Mercurial > hg > orthanc
annotate OrthancServer/ServerJobs/SplitStudyJob.cpp @ 2844:99863d6245b2
New URI: "/studies/.../split" to split a study
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 28 Sep 2018 16:48:43 +0200 |
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children | 218e2c864d1d |
rev | line source |
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2844
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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/Logging.h" |
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37 #include "../../Core/DicomParsing/FromDcmtkBridge.h" |
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38 |
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39 namespace Orthanc |
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40 { |
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41 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const |
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42 { |
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43 if (allowedTags_.find(tag) == allowedTags_.end()) |
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44 { |
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45 LOG(ERROR) << "Cannot modify the following tag while splitting a study " |
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46 << "(not in the patient/study modules): " |
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47 << FromDcmtkBridge::GetTagName(tag, "") << " (" << tag.Format() << ")"; |
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48 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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49 } |
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50 } |
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51 |
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52 |
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53 void SplitStudyJob::Setup(const std::string& sourceStudy) |
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54 { |
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55 SetPermissive(false); |
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56 |
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57 keepSource_ = false; |
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58 sourceStudy_ = sourceStudy; |
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59 targetStudyUid_ = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study); |
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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 ResourceType type; |
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67 |
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68 if (!context_.GetIndex().LookupResourceType(type, sourceStudy) || |
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69 type != ResourceType_Study) |
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70 { |
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71 LOG(ERROR) << "Cannot split unknown study: " << sourceStudy; |
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72 throw OrthancException(ErrorCode_UnknownResource); |
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73 } |
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74 |
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75 std::list<std::string> children; |
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76 context_.GetIndex().GetChildren(children, sourceStudy); |
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77 |
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78 for (std::list<std::string>::const_iterator |
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79 it = children.begin(); it != children.end(); ++it) |
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80 { |
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81 sourceSeries_.insert(*it); |
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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 bool SplitStudyJob::HandleInstance(const std::string& instance) |
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87 { |
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88 /** |
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89 * Retrieve the DICOM instance to be modified |
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90 **/ |
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91 |
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92 std::auto_ptr<ParsedDicomFile> modified; |
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93 |
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94 try |
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95 { |
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96 ServerContext::DicomCacheLocker locker(context_, instance); |
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97 modified.reset(locker.GetDicom().Clone(true)); |
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98 } |
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99 catch (OrthancException&) |
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100 { |
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101 LOG(WARNING) << "An instance was removed after the job was issued: " << instance; |
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102 return false; |
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103 } |
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104 |
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105 |
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106 /** |
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107 * Chose the target UIDs |
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108 **/ |
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109 |
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110 std::string series; |
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111 if (!modified->GetTagValue(series, DICOM_TAG_SERIES_INSTANCE_UID)) |
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112 { |
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113 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen |
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114 } |
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115 |
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116 std::string targetSeriesUid; |
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117 SeriesUidMap::const_iterator found = targetSeries_.find(series); |
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118 |
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119 if (found == targetSeries_.end()) |
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120 { |
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121 // Choose a random SeriesInstanceUID for this series |
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122 targetSeriesUid = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series); |
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123 targetSeries_[series] = targetSeriesUid; |
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124 } |
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125 else |
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126 { |
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127 targetSeriesUid = found->second; |
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128 } |
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129 |
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130 |
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131 /** |
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132 * Apply user-specified modifications |
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133 **/ |
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134 |
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135 for (Removals::const_iterator it = removals_.begin(); |
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136 it != removals_.end(); ++it) |
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137 { |
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138 modified->Remove(*it); |
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139 } |
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140 |
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141 for (Replacements::const_iterator it = replacements_.begin(); |
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142 it != replacements_.end(); ++it) |
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143 { |
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144 modified->ReplacePlainString(it->first, it->second); |
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145 } |
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146 |
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147 |
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148 /** |
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149 * Store the new instance into Orthanc |
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150 **/ |
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151 |
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152 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_); |
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153 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid); |
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154 |
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155 if (targetStudy_.empty()) |
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156 { |
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157 targetStudy_ = modified->GetHasher().HashStudy(); |
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158 } |
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159 |
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160 DicomInstanceToStore toStore; |
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161 toStore.SetOrigin(origin_); |
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162 toStore.SetParsedDicomFile(*modified); |
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163 |
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164 std::string modifiedInstance; |
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165 if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success) |
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166 { |
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167 LOG(ERROR) << "Error while storing a modified instance " << instance; |
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168 return false; |
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169 } |
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170 |
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171 return true; |
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172 } |
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173 |
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174 |
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175 bool SplitStudyJob::HandleTrailingStep() |
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176 { |
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177 if (!keepSource_) |
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178 { |
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179 const size_t n = GetInstancesCount(); |
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180 |
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181 for (size_t i = 0; i < n; i++) |
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182 { |
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183 Json::Value tmp; |
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184 context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance); |
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185 } |
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186 } |
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187 |
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188 return true; |
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189 } |
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190 |
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191 |
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192 SplitStudyJob::SplitStudyJob(ServerContext& context, |
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193 const std::string& sourceStudy) : |
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194 SetOfInstancesJob(true /* with trailing step */), |
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195 context_(context) |
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196 { |
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197 Setup(sourceStudy); |
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198 } |
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199 |
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200 |
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201 SplitStudyJob::SplitStudyJob(ServerContext& context, |
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202 const Json::Value& serialized) : |
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203 SetOfInstancesJob(serialized), |
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204 context_(context) |
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205 { |
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206 //assert(HasTrailingStep()); |
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207 //Setup(); |
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208 } |
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209 |
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210 |
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211 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin) |
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212 { |
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213 if (IsStarted()) |
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214 { |
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215 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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216 } |
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217 else |
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218 { |
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219 origin_ = origin; |
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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 void SplitStudyJob::SetOrigin(const RestApiCall& call) |
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225 { |
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226 SetOrigin(DicomInstanceOrigin::FromRest(call)); |
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227 } |
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228 |
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229 |
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230 void SplitStudyJob::AddSourceSeries(const std::string& series) |
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231 { |
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232 if (IsStarted()) |
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233 { |
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234 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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235 } |
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236 else if (sourceSeries_.find(series) == sourceSeries_.end()) |
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237 { |
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238 LOG(ERROR) << "This series does not belong to the study to be split: " << series; |
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239 throw OrthancException(ErrorCode_UnknownResource); |
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240 } |
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241 else |
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242 { |
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243 // Add all the instances of the series as to be processed |
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244 std::list<std::string> instances; |
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245 context_.GetIndex().GetChildren(instances, series); |
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246 |
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247 for (std::list<std::string>::const_iterator |
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248 it = instances.begin(); it != instances.end(); ++it) |
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249 { |
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250 AddInstance(*it); |
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251 } |
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252 } |
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253 } |
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254 |
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255 |
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256 void SplitStudyJob::SetKeepSource(bool keep) |
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257 { |
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258 if (IsStarted()) |
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259 { |
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260 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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261 } |
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262 |
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263 keepSource_ = keep; |
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264 } |
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265 |
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266 |
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267 void SplitStudyJob::Remove(const DicomTag& tag) |
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268 { |
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269 if (IsStarted()) |
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270 { |
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271 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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272 } |
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273 |
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274 CheckAllowedTag(tag); |
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275 removals_.insert(tag); |
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276 } |
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277 |
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278 |
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279 void SplitStudyJob::Replace(const DicomTag& tag, |
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280 const std::string& value) |
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281 { |
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282 if (IsStarted()) |
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283 { |
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284 throw OrthancException(ErrorCode_BadSequenceOfCalls); |
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285 } |
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286 |
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287 CheckAllowedTag(tag); |
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288 replacements_[tag] = value; |
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289 } |
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290 |
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291 |
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292 void SplitStudyJob::GetPublicContent(Json::Value& value) |
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293 { |
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294 SetOfInstancesJob::GetPublicContent(value); |
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295 |
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296 if (!targetStudy_.empty()) |
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297 { |
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298 value["TargetStudy"] = targetStudy_; |
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299 } |
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300 |
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301 value["TargetStudyUID"] = targetStudyUid_; |
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302 } |
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303 |
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304 |
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305 bool SplitStudyJob::Serialize(Json::Value& target) |
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306 { |
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307 return true; |
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308 } |
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309 } |