Mercurial > hg > orthanc
annotate OrthancServer/ServerJobs/SplitStudyJob.cpp @ 3931:e6606d3ec892 transcoding
new configuration option: BuiltinDecoderTranscoderOrder
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 15 May 2020 09:22:31 +0200 |
parents | 023b2a9f3aa1 |
children | 3661e2a72482 |
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) 2017-2020 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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33 |
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34 #include "SplitStudyJob.h" |
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35 |
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36 #include "../../Core/DicomParsing/FromDcmtkBridge.h" |
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37 #include "../../Core/Logging.h" |
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38 #include "../../Core/SerializationToolbox.h" |
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39 #include "../ServerContext.h" |
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40 |
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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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49 "Cannot modify the following tag while splitting a study " | |
50 "(not in the patient/study modules): " + | |
51 FromDcmtkBridge::GetTagName(tag, "") + | |
52 " (" + tag.Format() + ")"); | |
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53 } |
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54 } |
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55 |
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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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66 |
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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 /** |
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71 * Retrieve the DICOM instance to be modified |
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72 **/ |
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73 |
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74 std::unique_ptr<ParsedDicomFile> modified; |
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75 |
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76 try |
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77 { |
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78 ServerContext::DicomCacheLocker locker(context_, instance); |
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79 modified.reset(locker.GetDicom().Clone(true)); |
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80 } |
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81 catch (OrthancException&) |
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82 { |
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83 LOG(WARNING) << "An instance was removed after the job was issued: " << instance; |
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84 return false; |
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85 } |
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86 |
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87 |
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88 /** |
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89 * Chose the target UIDs |
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90 **/ |
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91 |
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92 assert(modified->GetHasher().HashStudy() == sourceStudy_); |
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93 |
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94 std::string series = modified->GetHasher().HashSeries(); |
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95 |
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96 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series); |
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97 |
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98 if (targetSeriesUid == seriesUidMap_.end()) |
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99 { |
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100 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen |
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101 } |
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102 |
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103 |
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104 /** |
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105 * Apply user-specified modifications |
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106 **/ |
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107 |
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108 for (std::set<DicomTag>::const_iterator it = removals_.begin(); |
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109 it != removals_.end(); ++it) |
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110 { |
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111 modified->Remove(*it); |
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112 } |
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113 |
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114 for (Replacements::const_iterator it = replacements_.begin(); |
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115 it != replacements_.end(); ++it) |
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116 { |
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117 modified->ReplacePlainString(it->first, it->second); |
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118 } |
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119 |
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120 |
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121 /** |
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122 * Store the new instance into Orthanc |
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123 **/ |
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124 |
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125 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_); |
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126 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second); |
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127 |
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128 // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified |
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129 modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance)); |
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130 |
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131 if (targetStudy_.empty()) |
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132 { |
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133 targetStudy_ = modified->GetHasher().HashStudy(); |
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134 } |
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135 |
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136 DicomInstanceToStore toStore; |
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137 toStore.SetOrigin(origin_); |
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138 toStore.SetParsedDicomFile(*modified); |
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139 |
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140 std::string modifiedInstance; |
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141 if (context_.Store(modifiedInstance, toStore, |
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142 StoreInstanceMode_Default) != StoreStatus_Success) |
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143 { |
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144 LOG(ERROR) << "Error while storing a modified instance " << instance; |
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145 return false; |
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146 } |
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147 |
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148 return true; |
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149 } |
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150 |
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151 |
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152 bool SplitStudyJob::HandleTrailingStep() |
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153 { |
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154 if (!keepSource_) |
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155 { |
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156 const size_t n = GetInstancesCount(); |
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157 |
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158 for (size_t i = 0; i < n; i++) |
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159 { |
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160 Json::Value tmp; |
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161 context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance); |
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162 } |
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163 } |
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164 |
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165 return true; |
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166 } |
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167 |
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168 |
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169 SplitStudyJob::SplitStudyJob(ServerContext& context, |
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170 const std::string& sourceStudy) : |
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171 context_(context), |
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172 keepSource_(false), |
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173 sourceStudy_(sourceStudy), |
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174 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)) |
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175 { |
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176 Setup(); |
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177 |
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178 ResourceType type; |
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179 |
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180 if (!context_.GetIndex().LookupResourceType(type, sourceStudy) || |
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181 type != ResourceType_Study) |
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182 { |
2955 | 183 throw OrthancException(ErrorCode_UnknownResource, |
184 "Cannot split unknown study " + sourceStudy); | |
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185 } |
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186 } |
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187 |
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188 |
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189 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin) |
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190 { |
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191 if (IsStarted()) |
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192 { |
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193 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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194 } |
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195 else |
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196 { |
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197 origin_ = origin; |
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198 } |
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199 } |
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200 |
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201 |
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202 void SplitStudyJob::SetOrigin(const RestApiCall& call) |
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203 { |
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204 SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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205 } |
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206 |
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207 |
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208 void SplitStudyJob::AddSourceSeries(const std::string& series) |
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209 { |
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210 std::string parent; |
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211 |
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212 if (IsStarted()) |
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213 { |
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214 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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215 } |
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216 else if (!context_.GetIndex().LookupParent(parent, series, ResourceType_Study) || |
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217 parent != sourceStudy_) |
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218 { |
2955 | 219 throw OrthancException(ErrorCode_UnknownResource, |
220 "This series does not belong to the study to be split: " + series); | |
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221 } |
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222 else |
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223 { |
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224 // Generate a target SeriesInstanceUID for this series |
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225 seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series); |
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226 |
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227 // Add all the instances of the series as to be processed |
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228 std::list<std::string> instances; |
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229 context_.GetIndex().GetChildren(instances, series); |
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230 |
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231 for (std::list<std::string>::const_iterator |
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232 it = instances.begin(); it != instances.end(); ++it) |
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233 { |
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234 AddInstance(*it); |
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235 } |
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236 } |
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237 } |
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238 |
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239 |
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240 void SplitStudyJob::SetKeepSource(bool keep) |
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241 { |
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242 if (IsStarted()) |
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243 { |
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244 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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245 } |
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246 |
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247 keepSource_ = keep; |
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248 } |
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249 |
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250 |
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251 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid, |
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252 const std::string& series) const |
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253 { |
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254 SeriesUidMap::const_iterator found = seriesUidMap_.find(series); |
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255 |
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256 if (found == seriesUidMap_.end()) |
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257 { |
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258 return false; |
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259 } |
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260 else |
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261 { |
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262 uid = found->second; |
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263 return true; |
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264 } |
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265 } |
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266 |
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267 |
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268 void SplitStudyJob::Remove(const DicomTag& tag) |
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269 { |
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270 if (IsStarted()) |
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271 { |
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272 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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273 } |
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274 |
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275 CheckAllowedTag(tag); |
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276 removals_.insert(tag); |
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277 } |
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278 |
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279 |
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280 void SplitStudyJob::Replace(const DicomTag& tag, |
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281 const std::string& value) |
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282 { |
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283 if (IsStarted()) |
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284 { |
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285 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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286 } |
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287 |
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288 CheckAllowedTag(tag); |
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289 replacements_[tag] = value; |
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290 } |
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291 |
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292 |
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293 bool SplitStudyJob::LookupReplacement(std::string& value, |
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294 const DicomTag& tag) const |
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295 { |
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296 Replacements::const_iterator found = replacements_.find(tag); |
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297 |
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298 if (found == replacements_.end()) |
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299 { |
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300 return false; |
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301 } |
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302 else |
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303 { |
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304 value = found->second; |
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305 return true; |
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306 } |
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307 } |
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308 |
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309 |
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310 void SplitStudyJob::GetPublicContent(Json::Value& value) |
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311 { |
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312 SetOfInstancesJob::GetPublicContent(value); |
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313 |
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314 if (!targetStudy_.empty()) |
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315 { |
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316 value["TargetStudy"] = targetStudy_; |
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317 } |
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318 |
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319 value["TargetStudyUID"] = targetStudyUid_; |
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320 } |
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321 |
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322 |
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323 static const char* KEEP_SOURCE = "KeepSource"; |
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324 static const char* SOURCE_STUDY = "SourceStudy"; |
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325 static const char* TARGET_STUDY = "TargetStudy"; |
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326 static const char* TARGET_STUDY_UID = "TargetStudyUID"; |
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327 static const char* SERIES_UID_MAP = "SeriesUIDMap"; |
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328 static const char* ORIGIN = "Origin"; |
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329 static const char* REPLACEMENTS = "Replacements"; |
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330 static const char* REMOVALS = "Removals"; |
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331 |
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332 |
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333 SplitStudyJob::SplitStudyJob(ServerContext& context, |
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334 const Json::Value& serialized) : |
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335 SetOfInstancesJob(serialized), // (*) |
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336 context_(context) |
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337 { |
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338 if (!HasTrailingStep()) |
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339 { |
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340 // Should have been set by (*) |
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341 throw OrthancException(ErrorCode_InternalError); |
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342 } |
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343 |
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344 Setup(); |
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345 |
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346 keepSource_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SOURCE); |
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347 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY); |
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348 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY); |
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349 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID); |
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350 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP); |
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351 origin_ = DicomInstanceOrigin(serialized[ORIGIN]); |
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352 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS); |
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353 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS); |
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354 } |
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355 |
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356 |
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357 bool SplitStudyJob::Serialize(Json::Value& target) |
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358 { |
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359 if (!SetOfInstancesJob::Serialize(target)) |
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360 { |
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361 return false; |
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362 } |
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363 else |
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364 { |
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365 target[KEEP_SOURCE] = keepSource_; |
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366 target[SOURCE_STUDY] = sourceStudy_; |
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367 target[TARGET_STUDY] = targetStudy_; |
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368 target[TARGET_STUDY_UID] = targetStudyUid_; |
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369 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP); |
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370 origin_.Serialize(target[ORIGIN]); |
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371 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS); |
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372 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS); |
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373 |
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374 return true; |
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375 } |
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376 } |
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377 } |