Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerToolbox.cpp @ 4126:aad700c38719
merge
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Tue, 07 Jul 2020 20:27:50 +0200 |
parents | 9214e3a7b0a2 |
children | a4f28efdfccf |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
1900 | 3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
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5 * Copyright (C) 2017-2020 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 |
4045 | 37 #include "../../OrthancFramework/Sources/DicomFormat/DicomArray.h" |
38 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h" | |
39 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h" | |
40 #include "../../OrthancFramework/Sources/Logging.h" | |
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 |
234 | 46 #include <cassert> |
47 | |
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48 namespace Orthanc |
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49 { |
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50 static const DicomTag PATIENT_IDENTIFIERS[] = |
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51 { |
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52 DICOM_TAG_PATIENT_ID, |
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53 DICOM_TAG_PATIENT_NAME, |
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54 DICOM_TAG_PATIENT_BIRTH_DATE |
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55 }; |
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56 |
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57 static const DicomTag STUDY_IDENTIFIERS[] = |
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58 { |
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59 DICOM_TAG_PATIENT_ID, |
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60 DICOM_TAG_PATIENT_NAME, |
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61 DICOM_TAG_PATIENT_BIRTH_DATE, |
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62 DICOM_TAG_STUDY_INSTANCE_UID, |
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63 DICOM_TAG_ACCESSION_NUMBER, |
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64 DICOM_TAG_STUDY_DESCRIPTION, |
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65 DICOM_TAG_STUDY_DATE |
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66 }; |
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67 |
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68 static const DicomTag SERIES_IDENTIFIERS[] = |
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69 { |
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70 DICOM_TAG_SERIES_INSTANCE_UID |
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71 }; |
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72 |
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73 static const DicomTag INSTANCE_IDENTIFIERS[] = |
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74 { |
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75 DICOM_TAG_SOP_INSTANCE_UID |
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76 }; |
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77 |
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78 |
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79 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); |
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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 | 164 namespace ServerToolbox |
213
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165 { |
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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; |
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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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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 |
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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 |
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203 // next upgrade of the database schema. |
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204 |
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205 const char* plural = NULL; |
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206 |
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207 switch (level) |
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208 { |
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209 case ResourceType_Patient: |
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210 plural = "patients"; |
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211 break; |
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212 |
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213 case ResourceType_Study: |
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214 plural = "studies"; |
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215 break; |
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216 |
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217 case ResourceType_Series: |
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218 plural = "series"; |
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219 break; |
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220 |
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221 case ResourceType_Instance: |
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222 plural = "instances"; |
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223 break; |
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224 |
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225 default: |
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226 throw OrthancException(ErrorCode_InternalError); |
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227 } |
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228 |
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229 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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230 |
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231 std::list<std::string> resources; |
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232 database.GetAllPublicIds(resources, level); |
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233 |
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234 for (std::list<std::string>::const_iterator |
1847 | 235 it = resources.begin(); it != resources.end(); ++it) |
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236 { |
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237 // Locate the resource and one of its child instances |
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238 int64_t resource, instance; |
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239 ResourceType tmp; |
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240 |
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241 if (!database.LookupResource(resource, tmp, *it) || |
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242 tmp != level || |
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243 !FindOneChildInstance(instance, database, resource, level)) |
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244 { |
2955 | 245 throw OrthancException(ErrorCode_InternalError, |
246 "Cannot find an instance for " + | |
247 std::string(EnumerationToString(level)) + | |
248 " with identifier " + *it); | |
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249 } |
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250 |
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251 // Get the DICOM file attached to some instances in the resource |
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252 FileInfo attachment; |
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253 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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254 { |
2955 | 255 throw OrthancException(ErrorCode_InternalError, |
256 "Cannot retrieve the DICOM file associated with instance " + | |
257 database.GetPublicId(instance)); | |
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258 } |
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259 |
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260 try |
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261 { |
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262 // Read and parse the content of the DICOM file |
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263 StorageAccessor accessor(storageArea); |
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264 |
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265 std::string content; |
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266 accessor.Read(content, attachment); |
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267 |
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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 } |
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286 } |
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287 } |
2121 | 288 |
289 | |
290 void LoadIdentifiers(const DicomTag*& tags, | |
291 size_t& size, | |
292 ResourceType level) | |
293 { | |
294 switch (level) | |
295 { | |
296 case ResourceType_Patient: | |
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297 tags = PATIENT_IDENTIFIERS; |
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298 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 299 break; |
300 | |
301 case ResourceType_Study: | |
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302 tags = STUDY_IDENTIFIERS; |
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303 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 304 break; |
305 | |
306 case ResourceType_Series: | |
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307 tags = SERIES_IDENTIFIERS; |
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308 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 309 break; |
310 | |
311 case ResourceType_Instance: | |
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312 tags = INSTANCE_IDENTIFIERS; |
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313 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 314 break; |
315 | |
316 default: | |
317 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
318 } | |
319 } | |
320 | |
321 | |
322 std::string NormalizeIdentifier(const std::string& value) | |
323 { | |
324 std::string t; | |
325 t.reserve(value.size()); | |
326 | |
327 for (size_t i = 0; i < value.size(); i++) | |
328 { | |
329 if (value[i] == '%' || | |
330 value[i] == '_') | |
331 { | |
332 t.push_back(' '); // These characters might break wildcard queries in SQL | |
333 } | |
334 else if (isascii(value[i]) && | |
335 !iscntrl(value[i]) && | |
336 (!isspace(value[i]) || value[i] == ' ')) | |
337 { | |
338 t.push_back(value[i]); | |
339 } | |
340 } | |
341 | |
342 Toolbox::ToUpperCase(t); | |
343 | |
344 return Toolbox::StripSpaces(t); | |
345 } | |
346 | |
347 | |
348 bool IsIdentifier(const DicomTag& tag, | |
349 ResourceType level) | |
350 { | |
351 const DicomTag* tags; | |
352 size_t size; | |
353 | |
354 LoadIdentifiers(tags, size, level); | |
355 | |
356 for (size_t i = 0; i < size; i++) | |
357 { | |
358 if (tag == tags[i]) | |
359 { | |
360 return true; | |
361 } | |
362 } | |
363 | |
364 return false; | |
365 } | |
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366 |
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367 |
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368 void ReconstructResource(ServerContext& context, |
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369 const std::string& resource) |
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370 { |
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371 LOG(WARNING) << "Reconstructing resource " << resource; |
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372 |
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373 std::list<std::string> instances; |
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374 context.GetIndex().GetChildInstances(instances, resource); |
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375 |
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376 for (std::list<std::string>::const_iterator |
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377 it = instances.begin(); it != instances.end(); ++it) |
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378 { |
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379 ServerContext::DicomCacheLocker locker(context, *it); |
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380 |
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381 Json::Value dicomAsJson; |
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382 locker.GetDicom().DatasetToJson(dicomAsJson); |
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383 |
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384 std::string s = dicomAsJson.toStyledString(); |
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385 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size()); |
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386 |
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387 context.GetIndex().ReconstructInstance(locker.GetDicom()); |
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388 } |
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389 } |
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390 } |
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391 } |