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annotate OrthancServer/ServerToolbox.cpp @ 3093:2e1808b6146a db-changes

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reorganization of folders
author Sebastien Jodogne <s.jodogne@gmail.com>
date Sat, 05 Jan 2019 16:09:21 +0100
parents fb8ee0786b1e
children 61da3c9b4121
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
1900
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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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42 #include "../Plugins/Engine/OrthancPlugins.h"
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43 #include "Database/IDatabaseWrapper.h"
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44 #include "ServerContext.h"
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45
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46 #include <cassert>
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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() &&
3088
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diff changeset
141 metadata.size() == metadata_.size());
d498ece73562 preparing extension CreateResources
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142 }
d498ece73562 preparing extension CreateResources
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143
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144
3083
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145 static void StoreMainDicomTagsInternal(ResourcesContent& target,
683d572424b6 IDatabaseWrapper::SetResourcesContent
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146 int64_t resource,
683d572424b6 IDatabaseWrapper::SetResourcesContent
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147 const DicomMap& tags)
683d572424b6 IDatabaseWrapper::SetResourcesContent
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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)
683d572424b6 IDatabaseWrapper::SetResourcesContent
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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);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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174
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175 for (size_t i = 0; i < size; i++)
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176 {
683d572424b6 IDatabaseWrapper::SetResourcesContent
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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]));
683d572424b6 IDatabaseWrapper::SetResourcesContent
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179
683d572424b6 IDatabaseWrapper::SetResourcesContent
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180 const DicomValue* value = map.TestAndGetValue(tags[i]);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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181 if (value != NULL &&
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
182 !value->IsNull() &&
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
183 !value->IsBinary())
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
184 {
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
185 std::string s = ServerToolbox::NormalizeIdentifier(value->GetContent());
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
186 target.AddIdentifierTag(resource, tags[i], s);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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187 }
683d572424b6 IDatabaseWrapper::SetResourcesContent
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188 }
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
189 }
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diff changeset
190
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191
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diff changeset
192 void ResourcesContent::AddResource(int64_t resource,
683d572424b6 IDatabaseWrapper::SetResourcesContent
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193 ResourceType level,
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194 const DicomMap& dicomSummary)
683d572424b6 IDatabaseWrapper::SetResourcesContent
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195 {
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
196 StoreIdentifiers(*this, resource, level, dicomSummary);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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197
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diff changeset
198 DicomMap tags;
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
199
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
200 switch (level)
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
201 {
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
202 case ResourceType_Patient:
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
203 dicomSummary.ExtractPatientInformation(tags);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
204 break;
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205
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
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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diff changeset
208 dicomSummary.ExtractPatientInformation(tags);
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diff changeset
209 StoreMainDicomTagsInternal(*this, resource, tags);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
210
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
211 dicomSummary.ExtractStudyInformation(tags);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
212 break;
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
213
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
214 case ResourceType_Series:
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
215 dicomSummary.ExtractSeriesInformation(tags);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
216 break;
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diff changeset
217
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
218 case ResourceType_Instance:
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diff changeset
219 dicomSummary.ExtractInstanceInformation(tags);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
220 break;
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
221
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
222 default:
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
223 throw OrthancException(ErrorCode_InternalError);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
224 }
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
225
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
226 StoreMainDicomTagsInternal(*this, resource, tags);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
227 }
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
228
683d572424b6 IDatabaseWrapper::SetResourcesContent
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diff changeset
229
2120
4b02ec79728a refactoring
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diff changeset
230 namespace ServerToolbox
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
diff changeset
231 {
1668
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
232 void SimplifyTags(Json::Value& target,
1859
4e7c318a3f69 C-FIND SCP will return tags with sequence value representation
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diff changeset
233 const Json::Value& source,
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parents: 1847
diff changeset
234 DicomToJsonFormat format)
1668
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
235 {
2951
65b20d922e10 throw instead of assert when Dicom tags can not be simplified
am@osimis.io
parents: 2447
diff changeset
236 if (!source.isObject())
65b20d922e10 throw instead of assert when Dicom tags can not be simplified
am@osimis.io
parents: 2447
diff changeset
237 {
65b20d922e10 throw instead of assert when Dicom tags can not be simplified
am@osimis.io
parents: 2447
diff changeset
238 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
65b20d922e10 throw instead of assert when Dicom tags can not be simplified
am@osimis.io
parents: 2447
diff changeset
239 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
diff changeset
240
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
241 target = Json::objectValue;
de1413733c97 reconstructing main dicom tags
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diff changeset
242 Json::Value::Members members = source.getMemberNames();
de1413733c97 reconstructing main dicom tags
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diff changeset
243
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
244 for (size_t i = 0; i < members.size(); i++)
de1413733c97 reconstructing main dicom tags
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diff changeset
245 {
de1413733c97 reconstructing main dicom tags
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diff changeset
246 const Json::Value& v = source[members[i]];
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diff changeset
247 const std::string& type = v["Type"].asString();
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
diff changeset
248
1859
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diff changeset
249 std::string name;
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diff changeset
250 switch (format)
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parents: 1847
diff changeset
251 {
1860
c7d70f659190 DicomToJsonFormat_Simple -> DicomToJsonFormat_Human
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parents: 1859
diff changeset
252 case DicomToJsonFormat_Human:
1859
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diff changeset
253 name = v["Name"].asString();
4e7c318a3f69 C-FIND SCP will return tags with sequence value representation
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parents: 1847
diff changeset
254 break;
4e7c318a3f69 C-FIND SCP will return tags with sequence value representation
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parents: 1847
diff changeset
255
4e7c318a3f69 C-FIND SCP will return tags with sequence value representation
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1847
diff changeset
256 case DicomToJsonFormat_Short:
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diff changeset
257 name = members[i];
4e7c318a3f69 C-FIND SCP will return tags with sequence value representation
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parents: 1847
diff changeset
258 break;
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parents: 1847
diff changeset
259
4e7c318a3f69 C-FIND SCP will return tags with sequence value representation
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parents: 1847
diff changeset
260 default:
4e7c318a3f69 C-FIND SCP will return tags with sequence value representation
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parents: 1847
diff changeset
261 throw OrthancException(ErrorCode_ParameterOutOfRange);
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parents: 1847
diff changeset
262 }
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parents: 1847
diff changeset
263
1668
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diff changeset
264 if (type == "String")
de1413733c97 reconstructing main dicom tags
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diff changeset
265 {
de1413733c97 reconstructing main dicom tags
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diff changeset
266 target[name] = v["Value"].asString();
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
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());
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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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 }
213
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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
2129
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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
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
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333 // next upgrade of the database schema.
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334
1669
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
335 const char* plural = NULL;
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336
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diff changeset
337 switch (level)
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diff changeset
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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diff changeset
349 break;
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diff changeset
350
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diff changeset
351 case ResourceType_Instance:
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352 plural = "instances";
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diff changeset
353 break;
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diff changeset
354
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diff changeset
355 default:
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356 throw OrthancException(ErrorCode_InternalError);
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diff changeset
357 }
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diff changeset
358
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diff changeset
359 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
360
1668
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diff changeset
361 std::list<std::string> resources;
de1413733c97 reconstructing main dicom tags
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362 database.GetAllPublicIds(resources, level);
de1413733c97 reconstructing main dicom tags
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diff changeset
363
de1413733c97 reconstructing main dicom tags
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diff changeset
364 for (std::list<std::string>::const_iterator
1847
559956d5ceb2 cppcheck
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diff changeset
365 it = resources.begin(); it != resources.end(); ++it)
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
366 {
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367 // Locate the resource and one of its child instances
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diff changeset
368 int64_t resource, instance;
de1413733c97 reconstructing main dicom tags
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diff changeset
369 ResourceType tmp;
de1413733c97 reconstructing main dicom tags
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diff changeset
370
de1413733c97 reconstructing main dicom tags
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diff changeset
371 if (!database.LookupResource(resource, tmp, *it) ||
de1413733c97 reconstructing main dicom tags
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diff changeset
372 tmp != level ||
de1413733c97 reconstructing main dicom tags
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373 !FindOneChildInstance(instance, database, resource, level))
de1413733c97 reconstructing main dicom tags
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diff changeset
374 {
2955
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375 throw OrthancException(ErrorCode_InternalError,
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376 "Cannot find an instance for " +
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
377 std::string(EnumerationToString(level)) +
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378 " with identifier " + *it);
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
379 }
de1413733c97 reconstructing main dicom tags
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diff changeset
380
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381 // Get the DICOM file attached to some instances in the resource
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382 FileInfo attachment;
de1413733c97 reconstructing main dicom tags
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diff changeset
383 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
de1413733c97 reconstructing main dicom tags
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diff changeset
384 {
2955
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385 throw OrthancException(ErrorCode_InternalError,
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386 "Cannot retrieve the DICOM file associated with instance " +
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diff changeset
387 database.GetPublicId(instance));
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
388 }
de1413733c97 reconstructing main dicom tags
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diff changeset
389
1870
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
390 try
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
391 {
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
392 // Read and parse the content of the DICOM file
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diff changeset
393 StorageAccessor accessor(storageArea);
1673
0bbcfd9695e5 UpgradeDatabase in the sample plugin
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diff changeset
394
1870
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
395 std::string content;
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
396 accessor.Read(content, attachment);
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
397
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
398 ParsedDicomFile dicom(content);
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
399
1870
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
400 // Update the tags of this resource
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
401 DicomMap dicomSummary;
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
402 dicom.ExtractDicomSummary(dicomSummary);
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
403
1870
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
404 database.ClearMainDicomTags(resource);
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
405
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
406 ResourcesContent tags;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
407 tags.AddResource(resource, level, dicomSummary);
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
408 database.SetResourcesContent(tags);
1870
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
409 }
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
410 catch (OrthancException&)
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
411 {
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
412 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
413 << " associated with instance " << database.GetPublicId(instance);
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
414 throw;
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
415 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
416 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
417 }
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
418
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
419
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
420 void LoadIdentifiers(const DicomTag*& tags,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
421 size_t& size,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
422 ResourceType level)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
423 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
424 switch (level)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
425 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
426 case ResourceType_Patient:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
427 tags = PATIENT_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
428 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
429 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
430
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
431 case ResourceType_Study:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
432 tags = STUDY_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
433 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
434 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
435
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
436 case ResourceType_Series:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
437 tags = SERIES_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
438 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
439 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
440
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
441 case ResourceType_Instance:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
442 tags = INSTANCE_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
443 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
444 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
445
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
446 default:
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
447 throw OrthancException(ErrorCode_ParameterOutOfRange);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
448 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
449 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
450
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
451
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
452 std::string NormalizeIdentifier(const std::string& value)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
453 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
454 std::string t;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
455 t.reserve(value.size());
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
456
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
457 for (size_t i = 0; i < value.size(); i++)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
458 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
459 if (value[i] == '%' ||
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
460 value[i] == '_')
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
461 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
462 t.push_back(' '); // These characters might break wildcard queries in SQL
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
463 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
464 else if (isascii(value[i]) &&
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
465 !iscntrl(value[i]) &&
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
466 (!isspace(value[i]) || value[i] == ' '))
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
467 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
468 t.push_back(value[i]);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
469 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
470 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
471
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
472 Toolbox::ToUpperCase(t);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
473
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
474 return Toolbox::StripSpaces(t);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
475 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
476
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
477
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
478 bool IsIdentifier(const DicomTag& tag,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
479 ResourceType level)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
480 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
481 const DicomTag* tags;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
482 size_t size;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
483
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
484 LoadIdentifiers(tags, size, level);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
485
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
486 for (size_t i = 0; i < size; i++)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
487 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
488 if (tag == tags[i])
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
489 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
490 return true;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
491 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
492 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
493
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
494 return false;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
495 }
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
496
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
497
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
498 void ReconstructResource(ServerContext& context,
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
499 const std::string& resource)
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
500 {
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
501 LOG(WARNING) << "Reconstructing resource " << resource;
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
502
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
503 std::list<std::string> instances;
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
504 context.GetIndex().GetChildInstances(instances, resource);
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
505
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
506 for (std::list<std::string>::const_iterator
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
507 it = instances.begin(); it != instances.end(); ++it)
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
508 {
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
509 ServerContext::DicomCacheLocker locker(context, *it);
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
510
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
511 Json::Value dicomAsJson;
2409
e4045b3c9772 ignore-length argument if retrieving DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2380
diff changeset
512 locker.GetDicom().DatasetToJson(dicomAsJson);
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
513
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
514 std::string s = dicomAsJson.toStyledString();
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
515 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size());
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
516
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
517 context.GetIndex().ReconstructInstance(locker.GetDicom());
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
518 }
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
519 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
520 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
521 }