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annotate OrthancServer/Sources/ServerToolbox.cpp @ 4140:0ddc5297a8ab

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centralization of default parameters for JSON/DicomMap conversions from DCMTK
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 07 Aug 2020 10:46:50 +0200
parents a4f28efdfccf
children d9473bd5ed43
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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) 2017-2020 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 "../../OrthancFramework/Sources/DicomFormat/DicomArray.h"
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38 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h"
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39 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h"
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40 #include "../../OrthancFramework/Sources/Logging.h"
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41 #include "../../OrthancFramework/Sources/OrthancException.h"
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42 #include "Database/IDatabaseWrapper.h"
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43 #include "Database/ResourcesContent.h"
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44 #include "OrthancConfiguration.h"
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45 #include "ServerContext.h"
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47 #include <cassert>
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48
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49 namespace Orthanc
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50 {
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51 static const DicomTag PATIENT_IDENTIFIERS[] =
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52 {
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53 DICOM_TAG_PATIENT_ID,
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54 DICOM_TAG_PATIENT_NAME,
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55 DICOM_TAG_PATIENT_BIRTH_DATE
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56 };
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57
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58 static const DicomTag STUDY_IDENTIFIERS[] =
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59 {
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60 DICOM_TAG_PATIENT_ID,
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61 DICOM_TAG_PATIENT_NAME,
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62 DICOM_TAG_PATIENT_BIRTH_DATE,
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63 DICOM_TAG_STUDY_INSTANCE_UID,
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64 DICOM_TAG_ACCESSION_NUMBER,
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65 DICOM_TAG_STUDY_DESCRIPTION,
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66 DICOM_TAG_STUDY_DATE
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67 };
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68
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69 static const DicomTag SERIES_IDENTIFIERS[] =
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70 {
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71 DICOM_TAG_SERIES_INSTANCE_UID
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72 };
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73
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74 static const DicomTag INSTANCE_IDENTIFIERS[] =
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75 {
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76 DICOM_TAG_SOP_INSTANCE_UID
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77 };
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78
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79
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80 static void StoreMainDicomTagsInternal(ResourcesContent& target,
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81 int64_t resource,
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82 const DicomMap& tags)
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83 {
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84 DicomArray flattened(tags);
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85
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86 for (size_t i = 0; i < flattened.GetSize(); i++)
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87 {
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88 const DicomElement& element = flattened.GetElement(i);
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89 const DicomTag& tag = element.GetTag();
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90 const DicomValue& value = element.GetValue();
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91 if (!value.IsNull() &&
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92 !value.IsBinary())
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93 {
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94 target.AddMainDicomTag(resource, tag, element.GetValue().GetContent());
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95 }
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96 }
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97 }
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98
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99
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100 static void StoreIdentifiers(ResourcesContent& target,
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101 int64_t resource,
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102 ResourceType level,
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103 const DicomMap& map)
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104 {
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105 const DicomTag* tags;
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106 size_t size;
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107
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108 ServerToolbox::LoadIdentifiers(tags, size, level);
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109
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110 for (size_t i = 0; i < size; i++)
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111 {
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112 // The identifiers tags are a subset of the main DICOM tags
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113 assert(DicomMap::IsMainDicomTag(tags[i]));
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114
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115 const DicomValue* value = map.TestAndGetValue(tags[i]);
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116 if (value != NULL &&
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117 !value->IsNull() &&
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118 !value->IsBinary())
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119 {
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120 std::string s = ServerToolbox::NormalizeIdentifier(value->GetContent());
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121 target.AddIdentifierTag(resource, tags[i], s);
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122 }
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123 }
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124 }
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125
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126
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127 void ResourcesContent::AddResource(int64_t resource,
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128 ResourceType level,
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129 const DicomMap& dicomSummary)
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130 {
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131 StoreIdentifiers(*this, resource, level, dicomSummary);
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132
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133 DicomMap tags;
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134
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135 switch (level)
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136 {
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137 case ResourceType_Patient:
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138 dicomSummary.ExtractPatientInformation(tags);
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139 break;
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140
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141 case ResourceType_Study:
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142 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
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143 dicomSummary.ExtractPatientInformation(tags);
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144 StoreMainDicomTagsInternal(*this, resource, tags);
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145
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146 dicomSummary.ExtractStudyInformation(tags);
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147 break;
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148
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149 case ResourceType_Series:
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150 dicomSummary.ExtractSeriesInformation(tags);
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151 break;
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152
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153 case ResourceType_Instance:
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154 dicomSummary.ExtractInstanceInformation(tags);
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155 break;
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156
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157 default:
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158 throw OrthancException(ErrorCode_InternalError);
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159 }
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160
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161 StoreMainDicomTagsInternal(*this, resource, tags);
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162 }
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163
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164
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165 namespace ServerToolbox
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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166 {
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167 bool FindOneChildInstance(int64_t& result,
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168 IDatabaseWrapper& database,
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169 int64_t resource,
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170 ResourceType type)
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171 {
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172 for (;;)
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173 {
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174 if (type == ResourceType_Instance)
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175 {
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176 result = resource;
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177 return true;
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178 }
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179
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180 std::list<int64_t> children;
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181 database.GetChildrenInternalId(children, resource);
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182 if (children.empty())
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183 {
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184 return false;
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185 }
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186
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187 resource = children.front();
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188 type = GetChildResourceType(type);
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189 }
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190 }
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191
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192
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193 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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194 IStorageArea& storageArea,
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195 ResourceType level)
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196 {
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197 // WARNING: The database should be locked with a transaction!
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198
2129
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199 // TODO: This function might consume much memory if level ==
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200 // ResourceType_Instance. To improve this, first download the
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201 // list of studies, then remove the instances for each single
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202 // study (check out OrthancRestApi::InvalidateTags for an
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203 // example). Take this improvement into consideration for the
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204 // next upgrade of the database schema.
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205
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206 const char* plural = NULL;
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207
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208 switch (level)
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209 {
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210 case ResourceType_Patient:
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211 plural = "patients";
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212 break;
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213
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214 case ResourceType_Study:
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215 plural = "studies";
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216 break;
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217
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218 case ResourceType_Series:
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219 plural = "series";
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220 break;
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diff changeset
221
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222 case ResourceType_Instance:
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223 plural = "instances";
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224 break;
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diff changeset
225
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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226 default:
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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227 throw OrthancException(ErrorCode_InternalError);
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228 }
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diff changeset
229
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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230 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
231
1668
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diff changeset
232 std::list<std::string> resources;
de1413733c97 reconstructing main dicom tags
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233 database.GetAllPublicIds(resources, level);
de1413733c97 reconstructing main dicom tags
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234
de1413733c97 reconstructing main dicom tags
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diff changeset
235 for (std::list<std::string>::const_iterator
1847
559956d5ceb2 cppcheck
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diff changeset
236 it = resources.begin(); it != resources.end(); ++it)
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
237 {
de1413733c97 reconstructing main dicom tags
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238 // Locate the resource and one of its child instances
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239 int64_t resource, instance;
de1413733c97 reconstructing main dicom tags
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diff changeset
240 ResourceType tmp;
de1413733c97 reconstructing main dicom tags
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241
de1413733c97 reconstructing main dicom tags
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242 if (!database.LookupResource(resource, tmp, *it) ||
de1413733c97 reconstructing main dicom tags
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243 tmp != level ||
de1413733c97 reconstructing main dicom tags
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244 !FindOneChildInstance(instance, database, resource, level))
de1413733c97 reconstructing main dicom tags
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245 {
2955
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246 throw OrthancException(ErrorCode_InternalError,
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247 "Cannot find an instance for " +
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248 std::string(EnumerationToString(level)) +
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249 " with identifier " + *it);
1668
de1413733c97 reconstructing main dicom tags
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250 }
de1413733c97 reconstructing main dicom tags
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251
de1413733c97 reconstructing main dicom tags
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252 // Get the DICOM file attached to some instances in the resource
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253 FileInfo attachment;
de1413733c97 reconstructing main dicom tags
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diff changeset
254 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
de1413733c97 reconstructing main dicom tags
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diff changeset
255 {
2955
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256 throw OrthancException(ErrorCode_InternalError,
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257 "Cannot retrieve the DICOM file associated with instance " +
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258 database.GetPublicId(instance));
1668
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diff changeset
259 }
de1413733c97 reconstructing main dicom tags
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diff changeset
260
1870
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
261 try
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diff changeset
262 {
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diff changeset
263 // Read and parse the content of the DICOM file
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diff changeset
264 StorageAccessor accessor(storageArea);
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265
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diff changeset
266 std::string content;
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267 accessor.Read(content, attachment);
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268
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269 ParsedDicomFile dicom(content);
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270
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271 // Update the tags of this resource
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272 DicomMap dicomSummary;
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273 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom);
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274
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275 database.ClearMainDicomTags(resource);
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276
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277 ResourcesContent tags;
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278 tags.AddResource(resource, level, dicomSummary);
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279 database.SetResourcesContent(tags);
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280 }
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281 catch (OrthancException&)
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282 {
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283 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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284 << " associated with instance " << database.GetPublicId(instance);
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285 throw;
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286 }
213
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287 }
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288 }
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289
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290
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291 void LoadIdentifiers(const DicomTag*& tags,
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292 size_t& size,
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293 ResourceType level)
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294 {
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295 switch (level)
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296 {
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297 case ResourceType_Patient:
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298 tags = PATIENT_IDENTIFIERS;
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299 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
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300 break;
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301
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302 case ResourceType_Study:
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303 tags = STUDY_IDENTIFIERS;
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304 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
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305 break;
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306
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307 case ResourceType_Series:
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308 tags = SERIES_IDENTIFIERS;
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309 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
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310 break;
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311
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312 case ResourceType_Instance:
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313 tags = INSTANCE_IDENTIFIERS;
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314 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
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315 break;
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316
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317 default:
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318 throw OrthancException(ErrorCode_ParameterOutOfRange);
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319 }
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320 }
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321
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322
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323 std::string NormalizeIdentifier(const std::string& value)
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324 {
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325 std::string t;
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326 t.reserve(value.size());
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327
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328 for (size_t i = 0; i < value.size(); i++)
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329 {
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330 if (value[i] == '%' ||
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331 value[i] == '_')
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332 {
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333 t.push_back(' '); // These characters might break wildcard queries in SQL
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334 }
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335 else if (isascii(value[i]) &&
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336 !iscntrl(value[i]) &&
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337 (!isspace(value[i]) || value[i] == ' '))
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338 {
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339 t.push_back(value[i]);
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340 }
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341 }
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342
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343 Toolbox::ToUpperCase(t);
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344
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345 return Toolbox::StripSpaces(t);
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346 }
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347
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348
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349 bool IsIdentifier(const DicomTag& tag,
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350 ResourceType level)
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351 {
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352 const DicomTag* tags;
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353 size_t size;
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354
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355 LoadIdentifiers(tags, size, level);
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356
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357 for (size_t i = 0; i < size; i++)
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358 {
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359 if (tag == tags[i])
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360 {
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361 return true;
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362 }
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363 }
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364
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365 return false;
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366 }
2209
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367
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diff changeset
368
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diff changeset
369 void ReconstructResource(ServerContext& context,
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370 const std::string& resource)
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371 {
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372 LOG(WARNING) << "Reconstructing resource " << resource;
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373
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374 std::list<std::string> instances;
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375 context.GetIndex().GetChildInstances(instances, resource);
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376
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diff changeset
377 for (std::list<std::string>::const_iterator
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diff changeset
378 it = instances.begin(); it != instances.end(); ++it)
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diff changeset
379 {
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diff changeset
380 ServerContext::DicomCacheLocker locker(context, *it);
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381
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diff changeset
382 Json::Value dicomAsJson;
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0ddc5297a8ab centralization of default parameters for JSON/DicomMap conversions from DCMTK
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diff changeset
383 OrthancConfiguration::DefaultDicomDatasetToJson(dicomAsJson, locker.GetDicom());
2209
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diff changeset
384
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diff changeset
385 std::string s = dicomAsJson.toStyledString();
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diff changeset
386 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size());
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diff changeset
387
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diff changeset
388 context.GetIndex().ReconstructInstance(locker.GetDicom());
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diff changeset
389 }
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diff changeset
390 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
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391 }
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392 }