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annotate OrthancServer/Sources/ServerJobs/SplitStudyJob.cpp @ 5808:63c025cf6958 attach-custom-data

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cleanup
author Alain Mazy <am@orthanc.team>
date Tue, 24 Sep 2024 12:11:25 +0200
parents f7adfb22e20e
children
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rev   line source
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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) 2017-2023 Osimis S.A., Belgium
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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8 *
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9 * This program is free software: you can redistribute it and/or
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10 * modify it under the terms of the GNU General Public License as
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11 * published by the Free Software Foundation, either version 3 of the
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12 * License, or (at your option) any later version.
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13 *
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14 * This program is distributed in the hope that it will be useful, but
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15 * WITHOUT ANY WARRANTY; without even the implied warranty of
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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17 * General Public License for more details.
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18 *
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19 * You should have received a copy of the GNU General Public License
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20 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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21 **/
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22
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24 #include "SplitStudyJob.h"
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25
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26 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h"
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27 #include "../../../OrthancFramework/Sources/Logging.h"
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28 #include "../../../OrthancFramework/Sources/SerializationToolbox.h"
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29 #include "../ServerContext.h"
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30
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31
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32 namespace Orthanc
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33 {
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34 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
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35 {
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36 if (allowedTags_.find(tag) == allowedTags_.end())
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37 {
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38 throw OrthancException(ErrorCode_ParameterOutOfRange,
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39 "Cannot modify the following tag while splitting a study "
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40 "(not in the patient/study modules): " +
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41 FromDcmtkBridge::GetTagName(tag, "") +
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42 " (" + tag.Format() + ")");
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43 }
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44 }
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46
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47 void SplitStudyJob::Setup()
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48 {
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49 SetPermissive(false);
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50
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51 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
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52 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
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53 allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
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54 allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
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55 }
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57
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58 bool SplitStudyJob::HandleInstance(const std::string& instance)
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59 {
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60 if (!HasTrailingStep())
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61 {
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62 throw OrthancException(ErrorCode_BadSequenceOfCalls,
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63 "AddTrailingStep() should have been called after AddSourceSeries()");
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64 }
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65
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66 /**
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67 * Retrieve the DICOM instance to be modified
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68 **/
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69
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70 std::unique_ptr<ParsedDicomFile> modified;
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71
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72 try
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73 {
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74 ServerContext::DicomCacheLocker locker(GetContext(), instance);
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75 modified.reset(locker.GetDicom().Clone(true));
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76 }
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77 catch (OrthancException&)
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78 {
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79 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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80 return false;
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81 }
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82
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83
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84 /**
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85 * Chose the target UIDs
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86 **/
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87
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88 assert(modified->GetHasher().HashStudy() == sourceStudy_);
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89
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90 std::string series = modified->GetHasher().HashSeries();
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91
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92 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series);
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93
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94 if (targetSeriesUid == seriesUidMap_.end())
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95 {
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96 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen
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97 }
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98
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99
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100 /**
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101 * Apply user-specified modifications
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102 **/
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103
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104 for (std::set<DicomTag>::const_iterator it = removals_.begin();
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105 it != removals_.end(); ++it)
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106 {
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107 modified->Remove(*it);
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108 }
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109
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110 for (Replacements::const_iterator it = replacements_.begin();
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111 it != replacements_.end(); ++it)
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112 {
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113 modified->ReplacePlainString(it->first, it->second);
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114 }
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115
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116
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117 /**
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118 * Store the new instance into Orthanc
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119 **/
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120
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121 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
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122 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second);
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123
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124 // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified
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125 modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
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126
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127 if (targetStudy_.empty())
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128 {
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129 targetStudy_ = modified->GetHasher().HashStudy();
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130 }
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131
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132 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified));
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133 toStore->SetOrigin(origin_);
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134
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135 std::string modifiedInstance;
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136 ServerContext::StoreResult result = GetContext().Store(modifiedInstance, *toStore, StoreInstanceMode_Default);
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137 if (result.GetStatus() != StoreStatus_Success)
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138 {
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139 LOG(ERROR) << "Error while storing a modified instance " << instance;
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140 return false;
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141 }
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142
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143 return true;
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144 }
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145
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146
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147 SplitStudyJob::SplitStudyJob(ServerContext& context,
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148 const std::string& sourceStudy) :
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149 CleaningInstancesJob(context, false /* by default, remove source instances */),
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150 sourceStudy_(sourceStudy),
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151 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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152 {
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153 Setup();
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154
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155 ResourceType type;
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156
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157 if (!GetContext().GetIndex().LookupResourceType(type, sourceStudy) ||
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158 type != ResourceType_Study)
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159 {
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160 throw OrthancException(ErrorCode_UnknownResource,
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161 "Cannot split unknown study " + sourceStudy);
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162 }
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163 }
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164
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165
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166 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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167 {
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168 if (IsStarted())
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169 {
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170 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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171 }
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172 else
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173 {
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174 origin_ = origin;
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175 }
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176 }
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177
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178
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179 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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180 {
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181 SetOrigin(DicomInstanceOrigin::FromRest(call));
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182 }
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183
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184
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185 static void RegisterSeries(std::map<std::string, std::string>& target,
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186 const std::string& series)
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187 {
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188 // Generate a target SeriesInstanceUID for this series
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189 if (target.find(series) == target.end())
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190 {
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191 target[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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192 }
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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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211 {
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212 RegisterSeries(seriesUidMap_, series);
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213
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214 // Add all the instances of the series as to be processed
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215 std::list<std::string> instances;
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216 GetContext().GetIndex().GetChildren(instances, series);
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217
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218 for (std::list<std::string>::const_iterator
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219 it = instances.begin(); it != instances.end(); ++it)
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220 {
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221 AddInstance(*it);
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222 }
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223 }
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224 }
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225
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226
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227 void SplitStudyJob::AddSourceInstance(const std::string& instance)
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228 {
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229 std::string study, series;
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230
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231 if (IsStarted())
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232 {
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233 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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234 }
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235 else if (!GetContext().GetIndex().LookupParent(series, instance, ResourceType_Series) ||
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236 !GetContext().GetIndex().LookupParent(study, series, ResourceType_Study) ||
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237 study != sourceStudy_)
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238 {
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239 throw OrthancException(ErrorCode_UnknownResource,
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240 "This instance does not belong to the study to be split: " + instance);
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241 }
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242 else
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243 {
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244 RegisterSeries(seriesUidMap_, series);
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245 AddInstance(instance);
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246 }
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247 }
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248
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249
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250 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
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251 const std::string& series) const
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252 {
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253 SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
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254
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255 if (found == seriesUidMap_.end())
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256 {
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257 return false;
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258 }
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259 else
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260 {
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261 uid = found->second;
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262 return true;
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263 }
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264 }
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265
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266
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267 void SplitStudyJob::Remove(const DicomTag& tag)
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268 {
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269 if (IsStarted())
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270 {
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271 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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272 }
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273
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274 CheckAllowedTag(tag);
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275 removals_.insert(tag);
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276 }
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277
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278
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279 void SplitStudyJob::Replace(const DicomTag& tag,
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280 const std::string& value)
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281 {
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282 if (IsStarted())
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283 {
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284 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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285 }
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286
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287 CheckAllowedTag(tag);
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288 replacements_[tag] = value;
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289 }
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290
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291
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292 bool SplitStudyJob::LookupReplacement(std::string& value,
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293 const DicomTag& tag) const
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294 {
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295 Replacements::const_iterator found = replacements_.find(tag);
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296
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297 if (found == replacements_.end())
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298 {
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299 return false;
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300 }
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301 else
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302 {
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303 value = found->second;
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304 return true;
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305 }
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306 }
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307
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308
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309 void SplitStudyJob::GetPublicContent(Json::Value& value)
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310 {
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311 CleaningInstancesJob::GetPublicContent(value);
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312
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313 if (!targetStudy_.empty())
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314 {
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315 value["TargetStudy"] = targetStudy_;
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316 }
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317
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318 value["TargetStudyUID"] = targetStudyUid_;
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319 }
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320
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321
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322 static const char* SOURCE_STUDY = "SourceStudy";
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323 static const char* TARGET_STUDY = "TargetStudy";
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324 static const char* TARGET_STUDY_UID = "TargetStudyUID";
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325 static const char* SERIES_UID_MAP = "SeriesUIDMap";
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326 static const char* ORIGIN = "Origin";
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327 static const char* REPLACEMENTS = "Replacements";
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328 static const char* REMOVALS = "Removals";
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329
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diff changeset
330
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diff changeset
331 SplitStudyJob::SplitStudyJob(ServerContext& context,
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diff changeset
332 const Json::Value& serialized) :
3941
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333 CleaningInstancesJob(context, serialized,
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diff changeset
334 false /* by default, remove source instances */) // (*)
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diff changeset
335 {
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336 if (!HasTrailingStep())
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337 {
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diff changeset
338 // Should have been set by (*)
218e2c864d1d serialization of SplitStudyJob
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339 throw OrthancException(ErrorCode_InternalError);
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diff changeset
340 }
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diff changeset
341
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diff changeset
342 Setup();
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diff changeset
343
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diff changeset
344 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
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345 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
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diff changeset
346 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
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diff changeset
347 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
2845
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diff changeset
348 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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349 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
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350 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
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diff changeset
351 }
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diff changeset
352
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353
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354 bool SplitStudyJob::Serialize(Json::Value& target)
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355 {
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diff changeset
356 if (!CleaningInstancesJob::Serialize(target))
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diff changeset
357 {
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358 return false;
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359 }
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diff changeset
360 else
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diff changeset
361 {
218e2c864d1d serialization of SplitStudyJob
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diff changeset
362 target[SOURCE_STUDY] = sourceStudy_;
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diff changeset
363 target[TARGET_STUDY] = targetStudy_;
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diff changeset
364 target[TARGET_STUDY_UID] = targetStudyUid_;
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diff changeset
365 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
2845
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diff changeset
366 origin_.Serialize(target[ORIGIN]);
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367 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
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diff changeset
368 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
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diff changeset
369
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370 return true;
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diff changeset
371 }
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372 }
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373 }