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annotate OrthancServer/ServerToolbox.cpp @ 3088:d498ece73562 db-changes

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preparing extension CreateResources
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 04 Jan 2019 17:48:34 +0100
parents c829758b9ca0
children fb8ee0786b1e
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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 "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>& tags,
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104 std::vector<OrthancPluginResourcesContentMetadata>& metadata) const
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105 {
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106 tags.reserve(tags_.size());
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107 metadata.reserve(metadata_.size());
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108
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109 for (std::list<TagValue>::const_iterator
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110 it = tags_.begin(); it != tags_.end(); ++it)
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111 {
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112 OrthancPluginResourcesContentTags tmp;
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113 tmp.resource = it->resourceId_;
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114 tmp.isIdentifier = it->isIdentifier_;
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115 tmp.group = it->tag_.GetGroup();
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116 tmp.element = it->tag_.GetElement();
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117 tmp.value = it->value_.c_str();
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118 tags.push_back(tmp);
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119 }
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120
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121 for (std::list<Metadata>::const_iterator
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122 it = metadata_.begin(); it != metadata_.end(); ++it)
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123 {
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124 OrthancPluginResourcesContentMetadata tmp;
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125 tmp.resource = it->resourceId_;
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126 tmp.metadata = it->metadata_;
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127 tmp.value = it->value_.c_str();
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128 metadata.push_back(tmp);
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129 }
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130
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131 assert(tags.size() == tags_.size() &&
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132 metadata.size() == metadata_.size());
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133 }
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134
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135
3083
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136 static void StoreMainDicomTagsInternal(ResourcesContent& target,
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137 int64_t resource,
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138 const DicomMap& tags)
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139 {
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140 DicomArray flattened(tags);
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141
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142 for (size_t i = 0; i < flattened.GetSize(); i++)
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143 {
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144 const DicomElement& element = flattened.GetElement(i);
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145 const DicomTag& tag = element.GetTag();
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146 const DicomValue& value = element.GetValue();
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147 if (!value.IsNull() &&
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148 !value.IsBinary())
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149 {
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150 target.AddMainDicomTag(resource, tag, element.GetValue().GetContent());
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151 }
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152 }
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153 }
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154
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155
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156 static void StoreIdentifiers(ResourcesContent& target,
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157 int64_t resource,
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158 ResourceType level,
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159 const DicomMap& map)
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160 {
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161 const DicomTag* tags;
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162 size_t size;
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163
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164 ServerToolbox::LoadIdentifiers(tags, size, level);
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165
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166 for (size_t i = 0; i < size; i++)
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167 {
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168 // The identifiers tags are a subset of the main DICOM tags
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169 assert(DicomMap::IsMainDicomTag(tags[i]));
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170
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171 const DicomValue* value = map.TestAndGetValue(tags[i]);
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172 if (value != NULL &&
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173 !value->IsNull() &&
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174 !value->IsBinary())
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175 {
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176 std::string s = ServerToolbox::NormalizeIdentifier(value->GetContent());
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177 target.AddIdentifierTag(resource, tags[i], s);
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178 }
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179 }
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180 }
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181
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182
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183 void ResourcesContent::AddResource(int64_t resource,
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184 ResourceType level,
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185 const DicomMap& dicomSummary)
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186 {
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187 StoreIdentifiers(*this, resource, level, dicomSummary);
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188
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189 DicomMap tags;
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190
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191 switch (level)
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192 {
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193 case ResourceType_Patient:
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194 dicomSummary.ExtractPatientInformation(tags);
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195 break;
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196
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197 case ResourceType_Study:
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198 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
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199 dicomSummary.ExtractPatientInformation(tags);
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200 StoreMainDicomTagsInternal(*this, resource, tags);
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201
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202 dicomSummary.ExtractStudyInformation(tags);
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203 break;
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204
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205 case ResourceType_Series:
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206 dicomSummary.ExtractSeriesInformation(tags);
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diff changeset
207 break;
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208
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209 case ResourceType_Instance:
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210 dicomSummary.ExtractInstanceInformation(tags);
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diff changeset
211 break;
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212
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213 default:
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214 throw OrthancException(ErrorCode_InternalError);
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215 }
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216
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diff changeset
217 StoreMainDicomTagsInternal(*this, resource, tags);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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218 }
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219
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220
2120
4b02ec79728a refactoring
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221 namespace ServerToolbox
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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222 {
1668
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223 void SimplifyTags(Json::Value& target,
1859
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diff changeset
224 const Json::Value& source,
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225 DicomToJsonFormat format)
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diff changeset
226 {
2951
65b20d922e10 throw instead of assert when Dicom tags can not be simplified
am@osimis.io
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diff changeset
227 if (!source.isObject())
65b20d922e10 throw instead of assert when Dicom tags can not be simplified
am@osimis.io
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diff changeset
228 {
65b20d922e10 throw instead of assert when Dicom tags can not be simplified
am@osimis.io
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diff changeset
229 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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230 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
diff changeset
231
1668
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diff changeset
232 target = Json::objectValue;
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diff changeset
233 Json::Value::Members members = source.getMemberNames();
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diff changeset
234
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diff changeset
235 for (size_t i = 0; i < members.size(); i++)
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236 {
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diff changeset
237 const Json::Value& v = source[members[i]];
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diff changeset
238 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
239
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diff changeset
240 std::string name;
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diff changeset
241 switch (format)
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diff changeset
242 {
1860
c7d70f659190 DicomToJsonFormat_Simple -> DicomToJsonFormat_Human
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diff changeset
243 case DicomToJsonFormat_Human:
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diff changeset
244 name = v["Name"].asString();
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diff changeset
245 break;
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diff changeset
246
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diff changeset
247 case DicomToJsonFormat_Short:
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248 name = members[i];
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diff changeset
249 break;
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parents: 1847
diff changeset
250
4e7c318a3f69 C-FIND SCP will return tags with sequence value representation
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parents: 1847
diff changeset
251 default:
4e7c318a3f69 C-FIND SCP will return tags with sequence value representation
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diff changeset
252 throw OrthancException(ErrorCode_ParameterOutOfRange);
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253 }
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diff changeset
254
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diff changeset
255 if (type == "String")
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diff changeset
256 {
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diff changeset
257 target[name] = v["Value"].asString();
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diff changeset
258 }
de1413733c97 reconstructing main dicom tags
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diff changeset
259 else if (type == "TooLong" ||
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diff changeset
260 type == "Null")
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diff changeset
261 {
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diff changeset
262 target[name] = Json::nullValue;
de1413733c97 reconstructing main dicom tags
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diff changeset
263 }
de1413733c97 reconstructing main dicom tags
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diff changeset
264 else if (type == "Sequence")
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diff changeset
265 {
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diff changeset
266 const Json::Value& array = v["Value"];
de1413733c97 reconstructing main dicom tags
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diff changeset
267 assert(array.isArray());
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
diff changeset
268
1668
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diff changeset
269 Json::Value children = Json::arrayValue;
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diff changeset
270 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++)
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271 {
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diff changeset
272 Json::Value c;
1859
4e7c318a3f69 C-FIND SCP will return tags with sequence value representation
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273 SimplifyTags(c, array[i], format);
1668
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274 children.append(c);
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275 }
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diff changeset
276
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277 target[name] = children;
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278 }
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diff changeset
279 else
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280 {
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281 assert(0);
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282 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
diff changeset
283 }
1668
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diff changeset
284 }
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285
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286
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287 bool FindOneChildInstance(int64_t& result,
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288 IDatabaseWrapper& database,
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289 int64_t resource,
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diff changeset
290 ResourceType type)
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291 {
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292 for (;;)
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293 {
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294 if (type == ResourceType_Instance)
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295 {
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296 result = resource;
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297 return true;
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298 }
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299
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300 std::list<int64_t> children;
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301 database.GetChildrenInternalId(children, resource);
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302 if (children.empty())
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303 {
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304 return false;
de1413733c97 reconstructing main dicom tags
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305 }
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306
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307 resource = children.front();
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308 type = GetChildResourceType(type);
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309 }
de1413733c97 reconstructing main dicom tags
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310 }
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311
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312
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313 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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314 IStorageArea& storageArea,
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315 ResourceType level)
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316 {
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317 // WARNING: The database should be locked with a transaction!
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318
2129
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
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319 // TODO: This function might consume much memory if level ==
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
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320 // ResourceType_Instance. To improve this, first download the
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
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321 // list of studies, then remove the instances for each single
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
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322 // study (check out OrthancRestApi::InvalidateTags for an
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2123
diff changeset
323 // example). Take this improvement into consideration for the
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2123
diff changeset
324 // next upgrade of the database schema.
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
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diff changeset
325
1669
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
326 const char* plural = NULL;
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
327
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
328 switch (level)
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
329 {
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
330 case ResourceType_Patient:
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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331 plural = "patients";
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diff changeset
332 break;
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
333
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
334 case ResourceType_Study:
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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335 plural = "studies";
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diff changeset
336 break;
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
337
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diff changeset
338 case ResourceType_Series:
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diff changeset
339 plural = "series";
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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parents: 1668
diff changeset
340 break;
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parents: 1668
diff changeset
341
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
342 case ResourceType_Instance:
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
343 plural = "instances";
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
344 break;
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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parents: 1668
diff changeset
345
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
346 default:
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
347 throw OrthancException(ErrorCode_InternalError);
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parents: 1668
diff changeset
348 }
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diff changeset
349
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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parents: 1668
diff changeset
350 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
351
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
352 std::list<std::string> resources;
de1413733c97 reconstructing main dicom tags
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diff changeset
353 database.GetAllPublicIds(resources, level);
de1413733c97 reconstructing main dicom tags
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diff changeset
354
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
355 for (std::list<std::string>::const_iterator
1847
559956d5ceb2 cppcheck
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parents: 1747
diff changeset
356 it = resources.begin(); it != resources.end(); ++it)
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
357 {
de1413733c97 reconstructing main dicom tags
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diff changeset
358 // Locate the resource and one of its child instances
de1413733c97 reconstructing main dicom tags
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diff changeset
359 int64_t resource, instance;
de1413733c97 reconstructing main dicom tags
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diff changeset
360 ResourceType tmp;
de1413733c97 reconstructing main dicom tags
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diff changeset
361
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
362 if (!database.LookupResource(resource, tmp, *it) ||
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
363 tmp != level ||
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
364 !FindOneChildInstance(instance, database, resource, level))
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
365 {
2955
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parents: 2951
diff changeset
366 throw OrthancException(ErrorCode_InternalError,
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parents: 2951
diff changeset
367 "Cannot find an instance for " +
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2951
diff changeset
368 std::string(EnumerationToString(level)) +
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2951
diff changeset
369 " with identifier " + *it);
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
370 }
de1413733c97 reconstructing main dicom tags
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diff changeset
371
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
372 // Get the DICOM file attached to some instances in the resource
de1413733c97 reconstructing main dicom tags
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diff changeset
373 FileInfo attachment;
de1413733c97 reconstructing main dicom tags
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diff changeset
374 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
375 {
2955
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parents: 2951
diff changeset
376 throw OrthancException(ErrorCode_InternalError,
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2951
diff changeset
377 "Cannot retrieve the DICOM file associated with instance " +
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2951
diff changeset
378 database.GetPublicId(instance));
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
379 }
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
380
1870
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
381 try
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
382 {
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
383 // Read and parse the content of the DICOM file
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
384 StorageAccessor accessor(storageArea);
1673
0bbcfd9695e5 UpgradeDatabase in the sample plugin
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parents: 1669
diff changeset
385
1870
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
386 std::string content;
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
387 accessor.Read(content, attachment);
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
388
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
389 ParsedDicomFile dicom(content);
1668
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
390
1870
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
391 // Update the tags of this resource
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
392 DicomMap dicomSummary;
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
393 dicom.ExtractDicomSummary(dicomSummary);
1668
de1413733c97 reconstructing main dicom tags
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parents: 1486
diff changeset
394
1870
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
395 database.ClearMainDicomTags(resource);
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
396
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
397 ResourcesContent tags;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
398 tags.AddResource(resource, level, dicomSummary);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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parents: 3061
diff changeset
399 database.SetResourcesContent(tags);
1870
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
400 }
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
401 catch (OrthancException&)
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
402 {
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
403 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
404 << " associated with instance " << database.GetPublicId(instance);
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
405 throw;
a6c431193c79 Improved logging information if upgrade fails
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 1860
diff changeset
406 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
407 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
408 }
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
409
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
410
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
411 void LoadIdentifiers(const DicomTag*& tags,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
412 size_t& size,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
413 ResourceType level)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
414 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
415 switch (level)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
416 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
417 case ResourceType_Patient:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
418 tags = PATIENT_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
419 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
420 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
421
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
422 case ResourceType_Study:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
423 tags = STUDY_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
424 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
425 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
426
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
427 case ResourceType_Series:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
428 tags = SERIES_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
429 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
430 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
431
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
432 case ResourceType_Instance:
3083
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
433 tags = INSTANCE_IDENTIFIERS;
683d572424b6 IDatabaseWrapper::SetResourcesContent
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 3061
diff changeset
434 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
2121
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
435 break;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
436
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
437 default:
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
438 throw OrthancException(ErrorCode_ParameterOutOfRange);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
439 }
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
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
442
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
443 std::string NormalizeIdentifier(const std::string& value)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
444 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
445 std::string t;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
446 t.reserve(value.size());
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
447
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
448 for (size_t i = 0; i < value.size(); i++)
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 if (value[i] == '%' ||
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
451 value[i] == '_')
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
452 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
453 t.push_back(' '); // These characters might break wildcard queries in SQL
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
454 }
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
455 else if (isascii(value[i]) &&
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
456 !iscntrl(value[i]) &&
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
457 (!isspace(value[i]) || value[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 t.push_back(value[i]);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
460 }
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
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
463 Toolbox::ToUpperCase(t);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
464
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
465 return Toolbox::StripSpaces(t);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
466 }
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
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
469 bool IsIdentifier(const DicomTag& tag,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
470 ResourceType level)
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 const DicomTag* tags;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
473 size_t size;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
474
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
475 LoadIdentifiers(tags, size, level);
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 for (size_t i = 0; i < size; i++)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
478 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
479 if (tag == tags[i])
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 return true;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
482 }
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
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
485 return false;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
486 }
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
487
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
488
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
489 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
490 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
491 {
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
492 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
493
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
494 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
495 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
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 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
498 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
499 {
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 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
501
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 Json::Value dicomAsJson;
2409
e4045b3c9772 ignore-length argument if retrieving DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2380
diff changeset
503 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
504
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 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
506 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
507
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 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
509 }
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 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
511 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
512 }