Mercurial > hg > orthanc
annotate OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp @ 1385:772c8507c68d query-retrieve
integration mainline->query-retrieve
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Fri, 29 May 2015 15:00:45 +0200 |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
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5 * |
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6 * This program is free software: you can redistribute it and/or |
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7 * modify it under the terms of the GNU General Public License as |
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8 * published by the Free Software Foundation, either version 3 of the |
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9 * License, or (at your option) any later version. |
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10 * |
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11 * In addition, as a special exception, the copyright holders of this |
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12 * program give permission to link the code of its release with the |
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it |
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14 * that use the same license as the "OpenSSL" library), and distribute |
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15 * the linked executables. You must obey the GNU General Public License |
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16 * in all respects for all of the code used other than "OpenSSL". If you |
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17 * modify file(s) with this exception, you may extend this exception to |
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18 * your version of the file(s), but you are not obligated to do so. If |
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19 * you do not wish to do so, delete this exception statement from your |
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20 * version. If you delete this exception statement from all source files |
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21 * in the program, then also delete it here. |
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22 * |
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23 * This program is distributed in the hope that it will be useful, but |
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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26 * General Public License for more details. |
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27 * |
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28 * You should have received a copy of the GNU General Public License |
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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30 **/ |
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31 |
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32 |
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33 #include "../PrecompiledHeadersServer.h" |
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34 #include "OrthancRestApi.h" |
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35 |
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37 #include "../../Core/Uuid.h" |
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38 |
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39 #include <glog/logging.h> |
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40 |
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41 namespace Orthanc |
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42 { |
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43 // Modification of DICOM instances ------------------------------------------ |
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44 |
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45 enum TagOperation |
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46 { |
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47 TagOperation_Keep, |
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48 TagOperation_Remove |
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49 }; |
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50 |
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51 static void ParseListOfTags(DicomModification& target, |
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52 const Json::Value& query, |
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53 TagOperation operation) |
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54 { |
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55 if (!query.isArray()) |
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56 { |
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57 throw OrthancException(ErrorCode_BadRequest); |
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58 } |
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59 |
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60 for (Json::Value::ArrayIndex i = 0; i < query.size(); i++) |
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61 { |
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62 std::string name = query[i].asString(); |
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63 |
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64 DicomTag tag = FromDcmtkBridge::ParseTag(name); |
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65 |
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66 switch (operation) |
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67 { |
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68 case TagOperation_Keep: |
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69 target.Keep(tag); |
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70 VLOG(1) << "Keep: " << name << " " << tag << std::endl; |
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71 break; |
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72 |
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73 case TagOperation_Remove: |
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74 target.Remove(tag); |
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75 VLOG(1) << "Remove: " << name << " " << tag << std::endl; |
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76 break; |
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77 |
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78 default: |
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79 throw OrthancException(ErrorCode_InternalError); |
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80 } |
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81 } |
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82 } |
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83 |
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84 |
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85 static void ParseReplacements(DicomModification& target, |
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86 const Json::Value& replacements) |
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87 { |
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88 if (!replacements.isObject()) |
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89 { |
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90 throw OrthancException(ErrorCode_BadRequest); |
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91 } |
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92 |
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93 Json::Value::Members members = replacements.getMemberNames(); |
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94 for (size_t i = 0; i < members.size(); i++) |
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95 { |
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96 const std::string& name = members[i]; |
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97 std::string value = replacements[name].asString(); |
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98 |
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99 DicomTag tag = FromDcmtkBridge::ParseTag(name); |
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100 target.Replace(tag, value); |
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101 |
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102 VLOG(1) << "Replace: " << name << " " << tag << " == " << value << std::endl; |
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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 static std::string GeneratePatientName(ServerContext& context) |
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108 { |
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109 uint64_t seq = context.GetIndex().IncrementGlobalSequence(GlobalProperty_AnonymizationSequence); |
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110 return "Anonymized" + boost::lexical_cast<std::string>(seq); |
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111 } |
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112 |
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113 |
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115 bool OrthancRestApi::ParseModifyRequest(DicomModification& target, | |
116 const Json::Value& request) | |
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117 { |
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119 { |
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120 if (request.isMember("RemovePrivateTags")) |
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121 { |
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122 target.SetRemovePrivateTags(true); |
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123 } |
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124 |
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125 if (request.isMember("Remove")) |
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126 { |
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127 ParseListOfTags(target, request["Remove"], TagOperation_Remove); |
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128 } |
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129 |
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130 if (request.isMember("Replace")) |
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131 { |
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132 ParseReplacements(target, request["Replace"]); |
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133 } |
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134 |
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135 return true; |
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136 } |
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137 else |
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138 { |
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139 return false; |
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140 } |
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141 } |
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142 |
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143 |
1010 | 144 static bool ParseModifyRequest(DicomModification& target, |
145 const RestApiPostCall& call) | |
146 { | |
147 // curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}' | |
148 | |
149 Json::Value request; | |
150 if (call.ParseJsonRequest(request)) | |
151 { | |
152 return OrthancRestApi::ParseModifyRequest(target, request); | |
153 } | |
154 else | |
155 { | |
156 return false; | |
157 } | |
158 } | |
159 | |
160 | |
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161 static bool ParseAnonymizationRequest(DicomModification& target, |
974 | 162 RestApiPostCall& call) |
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163 { |
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164 // curl http://localhost:8042/instances/6e67da51-d119d6ae-c5667437-87b9a8a5-0f07c49f/anonymize -X POST -d '{"Replace":{"PatientName":"hello","0010-0020":"world"},"Keep":["StudyDescription", "SeriesDescription"],"KeepPrivateTags": null,"Remove":["Modality"]}' > Anonymized.dcm |
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165 |
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166 target.SetupAnonymization(); |
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167 std::string patientName = target.GetReplacement(DICOM_TAG_PATIENT_NAME); |
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168 |
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169 Json::Value request; |
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170 if (call.ParseJsonRequest(request) && request.isObject()) |
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171 { |
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172 if (request.isMember("KeepPrivateTags")) |
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173 { |
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174 target.SetRemovePrivateTags(false); |
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175 } |
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176 |
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177 if (request.isMember("Remove")) |
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178 { |
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179 ParseListOfTags(target, request["Remove"], TagOperation_Remove); |
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180 } |
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181 |
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182 if (request.isMember("Replace")) |
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183 { |
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184 ParseReplacements(target, request["Replace"]); |
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185 } |
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186 |
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187 if (request.isMember("Keep")) |
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188 { |
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189 ParseListOfTags(target, request["Keep"], TagOperation_Keep); |
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190 } |
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191 |
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192 if (target.IsReplaced(DICOM_TAG_PATIENT_NAME) && |
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193 target.GetReplacement(DICOM_TAG_PATIENT_NAME) == patientName) |
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194 { |
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195 // Overwrite the random Patient's Name by one that is more |
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196 // user-friendly (provided none was specified by the user) |
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197 target.Replace(DICOM_TAG_PATIENT_NAME, GeneratePatientName(OrthancRestApi::GetContext(call)), true); |
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198 } |
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199 |
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200 return true; |
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201 } |
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202 else |
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203 { |
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204 return false; |
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205 } |
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206 } |
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207 |
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208 |
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209 static void AnonymizeOrModifyInstance(DicomModification& modification, |
974 | 210 RestApiPostCall& call) |
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211 { |
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212 std::string id = call.GetUriComponent("id", ""); |
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213 |
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214 ServerContext::DicomCacheLocker locker(OrthancRestApi::GetContext(call), id); |
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215 |
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216 std::auto_ptr<ParsedDicomFile> modified(locker.GetDicom().Clone()); |
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217 modification.Apply(*modified); |
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218 modified->Answer(call.GetOutput()); |
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219 } |
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220 |
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221 |
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222 static void AnonymizeOrModifyResource(DicomModification& modification, |
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223 MetadataType metadataType, |
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224 ChangeType changeType, |
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225 ResourceType resourceType, |
974 | 226 RestApiPostCall& call) |
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227 { |
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228 bool isFirst = true; |
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229 Json::Value result(Json::objectValue); |
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230 |
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231 ServerContext& context = OrthancRestApi::GetContext(call); |
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232 |
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233 typedef std::list<std::string> Instances; |
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234 Instances instances; |
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235 std::string id = call.GetUriComponent("id", ""); |
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236 context.GetIndex().GetChildInstances(instances, id); |
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237 |
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238 if (instances.empty()) |
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239 { |
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240 return; |
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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 * Loop over all the instances of the resource. |
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246 **/ |
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247 |
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248 for (Instances::const_iterator it = instances.begin(); |
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249 it != instances.end(); ++it) |
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250 { |
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251 LOG(INFO) << "Modifying instance " << *it; |
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252 |
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253 std::auto_ptr<ServerContext::DicomCacheLocker> locker; |
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254 |
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255 try |
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256 { |
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257 locker.reset(new ServerContext::DicomCacheLocker(OrthancRestApi::GetContext(call), *it)); |
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258 } |
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259 catch (OrthancException&) |
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260 { |
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261 // This child instance has been removed in between |
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262 continue; |
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263 } |
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264 |
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265 |
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266 ParsedDicomFile& original = locker->GetDicom(); |
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267 DicomInstanceHasher originalHasher = original.GetHasher(); |
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268 |
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269 |
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270 /** |
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271 * Compute the resulting DICOM instance. |
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272 **/ |
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273 |
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274 std::auto_ptr<ParsedDicomFile> modified(original.Clone()); |
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275 modification.Apply(*modified); |
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276 |
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277 DicomInstanceToStore toStore; |
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278 toStore.SetParsedDicomFile(*modified); |
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279 |
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280 |
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281 /** |
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282 * Prepare the metadata information to associate with the |
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283 * resulting DICOM instance (AnonymizedFrom/ModifiedFrom). |
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284 **/ |
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285 |
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286 DicomInstanceHasher modifiedHasher = modified->GetHasher(); |
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287 |
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288 if (originalHasher.HashSeries() != modifiedHasher.HashSeries()) |
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289 { |
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290 toStore.AddMetadata(ResourceType_Series, metadataType, originalHasher.HashSeries()); |
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291 } |
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292 |
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293 if (originalHasher.HashStudy() != modifiedHasher.HashStudy()) |
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294 { |
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295 toStore.AddMetadata(ResourceType_Study, metadataType, originalHasher.HashStudy()); |
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296 } |
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297 |
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298 if (originalHasher.HashPatient() != modifiedHasher.HashPatient()) |
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299 { |
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300 toStore.AddMetadata(ResourceType_Patient, metadataType, originalHasher.HashPatient()); |
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301 } |
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302 |
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303 assert(*it == originalHasher.HashInstance()); |
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304 toStore.AddMetadata(ResourceType_Instance, metadataType, *it); |
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305 |
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306 |
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307 /** |
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308 * Store the resulting DICOM instance into the Orthanc store. |
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309 **/ |
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310 |
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311 std::string modifiedInstance; |
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312 if (context.Store(modifiedInstance, toStore) != StoreStatus_Success) |
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313 { |
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314 LOG(ERROR) << "Error while storing a modified instance " << *it; |
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315 return; |
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316 } |
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317 |
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318 // Sanity checks in debug mode |
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319 assert(modifiedInstance == modifiedHasher.HashInstance()); |
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320 |
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321 |
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322 /** |
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323 * Compute the JSON object that is returned by the REST call. |
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324 **/ |
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325 |
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326 if (isFirst) |
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327 { |
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328 std::string newId; |
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329 |
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330 switch (resourceType) |
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331 { |
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332 case ResourceType_Series: |
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333 newId = modifiedHasher.HashSeries(); |
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334 break; |
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335 |
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336 case ResourceType_Study: |
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337 newId = modifiedHasher.HashStudy(); |
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338 break; |
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339 |
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340 case ResourceType_Patient: |
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341 newId = modifiedHasher.HashPatient(); |
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342 break; |
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343 |
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344 default: |
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345 throw OrthancException(ErrorCode_InternalError); |
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346 } |
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347 |
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348 result["Type"] = EnumerationToString(resourceType); |
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349 result["ID"] = newId; |
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350 result["Path"] = GetBasePath(resourceType, newId); |
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351 result["PatientID"] = modifiedHasher.HashPatient(); |
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352 isFirst = false; |
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353 } |
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354 } |
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355 |
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356 call.GetOutput().AnswerJson(result); |
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357 } |
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358 |
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359 |
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360 |
974 | 361 static void ModifyInstance(RestApiPostCall& call) |
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362 { |
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363 DicomModification modification; |
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364 modification.SetAllowManualIdentifiers(true); |
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365 |
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366 if (ParseModifyRequest(modification, call)) |
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367 { |
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368 if (modification.IsReplaced(DICOM_TAG_PATIENT_ID)) |
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369 { |
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370 modification.SetLevel(ResourceType_Patient); |
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371 } |
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372 else if (modification.IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID)) |
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373 { |
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374 modification.SetLevel(ResourceType_Study); |
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375 } |
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376 else if (modification.IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID)) |
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377 { |
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378 modification.SetLevel(ResourceType_Series); |
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379 } |
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380 else |
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381 { |
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382 modification.SetLevel(ResourceType_Instance); |
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383 } |
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384 |
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385 AnonymizeOrModifyInstance(modification, call); |
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386 } |
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387 } |
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388 |
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389 |
974 | 390 static void AnonymizeInstance(RestApiPostCall& call) |
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391 { |
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392 DicomModification modification; |
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393 modification.SetAllowManualIdentifiers(true); |
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394 |
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395 if (ParseAnonymizationRequest(modification, call)) |
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396 { |
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397 AnonymizeOrModifyInstance(modification, call); |
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398 } |
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399 } |
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400 |
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401 |
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402 template <enum ChangeType changeType, |
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403 enum ResourceType resourceType> |
974 | 404 static void ModifyResource(RestApiPostCall& call) |
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405 { |
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406 DicomModification modification; |
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407 |
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408 if (ParseModifyRequest(modification, call)) |
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409 { |
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410 modification.SetLevel(resourceType); |
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411 AnonymizeOrModifyResource(modification, MetadataType_ModifiedFrom, |
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412 changeType, resourceType, call); |
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413 } |
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414 } |
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changeset
|
415 |
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|
416 |
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417 template <enum ChangeType changeType, |
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418 enum ResourceType resourceType> |
974 | 419 static void AnonymizeResource(RestApiPostCall& call) |
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420 { |
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421 DicomModification modification; |
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422 |
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423 if (ParseAnonymizationRequest(modification, call)) |
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424 { |
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425 AnonymizeOrModifyResource(modification, MetadataType_AnonymizedFrom, |
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426 changeType, resourceType, call); |
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427 } |
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428 } |
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429 |
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430 |
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431 static void CreateDicom(RestApiPostCall& call) |
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432 { |
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433 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World"}' |
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434 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World","PixelData":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAABAAAAAQCAAAAAA6mKC9AAAACXBIWXMAAAsTAAALEwEAmpwYAAAAB3RJTUUH3gUGDDcB53FulQAAAElJREFUGNNtj0sSAEEEQ1+U+185s1CtmRkblQ9CZldsKHJDk6DLGLJa6chjh0ooQmpjXMM86zPwydGEj6Ed/UGykkEM8X+p3u8/8LcOJIWLGeMAAAAASUVORK5CYII="}' |
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435 |
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436 Json::Value replacements; |
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437 if (call.ParseJsonRequest(replacements) && replacements.isObject()) |
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438 { |
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439 ParsedDicomFile dicom; |
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440 |
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441 Json::Value::Members members = replacements.getMemberNames(); |
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442 for (size_t i = 0; i < members.size(); i++) |
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443 { |
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444 const std::string& name = members[i]; |
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445 std::string value = replacements[name].asString(); |
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446 |
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447 DicomTag tag = FromDcmtkBridge::ParseTag(name); |
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448 if (tag == DICOM_TAG_PIXEL_DATA) |
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449 { |
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450 dicom.EmbedImage(value); |
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451 } |
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452 else |
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453 { |
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454 dicom.Replace(tag, value); |
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|
455 } |
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diff
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|
456 } |
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diff
changeset
|
457 |
1005
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refactoring of ServerContext::Store
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diff
changeset
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458 DicomInstanceToStore toStore; |
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459 toStore.SetParsedDicomFile(dicom); |
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diff
changeset
|
460 |
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461 std::string id; |
1005
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diff
changeset
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462 StoreStatus status = OrthancRestApi::GetContext(call).Store(id, toStore); |
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|
463 |
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464 if (status == StoreStatus_Failure) |
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465 { |
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466 LOG(ERROR) << "Error while storing a manually-created instance"; |
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467 return; |
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468 } |
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changeset
|
469 |
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changeset
|
470 OrthancRestApi::GetApi(call).AnswerStoredInstance(call, id, status); |
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471 } |
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diff
changeset
|
472 } |
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diff
changeset
|
473 |
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diff
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|
474 |
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|
475 void OrthancRestApi::RegisterAnonymizeModify() |
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|
476 { |
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|
477 Register("/instances/{id}/modify", ModifyInstance); |
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478 Register("/series/{id}/modify", ModifyResource<ChangeType_ModifiedSeries, ResourceType_Series>); |
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diff
changeset
|
479 Register("/studies/{id}/modify", ModifyResource<ChangeType_ModifiedStudy, ResourceType_Study>); |
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changeset
|
480 Register("/patients/{id}/modify", ModifyResource<ChangeType_ModifiedPatient, ResourceType_Patient>); |
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diff
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|
481 |
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diff
changeset
|
482 Register("/instances/{id}/anonymize", AnonymizeInstance); |
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diff
changeset
|
483 Register("/series/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedSeries, ResourceType_Series>); |
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diff
changeset
|
484 Register("/studies/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedStudy, ResourceType_Study>); |
ac18946afa74
refactoring of anonymization/modification
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diff
changeset
|
485 Register("/patients/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedPatient, ResourceType_Patient>); |
796
e7b1ca0f1e04
creation of dicom files
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parents:
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diff
changeset
|
486 |
1120
009dce4ea2f6
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Sebastien Jodogne <s.jodogne@gmail.com>
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1010
diff
changeset
|
487 Register("/tools/create-dicom", CreateDicom); |
751
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refactoring of OrthancRestApi
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diff
changeset
|
488 } |
5197fd35333c
refactoring of OrthancRestApi
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diff
changeset
|
489 } |