Mercurial > hg > orthanc
annotate OrthancServer/ServerJobs/SplitStudyJob.cpp @ 2845:218e2c864d1d
serialization of SplitStudyJob
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 28 Sep 2018 17:59:44 +0200 |
parents | 99863d6245b2 |
children | d386abc18133 |
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) 2017-2018 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 |
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40 namespace Orthanc |
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41 { |
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42 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const |
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43 { |
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44 if (allowedTags_.find(tag) == allowedTags_.end()) |
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45 { |
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46 LOG(ERROR) << "Cannot modify the following tag while splitting a study " |
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47 << "(not in the patient/study modules): " |
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48 << FromDcmtkBridge::GetTagName(tag, "") << " (" << tag.Format() << ")"; |
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49 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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50 } |
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51 } |
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52 |
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53 |
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54 void SplitStudyJob::Setup() |
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55 { |
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56 SetPermissive(false); |
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57 |
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58 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient); |
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59 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study); |
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60 allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID); |
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61 allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID); |
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62 } |
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63 |
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64 |
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65 bool SplitStudyJob::HandleInstance(const std::string& instance) |
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66 { |
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67 /** |
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68 * Retrieve the DICOM instance to be modified |
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69 **/ |
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70 |
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71 std::auto_ptr<ParsedDicomFile> modified; |
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72 |
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73 try |
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74 { |
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75 ServerContext::DicomCacheLocker locker(context_, instance); |
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76 modified.reset(locker.GetDicom().Clone(true)); |
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77 } |
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78 catch (OrthancException&) |
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79 { |
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80 LOG(WARNING) << "An instance was removed after the job was issued: " << instance; |
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81 return false; |
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82 } |
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83 |
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84 |
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85 /** |
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86 * Chose the target UIDs |
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87 **/ |
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88 |
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89 std::string series; |
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90 if (!modified->GetTagValue(series, DICOM_TAG_SERIES_INSTANCE_UID)) |
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91 { |
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92 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen |
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93 } |
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94 |
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95 std::string targetSeriesUid; |
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96 SeriesUidMap::const_iterator found = targetSeries_.find(series); |
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97 |
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98 if (found == targetSeries_.end()) |
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99 { |
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100 // Choose a random SeriesInstanceUID for this series |
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101 targetSeriesUid = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series); |
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102 targetSeries_[series] = targetSeriesUid; |
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103 } |
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104 else |
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105 { |
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106 targetSeriesUid = found->second; |
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107 } |
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108 |
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109 |
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110 /** |
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111 * Apply user-specified modifications |
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112 **/ |
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113 |
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114 for (std::set<DicomTag>::const_iterator it = removals_.begin(); |
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115 it != removals_.end(); ++it) |
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116 { |
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117 modified->Remove(*it); |
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118 } |
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119 |
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120 for (Replacements::const_iterator it = replacements_.begin(); |
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121 it != replacements_.end(); ++it) |
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122 { |
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123 modified->ReplacePlainString(it->first, it->second); |
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124 } |
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125 |
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126 |
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127 /** |
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128 * Store the new instance into Orthanc |
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129 **/ |
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130 |
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131 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_); |
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132 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid); |
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133 |
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134 if (targetStudy_.empty()) |
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135 { |
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136 targetStudy_ = modified->GetHasher().HashStudy(); |
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137 } |
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138 |
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139 DicomInstanceToStore toStore; |
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140 toStore.SetOrigin(origin_); |
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141 toStore.SetParsedDicomFile(*modified); |
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142 |
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143 std::string modifiedInstance; |
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144 if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success) |
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145 { |
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146 LOG(ERROR) << "Error while storing a modified instance " << instance; |
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147 return false; |
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148 } |
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149 |
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150 return true; |
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151 } |
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152 |
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153 |
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154 bool SplitStudyJob::HandleTrailingStep() |
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155 { |
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156 if (!keepSource_) |
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157 { |
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158 const size_t n = GetInstancesCount(); |
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159 |
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160 for (size_t i = 0; i < n; i++) |
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161 { |
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162 Json::Value tmp; |
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163 context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance); |
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164 } |
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165 } |
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166 |
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167 return true; |
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168 } |
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169 |
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170 |
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171 SplitStudyJob::SplitStudyJob(ServerContext& context, |
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172 const std::string& sourceStudy) : |
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173 SetOfInstancesJob(true /* with trailing step */), |
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174 context_(context), |
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175 keepSource_(false), |
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176 sourceStudy_(sourceStudy), |
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177 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study)) |
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178 { |
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179 Setup(); |
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180 |
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181 ResourceType type; |
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182 |
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183 if (!context_.GetIndex().LookupResourceType(type, sourceStudy) || |
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184 type != ResourceType_Study) |
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185 { |
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186 LOG(ERROR) << "Cannot split unknown study: " << sourceStudy; |
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187 throw OrthancException(ErrorCode_UnknownResource); |
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188 } |
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189 |
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190 std::list<std::string> children; |
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191 context_.GetIndex().GetChildren(children, sourceStudy); |
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192 |
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193 for (std::list<std::string>::const_iterator |
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194 it = children.begin(); it != children.end(); ++it) |
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195 { |
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196 sourceSeries_.insert(*it); |
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197 } |
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198 } |
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199 |
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200 |
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201 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin) |
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202 { |
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203 if (IsStarted()) |
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204 { |
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205 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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206 } |
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207 else |
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208 { |
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209 origin_ = origin; |
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210 } |
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211 } |
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212 |
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213 |
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214 void SplitStudyJob::SetOrigin(const RestApiCall& call) |
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215 { |
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216 SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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217 } |
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218 |
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219 |
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220 void SplitStudyJob::AddSourceSeries(const std::string& series) |
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221 { |
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222 if (IsStarted()) |
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223 { |
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224 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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225 } |
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226 else if (sourceSeries_.find(series) == sourceSeries_.end()) |
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227 { |
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228 LOG(ERROR) << "This series does not belong to the study to be split: " << series; |
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229 throw OrthancException(ErrorCode_UnknownResource); |
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230 } |
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231 else |
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232 { |
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233 // Add all the instances of the series as to be processed |
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234 std::list<std::string> instances; |
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235 context_.GetIndex().GetChildren(instances, series); |
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236 |
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237 for (std::list<std::string>::const_iterator |
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238 it = instances.begin(); it != instances.end(); ++it) |
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239 { |
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240 AddInstance(*it); |
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241 } |
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242 } |
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243 } |
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244 |
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245 |
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246 void SplitStudyJob::SetKeepSource(bool keep) |
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247 { |
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248 if (IsStarted()) |
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249 { |
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250 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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251 } |
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252 |
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253 keepSource_ = keep; |
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254 } |
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255 |
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256 |
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257 void SplitStudyJob::Remove(const DicomTag& tag) |
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258 { |
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259 if (IsStarted()) |
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260 { |
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261 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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262 } |
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263 |
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264 CheckAllowedTag(tag); |
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265 removals_.insert(tag); |
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266 } |
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267 |
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268 |
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269 void SplitStudyJob::Replace(const DicomTag& tag, |
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270 const std::string& value) |
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271 { |
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272 if (IsStarted()) |
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273 { |
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274 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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275 } |
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276 |
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277 CheckAllowedTag(tag); |
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278 replacements_[tag] = value; |
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279 } |
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280 |
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281 |
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282 void SplitStudyJob::GetPublicContent(Json::Value& value) |
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283 { |
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284 SetOfInstancesJob::GetPublicContent(value); |
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285 |
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286 if (!targetStudy_.empty()) |
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287 { |
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288 value["TargetStudy"] = targetStudy_; |
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289 } |
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290 |
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291 value["TargetStudyUID"] = targetStudyUid_; |
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292 } |
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293 |
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294 |
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295 static const char* SOURCE_STUDY = "SourceStudy"; |
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296 static const char* SOURCE_SERIES = "SourceSeries"; |
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297 static const char* KEEP_SOURCE = "KeepSource"; |
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298 static const char* TARGET_STUDY = "TargetStudy"; |
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299 static const char* TARGET_STUDY_UID = "TargetStudyUID"; |
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300 static const char* TARGET_SERIES = "TargetSeries"; |
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301 static const char* ORIGIN = "Origin"; |
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302 static const char* REPLACEMENTS = "Replacements"; |
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303 static const char* REMOVALS = "Removals"; |
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304 |
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305 |
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306 SplitStudyJob::SplitStudyJob(ServerContext& context, |
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307 const Json::Value& serialized) : |
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308 SetOfInstancesJob(serialized), // (*) |
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309 context_(context) |
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310 { |
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311 if (!HasTrailingStep()) |
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312 { |
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313 // Should have been set by (*) |
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314 throw OrthancException(ErrorCode_InternalError); |
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315 } |
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316 |
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317 Setup(); |
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318 |
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319 keepSource_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SOURCE); |
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320 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY); |
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321 SerializationToolbox::ReadSetOfStrings(sourceSeries_, serialized, SOURCE_SERIES); |
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322 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY); |
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323 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID); |
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324 SerializationToolbox::ReadMapOfStrings(targetSeries_, serialized, TARGET_SERIES); |
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325 origin_ = DicomInstanceOrigin(serialized[ORIGIN]); |
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326 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS); |
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327 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS); |
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328 } |
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329 |
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330 |
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331 bool SplitStudyJob::Serialize(Json::Value& target) |
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332 { |
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333 if (!SetOfInstancesJob::Serialize(target)) |
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334 { |
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335 return false; |
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336 } |
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337 else |
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338 { |
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339 target[KEEP_SOURCE] = keepSource_; |
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340 target[SOURCE_STUDY] = sourceStudy_; |
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341 SerializationToolbox::WriteSetOfStrings(target, sourceSeries_, SOURCE_SERIES); |
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342 target[TARGET_STUDY] = targetStudy_; |
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343 target[TARGET_STUDY_UID] = targetStudyUid_; |
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344 SerializationToolbox::WriteMapOfStrings(target, targetSeries_, TARGET_SERIES); |
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345 origin_.Serialize(target[ORIGIN]); |
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346 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS); |
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347 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS); |
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348 |
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349 return true; |
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350 } |
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351 } |
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352 } |