Mercurial > hg > orthanc
annotate OrthancServer/ServerToolbox.cpp @ 3089:fb8ee0786b1e db-changes
new extension for database plugin SDK: setResourcesContent
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Sat, 05 Jan 2019 11:39:31 +0100 |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
1900 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
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5 * Copyright (C) 2017-2019 Osimis S.A., Belgium |
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6 * |
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7 * This program is free software: you can redistribute it and/or |
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8 * modify it under the terms of the GNU General Public License as |
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9 * published by the Free Software Foundation, either version 3 of the |
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10 * License, or (at your option) any later version. |
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11 * |
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12 * In addition, as a special exception, the copyright holders of this |
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13 * program give permission to link the code of its release with the |
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it |
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15 * that use the same license as the "OpenSSL" library), and distribute |
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16 * the linked executables. You must obey the GNU General Public License |
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17 * in all respects for all of the code used other than "OpenSSL". If you |
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18 * modify file(s) with this exception, you may extend this exception to |
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19 * your version of the file(s), but you are not obligated to do so. If |
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20 * you do not wish to do so, delete this exception statement from your |
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21 * version. If you delete this exception statement from all source files |
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22 * in the program, then also delete it here. |
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23 * |
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24 * This program is distributed in the hope that it will be useful, but |
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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27 * General Public License for more details. |
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28 * |
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29 * You should have received a copy of the GNU General Public License |
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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31 **/ |
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32 |
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33 |
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34 #include "PrecompiledHeadersServer.h" |
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35 #include "ServerToolbox.h" |
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36 |
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37 #include "../Core/DicomFormat/DicomArray.h" |
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38 #include "../Core/DicomParsing/ParsedDicomFile.h" |
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39 #include "../Core/FileStorage/StorageAccessor.h" |
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40 #include "../Core/Logging.h" |
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41 #include "../Core/OrthancException.h" |
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43 #include "IDatabaseWrapper.h" |
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44 #include "ServerContext.h" |
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45 |
234 | 46 #include <cassert> |
47 | |
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48 namespace Orthanc |
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49 { |
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50 static const DicomTag PATIENT_IDENTIFIERS[] = |
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51 { |
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52 DICOM_TAG_PATIENT_ID, |
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53 DICOM_TAG_PATIENT_NAME, |
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54 DICOM_TAG_PATIENT_BIRTH_DATE |
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55 }; |
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56 |
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57 static const DicomTag STUDY_IDENTIFIERS[] = |
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58 { |
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59 DICOM_TAG_PATIENT_ID, |
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60 DICOM_TAG_PATIENT_NAME, |
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61 DICOM_TAG_PATIENT_BIRTH_DATE, |
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62 DICOM_TAG_STUDY_INSTANCE_UID, |
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63 DICOM_TAG_ACCESSION_NUMBER, |
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64 DICOM_TAG_STUDY_DESCRIPTION, |
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65 DICOM_TAG_STUDY_DATE |
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66 }; |
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67 |
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68 static const DicomTag SERIES_IDENTIFIERS[] = |
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69 { |
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70 DICOM_TAG_SERIES_INSTANCE_UID |
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71 }; |
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72 |
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73 static const DicomTag INSTANCE_IDENTIFIERS[] = |
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74 { |
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75 DICOM_TAG_SOP_INSTANCE_UID |
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76 }; |
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77 |
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78 |
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79 void ResourcesContent::Store(Compatibility::ISetResourcesContent& compatibility) const |
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80 { |
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81 for (std::list<TagValue>::const_iterator |
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82 it = tags_.begin(); it != tags_.end(); ++it) |
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83 { |
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84 if (it->isIdentifier_) |
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85 { |
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86 compatibility.SetIdentifierTag(it->resourceId_, it->tag_, it->value_); |
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87 } |
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88 else |
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89 { |
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90 compatibility.SetMainDicomTag(it->resourceId_, it->tag_, it->value_); |
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91 } |
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92 } |
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93 |
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94 for (std::list<Metadata>::const_iterator |
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95 it = metadata_.begin(); it != metadata_.end(); ++it) |
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96 { |
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97 compatibility.SetMetadata(it->resourceId_, it->metadata_, it->value_); |
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98 } |
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99 } |
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100 |
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101 |
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102 void ResourcesContent::EncodeForPlugins( |
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103 std::vector<OrthancPluginResourcesContentTags>& identifierTags, |
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104 std::vector<OrthancPluginResourcesContentTags>& mainDicomTags, |
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105 std::vector<OrthancPluginResourcesContentMetadata>& metadata) const |
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106 { |
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107 identifierTags.reserve(tags_.size()); |
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108 mainDicomTags.reserve(tags_.size()); |
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109 metadata.reserve(metadata_.size()); |
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110 |
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111 for (std::list<TagValue>::const_iterator |
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112 it = tags_.begin(); it != tags_.end(); ++it) |
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113 { |
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114 OrthancPluginResourcesContentTags tmp; |
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115 tmp.resource = it->resourceId_; |
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116 tmp.group = it->tag_.GetGroup(); |
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117 tmp.element = it->tag_.GetElement(); |
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118 tmp.value = it->value_.c_str(); |
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119 |
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120 if (it->isIdentifier_) |
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121 { |
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122 identifierTags.push_back(tmp); |
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123 } |
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124 else |
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125 { |
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126 mainDicomTags.push_back(tmp); |
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127 } |
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128 } |
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129 |
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130 for (std::list<Metadata>::const_iterator |
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131 it = metadata_.begin(); it != metadata_.end(); ++it) |
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132 { |
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133 OrthancPluginResourcesContentMetadata tmp; |
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134 tmp.resource = it->resourceId_; |
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135 tmp.metadata = it->metadata_; |
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136 tmp.value = it->value_.c_str(); |
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137 metadata.push_back(tmp); |
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138 } |
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139 |
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140 assert(identifierTags.size() + mainDicomTags.size() == tags_.size() && |
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141 metadata.size() == metadata_.size()); |
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142 } |
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143 |
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144 |
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145 static void StoreMainDicomTagsInternal(ResourcesContent& target, |
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146 int64_t resource, |
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147 const DicomMap& tags) |
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148 { |
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149 DicomArray flattened(tags); |
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150 |
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151 for (size_t i = 0; i < flattened.GetSize(); i++) |
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152 { |
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153 const DicomElement& element = flattened.GetElement(i); |
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154 const DicomTag& tag = element.GetTag(); |
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155 const DicomValue& value = element.GetValue(); |
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156 if (!value.IsNull() && |
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157 !value.IsBinary()) |
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158 { |
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159 target.AddMainDicomTag(resource, tag, element.GetValue().GetContent()); |
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160 } |
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161 } |
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162 } |
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163 |
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164 |
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165 static void StoreIdentifiers(ResourcesContent& target, |
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166 int64_t resource, |
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167 ResourceType level, |
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168 const DicomMap& map) |
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169 { |
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170 const DicomTag* tags; |
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171 size_t size; |
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172 |
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173 ServerToolbox::LoadIdentifiers(tags, size, level); |
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174 |
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175 for (size_t i = 0; i < size; i++) |
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176 { |
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177 // The identifiers tags are a subset of the main DICOM tags |
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178 assert(DicomMap::IsMainDicomTag(tags[i])); |
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179 |
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180 const DicomValue* value = map.TestAndGetValue(tags[i]); |
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181 if (value != NULL && |
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182 !value->IsNull() && |
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183 !value->IsBinary()) |
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184 { |
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185 std::string s = ServerToolbox::NormalizeIdentifier(value->GetContent()); |
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186 target.AddIdentifierTag(resource, tags[i], s); |
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187 } |
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188 } |
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189 } |
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190 |
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191 |
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192 void ResourcesContent::AddResource(int64_t resource, |
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193 ResourceType level, |
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194 const DicomMap& dicomSummary) |
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195 { |
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196 StoreIdentifiers(*this, resource, level, dicomSummary); |
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197 |
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198 DicomMap tags; |
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199 |
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200 switch (level) |
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201 { |
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202 case ResourceType_Patient: |
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203 dicomSummary.ExtractPatientInformation(tags); |
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204 break; |
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205 |
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206 case ResourceType_Study: |
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207 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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208 dicomSummary.ExtractPatientInformation(tags); |
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209 StoreMainDicomTagsInternal(*this, resource, tags); |
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210 |
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211 dicomSummary.ExtractStudyInformation(tags); |
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212 break; |
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213 |
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214 case ResourceType_Series: |
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215 dicomSummary.ExtractSeriesInformation(tags); |
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216 break; |
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217 |
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218 case ResourceType_Instance: |
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219 dicomSummary.ExtractInstanceInformation(tags); |
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220 break; |
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221 |
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222 default: |
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223 throw OrthancException(ErrorCode_InternalError); |
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224 } |
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225 |
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226 StoreMainDicomTagsInternal(*this, resource, tags); |
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227 } |
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228 |
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229 |
2120 | 230 namespace ServerToolbox |
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231 { |
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232 void SimplifyTags(Json::Value& target, |
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233 const Json::Value& source, |
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234 DicomToJsonFormat format) |
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235 { |
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236 if (!source.isObject()) |
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237 { |
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238 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat); |
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239 } |
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240 |
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241 target = Json::objectValue; |
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242 Json::Value::Members members = source.getMemberNames(); |
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243 |
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244 for (size_t i = 0; i < members.size(); i++) |
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245 { |
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246 const Json::Value& v = source[members[i]]; |
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247 const std::string& type = v["Type"].asString(); |
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248 |
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249 std::string name; |
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250 switch (format) |
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251 { |
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252 case DicomToJsonFormat_Human: |
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253 name = v["Name"].asString(); |
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254 break; |
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255 |
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256 case DicomToJsonFormat_Short: |
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257 name = members[i]; |
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258 break; |
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259 |
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260 default: |
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261 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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262 } |
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263 |
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264 if (type == "String") |
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265 { |
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266 target[name] = v["Value"].asString(); |
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267 } |
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268 else if (type == "TooLong" || |
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269 type == "Null") |
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270 { |
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271 target[name] = Json::nullValue; |
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272 } |
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273 else if (type == "Sequence") |
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274 { |
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275 const Json::Value& array = v["Value"]; |
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276 assert(array.isArray()); |
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277 |
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278 Json::Value children = Json::arrayValue; |
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279 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++) |
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280 { |
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281 Json::Value c; |
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282 SimplifyTags(c, array[i], format); |
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283 children.append(c); |
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284 } |
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285 |
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286 target[name] = children; |
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287 } |
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288 else |
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289 { |
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290 assert(0); |
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291 } |
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292 } |
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293 } |
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294 |
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295 |
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296 bool FindOneChildInstance(int64_t& result, |
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297 IDatabaseWrapper& database, |
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298 int64_t resource, |
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299 ResourceType type) |
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300 { |
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301 for (;;) |
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302 { |
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303 if (type == ResourceType_Instance) |
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304 { |
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305 result = resource; |
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306 return true; |
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307 } |
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308 |
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309 std::list<int64_t> children; |
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310 database.GetChildrenInternalId(children, resource); |
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311 if (children.empty()) |
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312 { |
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313 return false; |
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314 } |
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315 |
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316 resource = children.front(); |
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317 type = GetChildResourceType(type); |
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318 } |
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319 } |
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320 |
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321 |
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322 void ReconstructMainDicomTags(IDatabaseWrapper& database, |
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323 IStorageArea& storageArea, |
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324 ResourceType level) |
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325 { |
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326 // WARNING: The database should be locked with a transaction! |
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327 |
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328 // TODO: This function might consume much memory if level == |
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329 // ResourceType_Instance. To improve this, first download the |
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330 // list of studies, then remove the instances for each single |
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331 // study (check out OrthancRestApi::InvalidateTags for an |
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332 // example). Take this improvement into consideration for the |
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333 // next upgrade of the database schema. |
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334 |
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335 const char* plural = NULL; |
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336 |
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337 switch (level) |
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338 { |
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339 case ResourceType_Patient: |
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340 plural = "patients"; |
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341 break; |
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342 |
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343 case ResourceType_Study: |
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344 plural = "studies"; |
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345 break; |
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346 |
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347 case ResourceType_Series: |
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348 plural = "series"; |
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349 break; |
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350 |
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351 case ResourceType_Instance: |
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352 plural = "instances"; |
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353 break; |
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354 |
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355 default: |
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356 throw OrthancException(ErrorCode_InternalError); |
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357 } |
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358 |
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359 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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360 |
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361 std::list<std::string> resources; |
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362 database.GetAllPublicIds(resources, level); |
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363 |
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364 for (std::list<std::string>::const_iterator |
1847 | 365 it = resources.begin(); it != resources.end(); ++it) |
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366 { |
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367 // Locate the resource and one of its child instances |
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368 int64_t resource, instance; |
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369 ResourceType tmp; |
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370 |
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371 if (!database.LookupResource(resource, tmp, *it) || |
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372 tmp != level || |
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373 !FindOneChildInstance(instance, database, resource, level)) |
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374 { |
2955 | 375 throw OrthancException(ErrorCode_InternalError, |
376 "Cannot find an instance for " + | |
377 std::string(EnumerationToString(level)) + | |
378 " with identifier " + *it); | |
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379 } |
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380 |
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381 // Get the DICOM file attached to some instances in the resource |
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382 FileInfo attachment; |
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383 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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384 { |
2955 | 385 throw OrthancException(ErrorCode_InternalError, |
386 "Cannot retrieve the DICOM file associated with instance " + | |
387 database.GetPublicId(instance)); | |
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388 } |
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389 |
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390 try |
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391 { |
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392 // Read and parse the content of the DICOM file |
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393 StorageAccessor accessor(storageArea); |
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394 |
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395 std::string content; |
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396 accessor.Read(content, attachment); |
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397 |
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398 ParsedDicomFile dicom(content); |
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399 |
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400 // Update the tags of this resource |
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401 DicomMap dicomSummary; |
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402 dicom.ExtractDicomSummary(dicomSummary); |
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403 |
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404 database.ClearMainDicomTags(resource); |
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405 |
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406 ResourcesContent tags; |
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407 tags.AddResource(resource, level, dicomSummary); |
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408 database.SetResourcesContent(tags); |
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409 } |
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410 catch (OrthancException&) |
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411 { |
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412 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() |
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413 << " associated with instance " << database.GetPublicId(instance); |
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414 throw; |
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415 } |
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416 } |
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417 } |
2121 | 418 |
419 | |
420 void LoadIdentifiers(const DicomTag*& tags, | |
421 size_t& size, | |
422 ResourceType level) | |
423 { | |
424 switch (level) | |
425 { | |
426 case ResourceType_Patient: | |
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427 tags = PATIENT_IDENTIFIERS; |
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428 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 429 break; |
430 | |
431 case ResourceType_Study: | |
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432 tags = STUDY_IDENTIFIERS; |
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433 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 434 break; |
435 | |
436 case ResourceType_Series: | |
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437 tags = SERIES_IDENTIFIERS; |
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438 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 439 break; |
440 | |
441 case ResourceType_Instance: | |
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442 tags = INSTANCE_IDENTIFIERS; |
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443 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 444 break; |
445 | |
446 default: | |
447 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
448 } | |
449 } | |
450 | |
451 | |
452 std::string NormalizeIdentifier(const std::string& value) | |
453 { | |
454 std::string t; | |
455 t.reserve(value.size()); | |
456 | |
457 for (size_t i = 0; i < value.size(); i++) | |
458 { | |
459 if (value[i] == '%' || | |
460 value[i] == '_') | |
461 { | |
462 t.push_back(' '); // These characters might break wildcard queries in SQL | |
463 } | |
464 else if (isascii(value[i]) && | |
465 !iscntrl(value[i]) && | |
466 (!isspace(value[i]) || value[i] == ' ')) | |
467 { | |
468 t.push_back(value[i]); | |
469 } | |
470 } | |
471 | |
472 Toolbox::ToUpperCase(t); | |
473 | |
474 return Toolbox::StripSpaces(t); | |
475 } | |
476 | |
477 | |
478 bool IsIdentifier(const DicomTag& tag, | |
479 ResourceType level) | |
480 { | |
481 const DicomTag* tags; | |
482 size_t size; | |
483 | |
484 LoadIdentifiers(tags, size, level); | |
485 | |
486 for (size_t i = 0; i < size; i++) | |
487 { | |
488 if (tag == tags[i]) | |
489 { | |
490 return true; | |
491 } | |
492 } | |
493 | |
494 return false; | |
495 } | |
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496 |
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497 |
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498 void ReconstructResource(ServerContext& context, |
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499 const std::string& resource) |
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500 { |
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501 LOG(WARNING) << "Reconstructing resource " << resource; |
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502 |
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503 std::list<std::string> instances; |
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504 context.GetIndex().GetChildInstances(instances, resource); |
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505 |
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506 for (std::list<std::string>::const_iterator |
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507 it = instances.begin(); it != instances.end(); ++it) |
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508 { |
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509 ServerContext::DicomCacheLocker locker(context, *it); |
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510 |
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511 Json::Value dicomAsJson; |
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512 locker.GetDicom().DatasetToJson(dicomAsJson); |
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513 |
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514 std::string s = dicomAsJson.toStyledString(); |
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515 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size()); |
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516 |
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517 context.GetIndex().ReconstructInstance(locker.GetDicom()); |
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518 } |
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519 } |
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520 } |
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521 } |