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annotate OrthancServer/ServerToolbox.cpp @ 1745:38dda23c7d7d db-changes

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LookupIdentifierQuery
author Sebastien Jodogne <s.jodogne@gmail.com>
date Mon, 26 Oct 2015 13:47:50 +0100
parents b3de74dec2d5
children ca69082ab200
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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 #include "LookupIdentifierQuery.h"
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42
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43 #include <cassert>
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44
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45 namespace Orthanc
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46 {
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47 namespace Toolbox
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48 {
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49 void SimplifyTags(Json::Value& target,
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50 const Json::Value& source)
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51 {
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52 assert(source.isObject());
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53
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54 target = Json::objectValue;
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55 Json::Value::Members members = source.getMemberNames();
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56
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57 for (size_t i = 0; i < members.size(); i++)
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58 {
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59 const Json::Value& v = source[members[i]];
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60 const std::string& name = v["Name"].asString();
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61 const std::string& type = v["Type"].asString();
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62
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63 if (type == "String")
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64 {
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65 target[name] = v["Value"].asString();
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66 }
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67 else if (type == "TooLong" ||
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68 type == "Null")
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69 {
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70 target[name] = Json::nullValue;
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71 }
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72 else if (type == "Sequence")
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73 {
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74 const Json::Value& array = v["Value"];
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75 assert(array.isArray());
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76
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77 Json::Value children = Json::arrayValue;
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78 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++)
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79 {
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80 Json::Value c;
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81 SimplifyTags(c, array[i]);
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82 children.append(c);
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83 }
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84
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85 target[name] = children;
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86 }
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87 else
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88 {
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89 assert(0);
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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
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95 static std::string ValueAsString(const DicomMap& summary,
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96 const DicomTag& tag)
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97 {
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98 const DicomValue& value = summary.GetValue(tag);
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99 if (value.IsNull())
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100 {
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101 return "(null)";
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102 }
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103 else
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104 {
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105 return value.GetContent();
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106 }
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107 }
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108
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109
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110 void LogMissingRequiredTag(const DicomMap& summary)
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111 {
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112 std::string s, t;
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113
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114 if (summary.HasTag(DICOM_TAG_PATIENT_ID))
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115 {
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116 if (t.size() > 0)
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117 t += ", ";
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118 t += "PatientID=" + ValueAsString(summary, DICOM_TAG_PATIENT_ID);
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119 }
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120 else
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121 {
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122 if (s.size() > 0)
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123 s += ", ";
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124 s += "PatientID";
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125 }
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126
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127 if (summary.HasTag(DICOM_TAG_STUDY_INSTANCE_UID))
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128 {
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129 if (t.size() > 0)
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130 t += ", ";
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131 t += "StudyInstanceUID=" + ValueAsString(summary, DICOM_TAG_STUDY_INSTANCE_UID);
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132 }
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133 else
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134 {
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135 if (s.size() > 0)
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136 s += ", ";
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137 s += "StudyInstanceUID";
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138 }
213
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139
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140 if (summary.HasTag(DICOM_TAG_SERIES_INSTANCE_UID))
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141 {
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142 if (t.size() > 0)
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143 t += ", ";
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144 t += "SeriesInstanceUID=" + ValueAsString(summary, DICOM_TAG_SERIES_INSTANCE_UID);
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145 }
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146 else
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147 {
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148 if (s.size() > 0)
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149 s += ", ";
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150 s += "SeriesInstanceUID";
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151 }
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152
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153 if (summary.HasTag(DICOM_TAG_SOP_INSTANCE_UID))
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154 {
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155 if (t.size() > 0)
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156 t += ", ";
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157 t += "SOPInstanceUID=" + ValueAsString(summary, DICOM_TAG_SOP_INSTANCE_UID);
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158 }
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159 else
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160 {
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161 if (s.size() > 0)
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162 s += ", ";
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163 s += "SOPInstanceUID";
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164 }
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165
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166 if (t.size() == 0)
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167 {
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168 LOG(ERROR) << "Store has failed because all the required tags (" << s << ") are missing (is it a DICOMDIR file?)";
213
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169 }
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170 else
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171 {
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172 LOG(ERROR) << "Store has failed because required tags (" << s << ") are missing for the following instance: " << t;
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173 }
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174 }
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175
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176
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177 static void SetMainDicomTagsInternal(IDatabaseWrapper& database,
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178 int64_t resource,
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179 const DicomMap& tags)
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180 {
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181 DicomArray flattened(tags);
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182
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183 for (size_t i = 0; i < flattened.GetSize(); i++)
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184 {
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185 const DicomElement& element = flattened.GetElement(i);
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186 const DicomTag& tag = element.GetTag();
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187 const DicomValue& value = element.GetValue();
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188 if (!value.IsNull() &&
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189 !value.IsBinary())
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190 {
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191 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent());
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192 }
1716
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193 }
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194 }
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195
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196
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197 void SetMainDicomTags(IDatabaseWrapper& database,
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198 int64_t resource,
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199 ResourceType level,
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200 const DicomMap& dicomSummary)
1668
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201 {
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202 // WARNING: The database should be locked with a transaction!
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203
1745
38dda23c7d7d LookupIdentifierQuery
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204 LookupIdentifierQuery::StoreIdentifiers(database, resource, level, dicomSummary);
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205
1668
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206 DicomMap tags;
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207
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208 switch (level)
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209 {
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210 case ResourceType_Patient:
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38dda23c7d7d LookupIdentifierQuery
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211 dicomSummary.ExtractPatientInformation(tags);
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212 break;
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213
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214 case ResourceType_Study:
1717
3926e6317a43 SetIdentifierTagInternal
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215 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
1745
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216 dicomSummary.ExtractPatientInformation(tags);
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217 SetMainDicomTagsInternal(database, resource, tags);
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diff changeset
218
1668
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219 dicomSummary.ExtractStudyInformation(tags);
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220 break;
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221
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222 case ResourceType_Series:
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223 dicomSummary.ExtractSeriesInformation(tags);
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224 break;
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225
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226 case ResourceType_Instance:
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227 dicomSummary.ExtractInstanceInformation(tags);
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228 break;
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229
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diff changeset
230 default:
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231 throw OrthancException(ErrorCode_InternalError);
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232 }
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233
1716
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diff changeset
234 SetMainDicomTagsInternal(database, resource, tags);
1668
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diff changeset
235 }
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diff changeset
236
de1413733c97 reconstructing main dicom tags
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diff changeset
237
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diff changeset
238 bool FindOneChildInstance(int64_t& result,
de1413733c97 reconstructing main dicom tags
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diff changeset
239 IDatabaseWrapper& database,
de1413733c97 reconstructing main dicom tags
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diff changeset
240 int64_t resource,
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diff changeset
241 ResourceType type)
de1413733c97 reconstructing main dicom tags
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242 {
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diff changeset
243 for (;;)
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244 {
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diff changeset
245 if (type == ResourceType_Instance)
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246 {
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diff changeset
247 result = resource;
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248 return true;
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249 }
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250
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251 std::list<int64_t> children;
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diff changeset
252 database.GetChildrenInternalId(children, resource);
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253 if (children.empty())
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254 {
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255 return false;
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diff changeset
256 }
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diff changeset
257
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diff changeset
258 resource = children.front();
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259 type = GetChildResourceType(type);
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260 }
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261 }
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diff changeset
262
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263
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diff changeset
264 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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diff changeset
265 IStorageArea& storageArea,
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266 ResourceType level)
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267 {
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diff changeset
268 // WARNING: The database should be locked with a transaction!
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diff changeset
269
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diff changeset
270 const char* plural = NULL;
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diff changeset
271
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diff changeset
272 switch (level)
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diff changeset
273 {
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274 case ResourceType_Patient:
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275 plural = "patients";
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276 break;
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277
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278 case ResourceType_Study:
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279 plural = "studies";
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280 break;
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281
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282 case ResourceType_Series:
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283 plural = "series";
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284 break;
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285
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286 case ResourceType_Instance:
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287 plural = "instances";
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288 break;
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289
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290 default:
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291 throw OrthancException(ErrorCode_InternalError);
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292 }
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293
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294 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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295
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296 std::list<std::string> resources;
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297 database.GetAllPublicIds(resources, level);
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298
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299 for (std::list<std::string>::const_iterator
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300 it = resources.begin(); it != resources.end(); it++)
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301 {
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302 // Locate the resource and one of its child instances
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303 int64_t resource, instance;
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304 ResourceType tmp;
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305
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306 if (!database.LookupResource(resource, tmp, *it) ||
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307 tmp != level ||
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308 !FindOneChildInstance(instance, database, resource, level))
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309 {
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310 throw OrthancException(ErrorCode_InternalError);
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311 }
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312
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313 // Get the DICOM file attached to some instances in the resource
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314 FileInfo attachment;
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315 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
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316 {
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317 throw OrthancException(ErrorCode_InternalError);
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318 }
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319
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320 // Read and parse the content of the DICOM file
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321 StorageAccessor accessor(storageArea);
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322
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323 std::string content;
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324 accessor.Read(content, attachment);
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325
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326 ParsedDicomFile dicom(content);
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327
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328 // Update the tags of this resource
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329 DicomMap dicomSummary;
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330 dicom.Convert(dicomSummary);
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331
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332 database.ClearMainDicomTags(resource);
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333 Toolbox::SetMainDicomTags(database, resource, level, dicomSummary);
213
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334 }
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335 }
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336 }
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337 }