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annotate OrthancServer/Sources/ServerJobs/SplitStudyJob.cpp @ 5374:b216b57bbe6a

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author Alain Mazy <am@osimis.io>
date Tue, 22 Aug 2023 12:30:05 +0200
parents 0ea402b4d901
children 48b8dae6dc77
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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) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU General Public License as
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10 * published by the Free Software Foundation, either version 3 of the
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11 * License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU General Public License
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19 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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20 **/
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21
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23 #include "SplitStudyJob.h"
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24
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25 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h"
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26 #include "../../../OrthancFramework/Sources/Logging.h"
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27 #include "../../../OrthancFramework/Sources/SerializationToolbox.h"
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28 #include "../ServerContext.h"
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29
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30
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31 namespace Orthanc
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32 {
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33 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
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34 {
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35 if (allowedTags_.find(tag) == allowedTags_.end())
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36 {
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37 throw OrthancException(ErrorCode_ParameterOutOfRange,
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38 "Cannot modify the following tag while splitting a study "
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39 "(not in the patient/study modules): " +
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40 FromDcmtkBridge::GetTagName(tag, "") +
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41 " (" + tag.Format() + ")");
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42 }
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43 }
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45
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46 void SplitStudyJob::Setup()
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47 {
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48 SetPermissive(false);
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49
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50 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
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51 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
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52 allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
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53 allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
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54 }
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56
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57 bool SplitStudyJob::HandleInstance(const std::string& instance)
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58 {
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59 if (!HasTrailingStep())
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60 {
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61 throw OrthancException(ErrorCode_BadSequenceOfCalls,
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62 "AddTrailingStep() should have been called after AddSourceSeries()");
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63 }
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64
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65 /**
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66 * Retrieve the DICOM instance to be modified
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67 **/
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68
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69 std::unique_ptr<ParsedDicomFile> modified;
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70
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71 try
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72 {
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73 ServerContext::DicomCacheLocker locker(GetContext(), instance);
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74 modified.reset(locker.GetDicom().Clone(true));
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75 }
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76 catch (OrthancException&)
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77 {
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78 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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79 return false;
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80 }
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81
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82
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83 /**
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84 * Chose the target UIDs
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85 **/
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86
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87 assert(modified->GetHasher().HashStudy() == sourceStudy_);
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88
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89 std::string series = modified->GetHasher().HashSeries();
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90
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91 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series);
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92
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93 if (targetSeriesUid == seriesUidMap_.end())
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94 {
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95 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen
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96 }
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97
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98
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99 /**
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100 * Apply user-specified modifications
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101 **/
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102
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103 for (std::set<DicomTag>::const_iterator it = removals_.begin();
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104 it != removals_.end(); ++it)
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105 {
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106 modified->Remove(*it);
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107 }
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108
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109 for (Replacements::const_iterator it = replacements_.begin();
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110 it != replacements_.end(); ++it)
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111 {
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112 modified->ReplacePlainString(it->first, it->second);
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113 }
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114
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115
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116 /**
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117 * Store the new instance into Orthanc
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118 **/
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119
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120 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
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121 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second);
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122
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123 // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified
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124 modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
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125
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126 if (targetStudy_.empty())
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127 {
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128 targetStudy_ = modified->GetHasher().HashStudy();
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129 }
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130
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131 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified));
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132 toStore->SetOrigin(origin_);
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133
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134 std::string modifiedInstance;
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135 ServerContext::StoreResult result = GetContext().Store(modifiedInstance, *toStore, StoreInstanceMode_Default);
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136 if (result.GetStatus() != StoreStatus_Success)
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137 {
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138 LOG(ERROR) << "Error while storing a modified instance " << instance;
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139 return false;
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140 }
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141
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142 return true;
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143 }
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144
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145
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146 SplitStudyJob::SplitStudyJob(ServerContext& context,
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147 const std::string& sourceStudy) :
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148 CleaningInstancesJob(context, false /* by default, remove source instances */),
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149 sourceStudy_(sourceStudy),
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150 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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151 {
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152 Setup();
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153
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154 ResourceType type;
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155
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156 if (!GetContext().GetIndex().LookupResourceType(type, sourceStudy) ||
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157 type != ResourceType_Study)
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158 {
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159 throw OrthancException(ErrorCode_UnknownResource,
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160 "Cannot split unknown study " + sourceStudy);
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161 }
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162 }
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163
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164
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165 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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166 {
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167 if (IsStarted())
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168 {
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169 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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170 }
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171 else
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172 {
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173 origin_ = origin;
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174 }
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175 }
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176
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177
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178 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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179 {
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180 SetOrigin(DicomInstanceOrigin::FromRest(call));
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181 }
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182
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183
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184 static void RegisterSeries(std::map<std::string, std::string>& target,
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185 const std::string& series)
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186 {
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187 // Generate a target SeriesInstanceUID for this series
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188 if (target.find(series) == target.end())
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189 {
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190 target[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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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::AddSourceSeries(const std::string& series)
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196 {
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197 std::string parent;
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198
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199 if (IsStarted())
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200 {
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201 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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202 }
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203 else if (!GetContext().GetIndex().LookupParent(parent, series, ResourceType_Study) ||
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204 parent != sourceStudy_)
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205 {
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206 throw OrthancException(ErrorCode_UnknownResource,
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207 "This series does not belong to the study to be split: " + series);
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208 }
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209 else
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210 {
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211 RegisterSeries(seriesUidMap_, series);
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212
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213 // Add all the instances of the series as to be processed
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214 std::list<std::string> instances;
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215 GetContext().GetIndex().GetChildren(instances, series);
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216
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217 for (std::list<std::string>::const_iterator
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218 it = instances.begin(); it != instances.end(); ++it)
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219 {
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220 AddInstance(*it);
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221 }
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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 void SplitStudyJob::AddSourceInstance(const std::string& instance)
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227 {
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228 std::string study, series;
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229
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230 if (IsStarted())
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231 {
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232 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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233 }
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234 else if (!GetContext().GetIndex().LookupParent(series, instance, ResourceType_Series) ||
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235 !GetContext().GetIndex().LookupParent(study, series, ResourceType_Study) ||
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236 study != sourceStudy_)
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237 {
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238 throw OrthancException(ErrorCode_UnknownResource,
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239 "This instance does not belong to the study to be split: " + instance);
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240 }
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241 else
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242 {
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243 RegisterSeries(seriesUidMap_, series);
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244 AddInstance(instance);
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245 }
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246 }
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247
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248
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249 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
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250 const std::string& series) const
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251 {
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252 SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
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253
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254 if (found == seriesUidMap_.end())
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255 {
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256 return false;
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257 }
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258 else
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259 {
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260 uid = found->second;
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261 return true;
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262 }
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263 }
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264
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265
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266 void SplitStudyJob::Remove(const DicomTag& tag)
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267 {
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268 if (IsStarted())
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269 {
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270 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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271 }
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272
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273 CheckAllowedTag(tag);
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274 removals_.insert(tag);
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275 }
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276
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277
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278 void SplitStudyJob::Replace(const DicomTag& tag,
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279 const std::string& value)
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280 {
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281 if (IsStarted())
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282 {
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283 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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284 }
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285
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286 CheckAllowedTag(tag);
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287 replacements_[tag] = value;
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288 }
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289
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290
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291 bool SplitStudyJob::LookupReplacement(std::string& value,
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292 const DicomTag& tag) const
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293 {
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294 Replacements::const_iterator found = replacements_.find(tag);
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295
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296 if (found == replacements_.end())
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297 {
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298 return false;
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299 }
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300 else
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301 {
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302 value = found->second;
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303 return true;
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304 }
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305 }
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306
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307
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308 void SplitStudyJob::GetPublicContent(Json::Value& value)
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309 {
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310 CleaningInstancesJob::GetPublicContent(value);
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311
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312 if (!targetStudy_.empty())
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313 {
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314 value["TargetStudy"] = targetStudy_;
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315 }
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316
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317 value["TargetStudyUID"] = targetStudyUid_;
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318 }
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319
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320
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321 static const char* SOURCE_STUDY = "SourceStudy";
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322 static const char* TARGET_STUDY = "TargetStudy";
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323 static const char* TARGET_STUDY_UID = "TargetStudyUID";
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324 static const char* SERIES_UID_MAP = "SeriesUIDMap";
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325 static const char* ORIGIN = "Origin";
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326 static const char* REPLACEMENTS = "Replacements";
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327 static const char* REMOVALS = "Removals";
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328
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329
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330 SplitStudyJob::SplitStudyJob(ServerContext& context,
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331 const Json::Value& serialized) :
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332 CleaningInstancesJob(context, serialized,
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333 false /* by default, remove source instances */) // (*)
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334 {
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335 if (!HasTrailingStep())
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336 {
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337 // Should have been set by (*)
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338 throw OrthancException(ErrorCode_InternalError);
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339 }
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diff changeset
340
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diff changeset
341 Setup();
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diff changeset
342
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diff changeset
343 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
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344 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
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diff changeset
345 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
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346 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
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diff changeset
347 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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348 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
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349 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
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diff changeset
350 }
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351
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352
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353 bool SplitStudyJob::Serialize(Json::Value& target)
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354 {
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355 if (!CleaningInstancesJob::Serialize(target))
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diff changeset
356 {
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357 return false;
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358 }
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diff changeset
359 else
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diff changeset
360 {
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diff changeset
361 target[SOURCE_STUDY] = sourceStudy_;
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diff changeset
362 target[TARGET_STUDY] = targetStudy_;
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diff changeset
363 target[TARGET_STUDY_UID] = targetStudyUid_;
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diff changeset
364 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
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diff changeset
365 origin_.Serialize(target[ORIGIN]);
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366 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
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diff changeset
367 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
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diff changeset
368
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369 return true;
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diff changeset
370 }
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371 }
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372 }