAP = "SeriesUIDMap";
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304 static const char* ORIGIN = "Origin";
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305 static const char* REPLACEMENTS = "Replacements";
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306 static const char* REMOVALS = "Removals";
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307
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308
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309 SplitStudyJob::SplitStudyJob(ServerContext& context,
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310 const Json::Value& serialized) :
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311 CleaningInstancesJob(context, serialized,
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312 false /* by default, remove source instances */) // (*)
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313 {
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314 if (!HasTrailingStep())
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315 {
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316 // Should have been set by (*)
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317 throw OrthancException(ErrorCode_InternalError);
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318 }
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319
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320 Setup();
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321
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322 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
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323 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
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324 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
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325 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
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326 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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327 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
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328 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
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329 }
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330
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331
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332 bool SplitStudyJob::Serialize(Json::Value& target)
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333 {
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334 if (!CleaningInstancesJob::Serialize(target))
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335 {
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336 return false;
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337 }
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338 else
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339 {
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340 target[SOURCE_STUDY] = sourceStudy_;
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341 target[TARGET_STUDY] = targetStudy_;
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342 target[TARGET_STUDY_UID] = targetStudyUid_;
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343 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
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344 origin_.Serialize(target[ORIGIN]);
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345 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
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346 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
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347
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348 return true;
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349 }
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350 }
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351 }