Mercurial > hg > orthanc
annotate OrthancServer/ServerToolbox.cpp @ 1737:ec66a16aa398
removal of DicomStringValue and DicomNullValue
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 22 Oct 2015 07:52:24 +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 "ServerToolbox.h" |
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35 |
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36 #include "../Core/DicomFormat/DicomArray.h" |
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37 #include "../Core/FileStorage/StorageAccessor.h" |
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38 #include "../Core/Logging.h" |
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39 #include "../Core/OrthancException.h" |
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40 #include "ParsedDicomFile.h" |
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41 |
234 | 42 #include <cassert> |
43 | |
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44 namespace Orthanc |
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45 { |
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46 namespace Toolbox |
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47 { |
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48 void SimplifyTags(Json::Value& target, |
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49 const Json::Value& source) |
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50 { |
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51 assert(source.isObject()); |
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52 |
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53 target = Json::objectValue; |
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54 Json::Value::Members members = source.getMemberNames(); |
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55 |
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56 for (size_t i = 0; i < members.size(); i++) |
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57 { |
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58 const Json::Value& v = source[members[i]]; |
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59 const std::string& name = v["Name"].asString(); |
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60 const std::string& type = v["Type"].asString(); |
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61 |
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62 if (type == "String") |
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63 { |
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64 target[name] = v["Value"].asString(); |
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65 } |
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66 else if (type == "TooLong" || |
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67 type == "Null") |
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68 { |
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69 target[name] = Json::nullValue; |
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70 } |
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71 else if (type == "Sequence") |
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72 { |
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73 const Json::Value& array = v["Value"]; |
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74 assert(array.isArray()); |
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75 |
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76 Json::Value children = Json::arrayValue; |
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77 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++) |
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78 { |
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79 Json::Value c; |
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80 SimplifyTags(c, array[i]); |
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81 children.append(c); |
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82 } |
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83 |
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84 target[name] = children; |
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85 } |
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86 else |
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87 { |
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88 assert(0); |
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89 } |
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90 } |
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91 } |
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92 |
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93 |
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94 static std::string ValueAsString(const DicomMap& summary, |
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95 const DicomTag& tag) |
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96 { |
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97 const DicomValue& value = summary.GetValue(tag); |
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98 if (value.IsNull()) |
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99 { |
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100 return "(null)"; |
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101 } |
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102 else |
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103 { |
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104 return value.GetContent(); |
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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 void LogMissingRequiredTag(const DicomMap& summary) |
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110 { |
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111 std::string s, t; |
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112 |
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113 if (summary.HasTag(DICOM_TAG_PATIENT_ID)) |
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114 { |
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115 if (t.size() > 0) |
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116 t += ", "; |
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117 t += "PatientID=" + ValueAsString(summary, DICOM_TAG_PATIENT_ID); |
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118 } |
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119 else |
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120 { |
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121 if (s.size() > 0) |
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122 s += ", "; |
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123 s += "PatientID"; |
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124 } |
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125 |
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126 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID)) |
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127 { |
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128 if (t.size() > 0) |
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129 t += ", "; |
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130 t += "StudyInstanceUID=" + ValueAsString(summary, DICOM_TAG_STUDY_INSTANCE_UID); |
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131 } |
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132 else |
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133 { |
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134 if (s.size() > 0) |
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135 s += ", "; |
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136 s += "StudyInstanceUID"; |
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137 } |
213
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138 |
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139 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID)) |
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140 { |
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141 if (t.size() > 0) |
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142 t += ", "; |
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143 t += "SeriesInstanceUID=" + ValueAsString(summary, DICOM_TAG_SERIES_INSTANCE_UID); |
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144 } |
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145 else |
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146 { |
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147 if (s.size() > 0) |
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148 s += ", "; |
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149 s += "SeriesInstanceUID"; |
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150 } |
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151 |
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152 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID)) |
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153 { |
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154 if (t.size() > 0) |
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155 t += ", "; |
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156 t += "SOPInstanceUID=" + ValueAsString(summary, DICOM_TAG_SOP_INSTANCE_UID); |
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157 } |
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158 else |
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159 { |
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160 if (s.size() > 0) |
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161 s += ", "; |
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162 s += "SOPInstanceUID"; |
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163 } |
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164 |
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165 if (t.size() == 0) |
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166 { |
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167 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)"; |
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168 } |
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169 else |
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170 { |
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171 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t; |
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172 } |
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173 } |
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174 |
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175 |
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176 static void SetMainDicomTagsInternal(IDatabaseWrapper& database, |
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177 int64_t resource, |
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178 const DicomMap& tags) |
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179 { |
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180 DicomArray flattened(tags); |
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181 |
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182 for (size_t i = 0; i < flattened.GetSize(); i++) |
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183 { |
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184 const DicomElement& element = flattened.GetElement(i); |
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185 const DicomTag& tag = element.GetTag(); |
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186 const DicomValue& value = element.GetValue(); |
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187 if (!value.IsNull() && |
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188 !value.IsBinary()) |
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189 { |
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190 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent()); |
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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 |
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196 static void SetIdentifierTagInternal(IDatabaseWrapper& database, |
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197 int64_t resource, |
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198 const DicomMap& tags, |
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199 const DicomTag& tag) |
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200 { |
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201 const DicomValue* value = tags.TestAndGetValue(tag); |
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202 if (value != NULL && |
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203 !value->IsNull() && |
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204 !value->IsBinary()) |
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205 { |
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206 std::string s = value->GetContent(); |
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207 |
1725 | 208 if (tag != DICOM_TAG_PATIENT_ID && |
209 tag != DICOM_TAG_STUDY_INSTANCE_UID && | |
210 tag != DICOM_TAG_SERIES_INSTANCE_UID && | |
211 tag != DICOM_TAG_SOP_INSTANCE_UID && | |
212 tag != DICOM_TAG_ACCESSION_NUMBER) | |
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213 { |
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214 s = NormalizeIdentifierTag(s); |
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215 } |
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216 |
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217 database.SetIdentifierTag(resource, tag, s); |
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218 } |
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219 } |
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220 |
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221 |
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222 static void AttachPatientInformation(IDatabaseWrapper& database, |
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223 int64_t resource, |
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224 const DicomMap& dicomSummary) |
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225 { |
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226 DicomMap tags; |
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227 dicomSummary.ExtractPatientInformation(tags); |
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228 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_PATIENT_ID); |
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229 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_PATIENT_NAME); |
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230 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_PATIENT_BIRTH_DATE); |
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231 SetMainDicomTagsInternal(database, resource, tags); |
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232 } |
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233 |
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234 |
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235 void SetMainDicomTags(IDatabaseWrapper& database, |
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236 int64_t resource, |
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237 ResourceType level, |
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238 const DicomMap& dicomSummary) |
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239 { |
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240 // WARNING: The database should be locked with a transaction! |
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241 |
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242 DicomMap tags; |
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243 |
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244 switch (level) |
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245 { |
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246 case ResourceType_Patient: |
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247 AttachPatientInformation(database, resource, dicomSummary); |
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248 break; |
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249 |
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250 case ResourceType_Study: |
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251 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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252 AttachPatientInformation(database, resource, dicomSummary); |
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253 |
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254 dicomSummary.ExtractStudyInformation(tags); |
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255 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_STUDY_INSTANCE_UID); |
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256 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_ACCESSION_NUMBER); |
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257 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_STUDY_DESCRIPTION); |
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258 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_STUDY_DATE); |
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259 break; |
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260 |
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261 case ResourceType_Series: |
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262 dicomSummary.ExtractSeriesInformation(tags); |
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263 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_SERIES_INSTANCE_UID); |
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264 break; |
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265 |
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266 case ResourceType_Instance: |
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267 dicomSummary.ExtractInstanceInformation(tags); |
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268 SetIdentifierTagInternal(database, resource, tags, DICOM_TAG_SOP_INSTANCE_UID); |
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269 break; |
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270 |
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271 default: |
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272 throw OrthancException(ErrorCode_InternalError); |
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273 } |
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274 |
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275 SetMainDicomTagsInternal(database, resource, tags); |
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276 } |
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277 |
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278 |
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279 bool FindOneChildInstance(int64_t& result, |
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280 IDatabaseWrapper& database, |
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281 int64_t resource, |
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282 ResourceType type) |
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283 { |
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284 for (;;) |
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285 { |
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286 if (type == ResourceType_Instance) |
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287 { |
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288 result = resource; |
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289 return true; |
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290 } |
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291 |
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292 std::list<int64_t> children; |
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293 database.GetChildrenInternalId(children, resource); |
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294 if (children.empty()) |
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295 { |
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296 return false; |
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297 } |
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298 |
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299 resource = children.front(); |
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300 type = GetChildResourceType(type); |
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301 } |
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302 } |
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303 |
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304 |
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305 void ReconstructMainDicomTags(IDatabaseWrapper& database, |
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306 IStorageArea& storageArea, |
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307 ResourceType level) |
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308 { |
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309 // WARNING: The database should be locked with a transaction! |
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310 |
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311 const char* plural = NULL; |
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312 |
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313 switch (level) |
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314 { |
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315 case ResourceType_Patient: |
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316 plural = "patients"; |
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317 break; |
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318 |
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319 case ResourceType_Study: |
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320 plural = "studies"; |
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321 break; |
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322 |
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323 case ResourceType_Series: |
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324 plural = "series"; |
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325 break; |
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326 |
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327 case ResourceType_Instance: |
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328 plural = "instances"; |
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329 break; |
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330 |
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331 default: |
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332 throw OrthancException(ErrorCode_InternalError); |
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333 } |
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334 |
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335 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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336 |
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337 std::list<std::string> resources; |
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338 database.GetAllPublicIds(resources, level); |
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339 |
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340 for (std::list<std::string>::const_iterator |
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341 it = resources.begin(); it != resources.end(); it++) |
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342 { |
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343 // Locate the resource and one of its child instances |
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344 int64_t resource, instance; |
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345 ResourceType tmp; |
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346 |
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347 if (!database.LookupResource(resource, tmp, *it) || |
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348 tmp != level || |
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349 !FindOneChildInstance(instance, database, resource, level)) |
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350 { |
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351 throw OrthancException(ErrorCode_InternalError); |
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352 } |
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353 |
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354 // Get the DICOM file attached to some instances in the resource |
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355 FileInfo attachment; |
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356 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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357 { |
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358 throw OrthancException(ErrorCode_InternalError); |
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359 } |
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360 |
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361 // Read and parse the content of the DICOM file |
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362 StorageAccessor accessor(storageArea); |
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363 |
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364 std::string content; |
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365 accessor.Read(content, attachment); |
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366 |
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367 ParsedDicomFile dicom(content); |
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368 |
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369 // Update the tags of this resource |
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370 DicomMap dicomSummary; |
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371 dicom.Convert(dicomSummary); |
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372 |
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373 database.ClearMainDicomTags(resource); |
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374 Toolbox::SetMainDicomTags(database, resource, level, dicomSummary); |
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375 } |
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376 } |
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377 |
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378 |
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379 std::string NormalizeIdentifierTag(const std::string& value) |
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380 { |
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381 std::string s = Toolbox::ConvertToAscii(Toolbox::StripSpaces(value)); |
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382 Toolbox::ToUpperCase(s); |
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383 return s; |
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384 } |
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385 } |
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386 } |