Mercurial > hg > orthanc

annotate OrthancServer/Sources/ServerJobs/SplitStudyJob.cpp @ 4717:783f8a048035 openssl-3.x

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integration mainline->openssl-3.x
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 23 Jun 2021 16:23:23 +0200
parents f0038043fb97 bad8935cd5f2
children 70d2a97ca8cb
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2021 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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20
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22 #include "SplitStudyJob.h"
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23
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24 #include "../../../OrthancFramework/Sources/DicomParsing/FromDcmtkBridge.h"
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25 #include "../../../OrthancFramework/Sources/Logging.h"
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26 #include "../../../OrthancFramework/Sources/SerializationToolbox.h"
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27 #include "../ServerContext.h"
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29
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30 namespace Orthanc
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31 {
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32 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
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33 {
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34 if (allowedTags_.find(tag) == allowedTags_.end())
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35 {
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36 throw OrthancException(ErrorCode_ParameterOutOfRange,
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37 "Cannot modify the following tag while splitting a study "
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38 "(not in the patient/study modules): " +
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39 FromDcmtkBridge::GetTagName(tag, "") +
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40 " (" + tag.Format() + ")");
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41 }
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42 }
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44
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45 void SplitStudyJob::Setup()
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46 {
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47 SetPermissive(false);
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48
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49 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
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50 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
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51 allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
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52 allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
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53 }
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56 bool SplitStudyJob::HandleInstance(const std::string& instance)
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57 {
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58 if (!HasTrailingStep())
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59 {
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60 throw OrthancException(ErrorCode_BadSequenceOfCalls,
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61 "AddTrailingStep() should have been called after AddSourceSeries()");
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62 }
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63
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64 /**
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65 * Retrieve the DICOM instance to be modified
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66 **/
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67
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68 std::unique_ptr<ParsedDicomFile> modified;
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69
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70 try
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71 {
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72 ServerContext::DicomCacheLocker locker(GetContext(), instance);
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73 modified.reset(locker.GetDicom().Clone(true));
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74 }
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75 catch (OrthancException&)
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76 {
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77 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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78 return false;
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79 }
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80
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81
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82 /**
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83 * Chose the target UIDs
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84 **/
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85
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86 assert(modified->GetHasher().HashStudy() == sourceStudy_);
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87
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88 std::string series = modified->GetHasher().HashSeries();
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89
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90 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series);
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91
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92 if (targetSeriesUid == seriesUidMap_.end())
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93 {
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94 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen
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95 }
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96
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97
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98 /**
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99 * Apply user-specified modifications
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100 **/
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101
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102 for (std::set<DicomTag>::const_iterator it = removals_.begin();
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103 it != removals_.end(); ++it)
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104 {
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105 modified->Remove(*it);
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106 }
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107
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108 for (Replacements::const_iterator it = replacements_.begin();
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109 it != replacements_.end(); ++it)
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110 {
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111 modified->ReplacePlainString(it->first, it->second);
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112 }
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113
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114
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115 /**
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116 * Store the new instance into Orthanc
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117 **/
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118
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119 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
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120 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second);
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121
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122 // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified
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123 modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
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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 std::unique_ptr<DicomInstanceToStore> toStore(DicomInstanceToStore::CreateFromParsedDicomFile(*modified));
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131 toStore->SetOrigin(origin_);
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132
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133 std::string modifiedInstance;
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134 if (GetContext().Store(modifiedInstance, *toStore,
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135 StoreInstanceMode_Default) != 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 SplitStudyJob::SplitStudyJob(ServerContext& context,
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146 const std::string& sourceStudy) :
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147 CleaningInstancesJob(context, false /* by default, remove source instances */),
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148 sourceStudy_(sourceStudy),
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149 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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150 {
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151 Setup();
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152
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153 ResourceType type;
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154
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155 if (!GetContext().GetIndex().LookupResourceType(type, sourceStudy) ||
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156 type != ResourceType_Study)
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157 {
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158 throw OrthancException(ErrorCode_UnknownResource,
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159 "Cannot split unknown study " + sourceStudy);
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160 }
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161 }
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162
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163
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164 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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165 {
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166 if (IsStarted())
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167 {
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168 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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169 }
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170 else
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171 {
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172 origin_ = origin;
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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 RestApiCall& call)
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178 {
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179 SetOrigin(DicomInstanceOrigin::FromRest(call));
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180 }
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181
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182
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183 static void RegisterSeries(std::map<std::string, std::string>& target,
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184 const std::string& series)
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185 {
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186 // Generate a target SeriesInstanceUID for this series
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187 if (target.find(series) == target.end())
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188 {
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189 target[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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190 }
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191 }
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192
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193
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194 void SplitStudyJob::AddSourceSeries(const std::string& series)
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195 {
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196 std::string parent;
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197
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198 if (IsStarted())
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199 {
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200 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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201 }
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202 else if (!GetContext().GetIndex().LookupParent(parent, series, ResourceType_Study) ||
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203 parent != sourceStudy_)
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204 {
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205 throw OrthancException(ErrorCode_UnknownResource,
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206 "This series does not belong to the study to be split: " + series);
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207 }
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208 else
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209 {
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210 RegisterSeries(seriesUidMap_, series);
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211
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212 // Add all the instances of the series as to be processed
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213 std::list<std::string> instances;
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214 GetContext().GetIndex().GetChildren(instances, series);
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215
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216 for (std::list<std::string>::const_iterator
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217 it = instances.begin(); it != instances.end(); ++it)
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218 {
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219 AddInstance(*it);
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220 }
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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 void SplitStudyJob::AddSourceInstance(const std::string& instance)
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226 {
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227 std::string study, series;
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228
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229 if (IsStarted())
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230 {
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231 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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232 }
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233 else if (!GetContext().GetIndex().LookupParent(series, instance, ResourceType_Series) ||
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234 !GetContext().GetIndex().LookupParent(study, series, ResourceType_Study) ||
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235 study != sourceStudy_)
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236 {
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237 throw OrthancException(ErrorCode_UnknownResource,
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238 "This instance does not belong to the study to be split: " + instance);
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239 }
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240 else
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241 {
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242 RegisterSeries(seriesUidMap_, series);
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243 AddInstance(instance);
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244 }
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245 }
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246
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247
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248 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
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249 const std::string& series) const
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250 {
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251 SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
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252
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253 if (found == seriesUidMap_.end())
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254 {
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255 return false;
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256 }
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257 else
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258 {
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259 uid = found->second;
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260 return true;
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261 }
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262 }
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263
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264
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265 void SplitStudyJob::Remove(const DicomTag& tag)
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266 {
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267 if (IsStarted())
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268 {
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269 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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270 }
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271
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272 CheckAllowedTag(tag);
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273 removals_.insert(tag);
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274 }
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275
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276
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277 void SplitStudyJob::Replace(const DicomTag& tag,
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278 const std::string& value)
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279 {
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280 if (IsStarted())
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281 {
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282 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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283 }
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284
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285 CheckAllowedTag(tag);
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286 replacements_[tag] = value;
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287 }
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288
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289
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290 bool SplitStudyJob::LookupReplacement(std::string& value,
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291 const DicomTag& tag) const
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292 {
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293 Replacements::const_iterator found = replacements_.find(tag);
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294
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295 if (found == replacements_.end())
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296 {
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297 return false;
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298 }
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299 else
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300 {
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301 value = found->second;
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302 return true;
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303 }
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304 }
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305
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306
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307 void SplitStudyJob::GetPublicContent(Json::Value& value)
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308 {
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309 CleaningInstancesJob::GetPublicContent(value);
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310
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311 if (!targetStudy_.empty())
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312 {
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313 value["TargetStudy"] = targetStudy_;
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314 }
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315
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316 value["TargetStudyUID"] = targetStudyUid_;
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317 }
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318
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319
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320 static const char* SOURCE_STUDY = "SourceStudy";
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321 static const char* TARGET_STUDY = "TargetStudy";
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322 static const char* TARGET_STUDY_UID = "TargetStudyUID";
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323 static const char* SERIES_UID_MAP = "SeriesUIDMap";
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324 static const char* ORIGIN = "Origin";
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325 static const char* REPLACEMENTS = "Replacements";
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326 static const char* REMOVALS = "Removals";
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327
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328
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329 SplitStudyJob::SplitStudyJob(ServerContext& context,
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330 const Json::Value& serialized) :
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331 CleaningInstancesJob(context, serialized,
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332 false /* by default, remove source instances */) // (*)
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333 {
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334 if (!HasTrailingStep())
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335 {
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336 // Should have been set by (*)
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337 throw OrthancException(ErrorCode_InternalError);
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338 }
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339
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diff changeset
340 Setup();
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341
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342 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
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343 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
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344 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
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345 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
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346 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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347 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
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348 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
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349 }
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350
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351
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352 bool SplitStudyJob::Serialize(Json::Value& target)
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353 {
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354 if (!CleaningInstancesJob::Serialize(target))
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355 {
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356 return false;
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357 }
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358 else
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359 {
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360 target[SOURCE_STUDY] = sourceStudy_;
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361 target[TARGET_STUDY] = targetStudy_;
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362 target[TARGET_STUDY_UID] = targetStudyUid_;
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diff changeset
363 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
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diff changeset
364 origin_.Serialize(target[ORIGIN]);
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365 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
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366 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
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diff changeset
367
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368 return true;
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diff changeset
369 }
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370 }
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371 }