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annotate OrthancServer/Sources/ServerToolbox.cpp @ 4097:99e2054d1e8d

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fix unit tests for orthanc framework
author Sebastien Jodogne <s.jodogne@gmail.com>
date Wed, 01 Jul 2020 11:15:29 +0200
parents 9214e3a7b0a2
children a4f28efdfccf
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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 "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 static void StoreMainDicomTagsInternal(ResourcesContent& target,
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80 int64_t resource,
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81 const DicomMap& tags)
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82 {
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83 DicomArray flattened(tags);
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84
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85 for (size_t i = 0; i < flattened.GetSize(); i++)
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86 {
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87 const DicomElement& element = flattened.GetElement(i);
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88 const DicomTag& tag = element.GetTag();
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89 const DicomValue& value = element.GetValue();
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90 if (!value.IsNull() &&
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91 !value.IsBinary())
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92 {
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93 target.AddMainDicomTag(resource, tag, element.GetValue().GetContent());
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94 }
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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 static void StoreIdentifiers(ResourcesContent& target,
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100 int64_t resource,
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101 ResourceType level,
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102 const DicomMap& map)
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103 {
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104 const DicomTag* tags;
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105 size_t size;
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106
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107 ServerToolbox::LoadIdentifiers(tags, size, level);
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108
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109 for (size_t i = 0; i < size; i++)
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110 {
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111 // The identifiers tags are a subset of the main DICOM tags
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112 assert(DicomMap::IsMainDicomTag(tags[i]));
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113
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114 const DicomValue* value = map.TestAndGetValue(tags[i]);
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115 if (value != NULL &&
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116 !value->IsNull() &&
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117 !value->IsBinary())
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118 {
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119 std::string s = ServerToolbox::NormalizeIdentifier(value->GetContent());
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120 target.AddIdentifierTag(resource, tags[i], s);
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121 }
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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 void ResourcesContent::AddResource(int64_t resource,
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127 ResourceType level,
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128 const DicomMap& dicomSummary)
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129 {
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130 StoreIdentifiers(*this, resource, level, dicomSummary);
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131
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132 DicomMap tags;
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133
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134 switch (level)
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135 {
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136 case ResourceType_Patient:
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137 dicomSummary.ExtractPatientInformation(tags);
683d572424b6 IDatabaseWrapper::SetResourcesContent
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138 break;
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139
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140 case ResourceType_Study:
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141 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
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142 dicomSummary.ExtractPatientInformation(tags);
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143 StoreMainDicomTagsInternal(*this, resource, tags);
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144
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145 dicomSummary.ExtractStudyInformation(tags);
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146 break;
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147
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148 case ResourceType_Series:
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149 dicomSummary.ExtractSeriesInformation(tags);
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150 break;
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151
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152 case ResourceType_Instance:
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153 dicomSummary.ExtractInstanceInformation(tags);
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154 break;
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155
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156 default:
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157 throw OrthancException(ErrorCode_InternalError);
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158 }
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159
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160 StoreMainDicomTagsInternal(*this, resource, tags);
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161 }
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162
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163
2120
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164 namespace ServerToolbox
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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165 {
1668
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166 bool FindOneChildInstance(int64_t& result,
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167 IDatabaseWrapper& database,
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168 int64_t resource,
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169 ResourceType type)
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170 {
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171 for (;;)
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172 {
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173 if (type == ResourceType_Instance)
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174 {
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175 result = resource;
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176 return true;
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177 }
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178
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179 std::list<int64_t> children;
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180 database.GetChildrenInternalId(children, resource);
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181 if (children.empty())
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182 {
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183 return false;
de1413733c97 reconstructing main dicom tags
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184 }
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185
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186 resource = children.front();
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187 type = GetChildResourceType(type);
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188 }
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189 }
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diff changeset
190
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191
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192 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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193 IStorageArea& storageArea,
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194 ResourceType level)
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195 {
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196 // WARNING: The database should be locked with a transaction!
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197
2129
0c09d1af22f3 "/tools/invalidate-tags" to invalidate the JSON summary of all the DICOM files
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198 // TODO: This function might consume much memory if level ==
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199 // ResourceType_Instance. To improve this, first download the
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200 // list of studies, then remove the instances for each single
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201 // study (check out OrthancRestApi::InvalidateTags for an
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202 // 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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203 // next upgrade of the database schema.
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204
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a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
205 const char* plural = NULL;
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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206
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
207 switch (level)
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
208 {
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
209 case ResourceType_Patient:
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210 plural = "patients";
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
211 break;
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
212
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
213 case ResourceType_Study:
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
214 plural = "studies";
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
215 break;
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
216
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
217 case ResourceType_Series:
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
218 plural = "series";
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
219 break;
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diff changeset
220
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
221 case ResourceType_Instance:
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diff changeset
222 plural = "instances";
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diff changeset
223 break;
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
224
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
225 default:
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
226 throw OrthancException(ErrorCode_InternalError);
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
227 }
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
228
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
229 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
a412ad57f0f9 refactoring of sample plugins, OrthancPluginReconstructMainDicomTags
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diff changeset
230
1668
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diff changeset
231 std::list<std::string> resources;
de1413733c97 reconstructing main dicom tags
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diff changeset
232 database.GetAllPublicIds(resources, level);
de1413733c97 reconstructing main dicom tags
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diff changeset
233
de1413733c97 reconstructing main dicom tags
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diff changeset
234 for (std::list<std::string>::const_iterator
1847
559956d5ceb2 cppcheck
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parents: 1747
diff changeset
235 it = resources.begin(); it != resources.end(); ++it)
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
236 {
de1413733c97 reconstructing main dicom tags
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diff changeset
237 // Locate the resource and one of its child instances
de1413733c97 reconstructing main dicom tags
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diff changeset
238 int64_t resource, instance;
de1413733c97 reconstructing main dicom tags
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diff changeset
239 ResourceType tmp;
de1413733c97 reconstructing main dicom tags
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diff changeset
240
de1413733c97 reconstructing main dicom tags
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diff changeset
241 if (!database.LookupResource(resource, tmp, *it) ||
de1413733c97 reconstructing main dicom tags
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diff changeset
242 tmp != level ||
de1413733c97 reconstructing main dicom tags
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diff changeset
243 !FindOneChildInstance(instance, database, resource, level))
de1413733c97 reconstructing main dicom tags
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diff changeset
244 {
2955
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diff changeset
245 throw OrthancException(ErrorCode_InternalError,
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diff changeset
246 "Cannot find an instance for " +
Sebastien Jodogne <s.jodogne@gmail.com>
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diff changeset
247 std::string(EnumerationToString(level)) +
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248 " with identifier " + *it);
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
249 }
de1413733c97 reconstructing main dicom tags
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diff changeset
250
de1413733c97 reconstructing main dicom tags
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diff changeset
251 // Get the DICOM file attached to some instances in the resource
de1413733c97 reconstructing main dicom tags
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diff changeset
252 FileInfo attachment;
de1413733c97 reconstructing main dicom tags
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diff changeset
253 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
de1413733c97 reconstructing main dicom tags
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diff changeset
254 {
2955
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diff changeset
255 throw OrthancException(ErrorCode_InternalError,
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diff changeset
256 "Cannot retrieve the DICOM file associated with instance " +
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diff changeset
257 database.GetPublicId(instance));
1668
de1413733c97 reconstructing main dicom tags
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diff changeset
258 }
de1413733c97 reconstructing main dicom tags
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diff changeset
259
1870
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
260 try
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
261 {
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
262 // Read and parse the content of the DICOM file
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diff changeset
263 StorageAccessor accessor(storageArea);
1673
0bbcfd9695e5 UpgradeDatabase in the sample plugin
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diff changeset
264
1870
a6c431193c79 Improved logging information if upgrade fails
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diff changeset
265 std::string content;
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diff changeset
266 accessor.Read(content, attachment);
a6c431193c79 Improved logging information if upgrade fails
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parents: 1860
diff changeset
267
a6c431193c79 Improved logging information if upgrade fails
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268 ParsedDicomFile dicom(content);
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269
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270 // Update the tags of this resource
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271 DicomMap dicomSummary;
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272 dicom.ExtractDicomSummary(dicomSummary);
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273
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274 database.ClearMainDicomTags(resource);
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275
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276 ResourcesContent tags;
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277 tags.AddResource(resource, level, dicomSummary);
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278 database.SetResourcesContent(tags);
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279 }
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280 catch (OrthancException&)
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281 {
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282 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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283 << " associated with instance " << database.GetPublicId(instance);
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284 throw;
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285 }
213
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286 }
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287 }
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288
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289
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290 void LoadIdentifiers(const DicomTag*& tags,
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291 size_t& size,
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292 ResourceType level)
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293 {
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294 switch (level)
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295 {
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296 case ResourceType_Patient:
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297 tags = PATIENT_IDENTIFIERS;
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298 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
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299 break;
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300
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301 case ResourceType_Study:
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302 tags = STUDY_IDENTIFIERS;
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303 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
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304 break;
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305
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306 case ResourceType_Series:
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307 tags = SERIES_IDENTIFIERS;
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308 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
2121
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309 break;
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310
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311 case ResourceType_Instance:
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312 tags = INSTANCE_IDENTIFIERS;
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313 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
2121
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314 break;
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315
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316 default:
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317 throw OrthancException(ErrorCode_ParameterOutOfRange);
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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 std::string NormalizeIdentifier(const std::string& value)
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323 {
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324 std::string t;
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325 t.reserve(value.size());
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326
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327 for (size_t i = 0; i < value.size(); i++)
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328 {
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329 if (value[i] == '%' ||
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330 value[i] == '_')
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331 {
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332 t.push_back(' '); // These characters might break wildcard queries in SQL
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333 }
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334 else if (isascii(value[i]) &&
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335 !iscntrl(value[i]) &&
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336 (!isspace(value[i]) || value[i] == ' '))
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337 {
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338 t.push_back(value[i]);
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339 }
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340 }
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341
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342 Toolbox::ToUpperCase(t);
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343
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344 return Toolbox::StripSpaces(t);
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345 }
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346
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347
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348 bool IsIdentifier(const DicomTag& tag,
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349 ResourceType level)
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350 {
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351 const DicomTag* tags;
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352 size_t size;
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diff changeset
353
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diff changeset
354 LoadIdentifiers(tags, size, level);
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355
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diff changeset
356 for (size_t i = 0; i < size; i++)
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diff changeset
357 {
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diff changeset
358 if (tag == tags[i])
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diff changeset
359 {
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parents: 2120
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360 return true;
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parents: 2120
diff changeset
361 }
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diff changeset
362 }
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parents: 2120
diff changeset
363
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diff changeset
364 return false;
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parents: 2120
diff changeset
365 }
2209
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diff changeset
366
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
367
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
368 void ReconstructResource(ServerContext& context,
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
369 const std::string& resource)
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diff changeset
370 {
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parents: 2129
diff changeset
371 LOG(WARNING) << "Reconstructing resource " << resource;
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parents: 2129
diff changeset
372
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
373 std::list<std::string> instances;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
374 context.GetIndex().GetChildInstances(instances, resource);
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parents: 2129
diff changeset
375
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
376 for (std::list<std::string>::const_iterator
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
377 it = instances.begin(); it != instances.end(); ++it)
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parents: 2129
diff changeset
378 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
379 ServerContext::DicomCacheLocker locker(context, *it);
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parents: 2129
diff changeset
380
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diff changeset
381 Json::Value dicomAsJson;
2409
e4045b3c9772 ignore-length argument if retrieving DICOM tags
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parents: 2380
diff changeset
382 locker.GetDicom().DatasetToJson(dicomAsJson);
2209
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diff changeset
383
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
384 std::string s = dicomAsJson.toStyledString();
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
385 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size());
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
386
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
387 context.GetIndex().ReconstructInstance(locker.GetDicom());
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parents: 2129
diff changeset
388 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
389 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
diff changeset
390 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
diff changeset
391 }