Mercurial > hg > orthanc

annotate OrthancServer/OrthancRestApi/OrthancRestAnonymizeModify.cpp @ 796:e7b1ca0f1e04

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creation of dicom files
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 06 May 2014 12:09:11 +0200
parents d466b3606aca
children ecedd89055db
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2014 Medical Physics Department, CHU of Liege,
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4 * 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 "OrthancRestApi.h"
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34
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35 #include "../DicomModification.h"
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36 #include "../FromDcmtkBridge.h"
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37
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38 #include <glog/logging.h>
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39
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40 namespace Orthanc
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41 {
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42 // Modification of DICOM instances ------------------------------------------
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43
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44 enum TagOperation
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45 {
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46 TagOperation_Keep,
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47 TagOperation_Remove
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48 };
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49
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50 static void ParseListOfTags(DicomModification& target,
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51 const Json::Value& query,
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52 TagOperation operation)
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53 {
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54 if (!query.isArray())
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55 {
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56 throw OrthancException(ErrorCode_BadRequest);
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57 }
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58
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59 for (Json::Value::ArrayIndex i = 0; i < query.size(); i++)
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60 {
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61 std::string name = query[i].asString();
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62
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63 DicomTag tag = FromDcmtkBridge::ParseTag(name);
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64
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65 switch (operation)
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66 {
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67 case TagOperation_Keep:
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68 target.Keep(tag);
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69 VLOG(1) << "Keep: " << name << " " << tag << std::endl;
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70 break;
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71
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72 case TagOperation_Remove:
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73 target.Remove(tag);
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74 VLOG(1) << "Remove: " << name << " " << tag << std::endl;
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75 break;
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76
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77 default:
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78 throw OrthancException(ErrorCode_InternalError);
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79 }
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80 }
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81 }
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82
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83
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84 static void ParseReplacements(DicomModification& target,
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85 const Json::Value& replacements)
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86 {
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87 if (!replacements.isObject())
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88 {
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89 throw OrthancException(ErrorCode_BadRequest);
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90 }
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91
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92 Json::Value::Members members = replacements.getMemberNames();
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93 for (size_t i = 0; i < members.size(); i++)
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94 {
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95 const std::string& name = members[i];
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96 std::string value = replacements[name].asString();
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97
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98 DicomTag tag = FromDcmtkBridge::ParseTag(name);
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99 if (tag != DICOM_TAG_PIXEL_DATA)
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100 {
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101 target.Replace(tag, value);
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102 }
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103
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104 VLOG(1) << "Replace: " << name << " " << tag << " == " << value << std::endl;
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105 }
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106 }
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107
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108
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109 static std::string GeneratePatientName(ServerContext& context)
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110 {
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111 uint64_t seq = context.GetIndex().IncrementGlobalSequence(GlobalProperty_AnonymizationSequence);
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112 return "Anonymized" + boost::lexical_cast<std::string>(seq);
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113 }
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114
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115
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116 static bool ParseModifyRequest(DicomModification& target,
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117 const RestApi::PostCall& call)
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118 {
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119 // curl http://localhost:8042/series/95a6e2bf-9296e2cc-bf614e2f-22b391ee-16e010e0/modify -X POST -d '{"Replace":{"InstitutionName":"My own clinic"}}'
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120
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121 Json::Value request;
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122 if (call.ParseJsonRequest(request) && request.isObject())
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123 {
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124 if (request.isMember("RemovePrivateTags"))
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125 {
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126 target.SetRemovePrivateTags(true);
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127 }
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128
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129 if (request.isMember("Remove"))
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130 {
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131 ParseListOfTags(target, request["Remove"], TagOperation_Remove);
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132 }
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133
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134 if (request.isMember("Replace"))
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135 {
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136 ParseReplacements(target, request["Replace"]);
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137 }
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138
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139 return true;
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140 }
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141 else
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142 {
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143 return false;
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144 }
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145 }
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146
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147
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148 static bool ParseAnonymizationRequest(DicomModification& target,
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149 RestApi::PostCall& call)
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150 {
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151 // 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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152
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153 target.SetupAnonymization();
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154 std::string patientName = target.GetReplacement(DICOM_TAG_PATIENT_NAME);
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155
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156 Json::Value request;
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157 if (call.ParseJsonRequest(request) && request.isObject())
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158 {
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159 if (request.isMember("KeepPrivateTags"))
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160 {
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161 target.SetRemovePrivateTags(false);
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162 }
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163
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164 if (request.isMember("Remove"))
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165 {
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166 ParseListOfTags(target, request["Remove"], TagOperation_Remove);
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167 }
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168
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169 if (request.isMember("Replace"))
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170 {
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171 ParseReplacements(target, request["Replace"]);
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172 }
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173
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174 if (request.isMember("Keep"))
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175 {
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176 ParseListOfTags(target, request["Keep"], TagOperation_Keep);
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177 }
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178
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179 if (target.GetReplacement(DICOM_TAG_PATIENT_NAME) == patientName)
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180 {
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181 // Overwrite the random Patient's Name by one that is more
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182 // user-friendly (provided none was specified by the user)
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183 target.Replace(DICOM_TAG_PATIENT_NAME, GeneratePatientName(OrthancRestApi::GetContext(call)));
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184 }
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185
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186 return true;
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187 }
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188 else
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189 {
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190 return false;
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191 }
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192 }
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193
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194
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195 static void AnonymizeOrModifyInstance(DicomModification& modification,
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196 RestApi::PostCall& call)
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197 {
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198 std::string id = call.GetUriComponent("id", "");
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199
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200 ServerContext::DicomCacheLocker locker(OrthancRestApi::GetContext(call), id);
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201
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202 std::auto_ptr<ParsedDicomFile> modified(locker.GetDicom().Clone());
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203 modification.Apply(*modified);
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204 modified->Answer(call.GetOutput());
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205 }
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206
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207
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208 static void AnonymizeOrModifyResource(DicomModification& modification,
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209 MetadataType metadataType,
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210 ChangeType changeType,
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211 ResourceType resourceType,
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212 RestApi::PostCall& call)
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213 {
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214 bool isFirst = true;
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215 Json::Value result(Json::objectValue);
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216
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217 ServerContext& context = OrthancRestApi::GetContext(call);
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218
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diff changeset
219 typedef std::list<std::string> Instances;
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220 Instances instances;
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221 std::string id = call.GetUriComponent("id", "");
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222 context.GetIndex().GetChildInstances(instances, id);
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223
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diff changeset
224 if (instances.empty())
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diff changeset
225 {
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226 return;
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227 }
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228
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229
751
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230 /**
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231 * Loop over all the instances of the resource.
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232 **/
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diff changeset
233
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234 for (Instances::const_iterator it = instances.begin();
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235 it != instances.end(); ++it)
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diff changeset
236 {
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diff changeset
237 LOG(INFO) << "Modifying instance " << *it;
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238
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diff changeset
239 std::auto_ptr<ServerContext::DicomCacheLocker> locker;
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240
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diff changeset
241 try
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diff changeset
242 {
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diff changeset
243 locker.reset(new ServerContext::DicomCacheLocker(OrthancRestApi::GetContext(call), *it));
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244 }
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diff changeset
245 catch (OrthancException&)
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246 {
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247 // This child instance has been removed in between
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diff changeset
248 continue;
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249 }
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diff changeset
250
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diff changeset
251 ParsedDicomFile& original = locker->GetDicom();
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252 DicomInstanceHasher originalHasher = original.GetHasher();
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253
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diff changeset
254
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255 /**
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256 * Compute the resulting DICOM instance and store it into the Orthanc store.
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diff changeset
257 **/
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diff changeset
258
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259 std::auto_ptr<ParsedDicomFile> modified(original.Clone());
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diff changeset
260 modification.Apply(*modified);
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261
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diff changeset
262 std::string modifiedInstance;
791
381f90e2b69d refactoring
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diff changeset
263 if (context.Store(modifiedInstance, *modified) != StoreStatus_Success)
751
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diff changeset
264 {
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diff changeset
265 LOG(ERROR) << "Error while storing a modified instance " << *it;
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266 return;
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diff changeset
267 }
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268
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diff changeset
269
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diff changeset
270 /**
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271 * Record metadata information (AnonymizedFrom/ModifiedFrom).
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diff changeset
272 **/
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diff changeset
273
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diff changeset
274 DicomInstanceHasher modifiedHasher = modified->GetHasher();
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diff changeset
275
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276 if (originalHasher.HashSeries() != modifiedHasher.HashSeries())
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277 {
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278 context.GetIndex().SetMetadata(modifiedHasher.HashSeries(),
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279 metadataType, originalHasher.HashSeries());
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280 }
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281
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282 if (originalHasher.HashStudy() != modifiedHasher.HashStudy())
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283 {
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284 context.GetIndex().SetMetadata(modifiedHasher.HashStudy(),
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285 metadataType, originalHasher.HashStudy());
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286 }
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287
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288 if (originalHasher.HashPatient() != modifiedHasher.HashPatient())
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289 {
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290 context.GetIndex().SetMetadata(modifiedHasher.HashPatient(),
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291 metadataType, originalHasher.HashPatient());
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292 }
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293
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294 assert(*it == originalHasher.HashInstance());
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295 assert(modifiedInstance == modifiedHasher.HashInstance());
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296 context.GetIndex().SetMetadata(modifiedInstance, metadataType, *it);
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297
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298
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299 /**
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300 * Compute the JSON object that is returned by the REST call.
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301 **/
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302
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303 if (isFirst)
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304 {
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305 std::string newId;
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306
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307 switch (resourceType)
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308 {
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309 case ResourceType_Series:
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310 newId = modifiedHasher.HashSeries();
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311 break;
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312
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313 case ResourceType_Study:
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314 newId = modifiedHasher.HashStudy();
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315 break;
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316
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317 case ResourceType_Patient:
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318 newId = modifiedHasher.HashPatient();
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319 break;
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320
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321 default:
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322 throw OrthancException(ErrorCode_InternalError);
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323 }
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324
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325 result["Type"] = EnumerationToString(resourceType);
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326 result["ID"] = newId;
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327 result["Path"] = GetBasePath(resourceType, newId);
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328 result["PatientID"] = modifiedHasher.HashPatient();
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329 isFirst = false;
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330 }
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331 }
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332
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333 call.GetOutput().AnswerJson(result);
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334 }
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335
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336
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337
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338 static void ModifyInstance(RestApi::PostCall& call)
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339 {
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340 DicomModification modification;
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341
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342 if (ParseModifyRequest(modification, call))
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343 {
796
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344 if (modification.IsReplaced(DICOM_TAG_PATIENT_ID))
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345 {
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346 modification.SetLevel(ResourceType_Patient);
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347 }
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348 else if (modification.IsReplaced(DICOM_TAG_STUDY_INSTANCE_UID))
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349 {
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350 modification.SetLevel(ResourceType_Study);
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351 }
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352 else if (modification.IsReplaced(DICOM_TAG_SERIES_INSTANCE_UID))
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353 {
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354 modification.SetLevel(ResourceType_Series);
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355 }
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356 else
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357 {
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358 modification.SetLevel(ResourceType_Instance);
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359 }
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diff changeset
360
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361 AnonymizeOrModifyInstance(modification, call);
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362 }
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diff changeset
363 }
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parents:
diff changeset
364
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parents:
diff changeset
365
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diff changeset
366 static void AnonymizeInstance(RestApi::PostCall& call)
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diff changeset
367 {
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diff changeset
368 DicomModification modification;
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diff changeset
369
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diff changeset
370 if (ParseAnonymizationRequest(modification, call))
751
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diff changeset
371 {
787
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diff changeset
372 AnonymizeOrModifyInstance(modification, call);
751
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diff changeset
373 }
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parents:
diff changeset
374 }
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diff changeset
375
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diff changeset
376
787
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diff changeset
377 template <enum ChangeType changeType,
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diff changeset
378 enum ResourceType resourceType>
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diff changeset
379 static void ModifyResource(RestApi::PostCall& call)
751
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diff changeset
380 {
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diff changeset
381 DicomModification modification;
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diff changeset
382
787
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diff changeset
383 if (ParseModifyRequest(modification, call))
751
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diff changeset
384 {
796
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diff changeset
385 modification.SetLevel(resourceType);
787
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diff changeset
386 AnonymizeOrModifyResource(modification, MetadataType_ModifiedFrom,
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
387 changeType, resourceType, call);
751
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diff changeset
388 }
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parents:
diff changeset
389 }
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parents:
diff changeset
390
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
391
787
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diff changeset
392 template <enum ChangeType changeType,
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diff changeset
393 enum ResourceType resourceType>
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diff changeset
394 static void AnonymizeResource(RestApi::PostCall& call)
751
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diff changeset
395 {
787
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diff changeset
396 DicomModification modification;
751
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parents:
diff changeset
397
787
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diff changeset
398 if (ParseAnonymizationRequest(modification, call))
751
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
399 {
787
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diff changeset
400 AnonymizeOrModifyResource(modification, MetadataType_AnonymizedFrom,
ac18946afa74 refactoring of anonymization/modification
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parents: 782
diff changeset
401 changeType, resourceType, call);
751
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parents:
diff changeset
402 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
403 }
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
404
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
405
796
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
406 static void Create(RestApi::PostCall& call)
e7b1ca0f1e04 creation of dicom files
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diff changeset
407 {
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parents: 795
diff changeset
408 // curl http://localhost:8042/tools/create-dicom -X POST -d '{"PatientName":"Hello^World"}'
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diff changeset
409
e7b1ca0f1e04 creation of dicom files
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diff changeset
410 Json::Value request;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
diff changeset
411 if (call.ParseJsonRequest(request) && request.isObject())
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diff changeset
412 {
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diff changeset
413 DicomModification modification;
e7b1ca0f1e04 creation of dicom files
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
414 ParseReplacements(modification, request);
e7b1ca0f1e04 creation of dicom files
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diff changeset
415
e7b1ca0f1e04 creation of dicom files
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diff changeset
416 ParsedDicomFile dicom;
e7b1ca0f1e04 creation of dicom files
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parents: 795
diff changeset
417 modification.Apply(dicom);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
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418
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419 std::string id;
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parents: 795
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420 StoreStatus status = OrthancRestApi::GetContext(call).Store(id, dicom);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
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421
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parents: 795
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422 if (status == StoreStatus_Failure)
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423 {
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424 LOG(ERROR) << "Error while storing a manually-created instance";
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
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425 return;
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parents: 795
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426 }
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parents: 795
diff changeset
427
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
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428 OrthancRestApi::GetApi(call).AnswerStoredInstance(call, id, status);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 795
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429 }
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parents: 795
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430 }
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parents: 795
diff changeset
431
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parents: 795
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432
751
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433 void OrthancRestApi::RegisterAnonymizeModify()
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
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434 {
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435 Register("/instances/{id}/modify", ModifyInstance);
787
ac18946afa74 refactoring of anonymization/modification
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diff changeset
436 Register("/series/{id}/modify", ModifyResource<ChangeType_ModifiedSeries, ResourceType_Series>);
ac18946afa74 refactoring of anonymization/modification
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parents: 782
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437 Register("/studies/{id}/modify", ModifyResource<ChangeType_ModifiedStudy, ResourceType_Study>);
796
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parents: 795
diff changeset
438 Register("/patients/{id}/modify", ModifyResource<ChangeType_ModifiedPatient, ResourceType_Patient>);
751
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parents:
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439
5197fd35333c refactoring of OrthancRestApi
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440 Register("/instances/{id}/anonymize", AnonymizeInstance);
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parents: 782
diff changeset
441 Register("/series/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedSeries, ResourceType_Series>);
ac18946afa74 refactoring of anonymization/modification
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
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442 Register("/studies/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedStudy, ResourceType_Study>);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 782
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443 Register("/patients/{id}/anonymize", AnonymizeResource<ChangeType_ModifiedPatient, ResourceType_Patient>);
796
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parents: 795
diff changeset
444
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parents: 795
diff changeset
445 Register("/tools/create-dicom", Create);
751
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parents:
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446 }
5197fd35333c refactoring of OrthancRestApi
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diff changeset
447 }