Mercurial > hg > orthanc
annotate OrthancServer/Sources/ServerToolbox.cpp @ 4718:88d16656b8b5
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 23 Jun 2021 19:00:07 +0200 |
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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) 2017-2021 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/DicomParsing/ParsedDicomFile.h" |
38 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h" | |
39 #include "../../OrthancFramework/Sources/Logging.h" | |
40 #include "../../OrthancFramework/Sources/OrthancException.h" | |
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41 #include "Database/IDatabaseWrapper.h" |
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42 #include "Database/ResourcesContent.h" |
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43 #include "OrthancConfiguration.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 |
2120 | 79 namespace ServerToolbox |
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80 { |
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81 bool FindOneChildInstance(int64_t& result, |
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82 IDatabaseWrapper::ITransaction& transaction, |
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83 int64_t resource, |
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84 ResourceType type) |
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85 { |
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86 for (;;) |
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87 { |
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88 if (type == ResourceType_Instance) |
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89 { |
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90 result = resource; |
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91 return true; |
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92 } |
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93 |
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94 std::list<int64_t> children; |
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95 transaction.GetChildrenInternalId(children, resource); |
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96 if (children.empty()) |
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97 { |
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98 return false; |
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99 } |
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100 |
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101 resource = children.front(); |
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102 type = GetChildResourceType(type); |
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103 } |
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104 } |
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105 |
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106 |
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107 void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction, |
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108 IStorageArea& storageArea, |
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109 ResourceType level) |
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110 { |
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111 // WARNING: The database should be locked with a transaction! |
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112 |
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113 // TODO: This function might consume much memory if level == |
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114 // ResourceType_Instance. To improve this, first download the |
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115 // list of studies, then remove the instances for each single |
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116 // study (check out OrthancRestApi::InvalidateTags for an |
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117 // example). Take this improvement into consideration for the |
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118 // next upgrade of the database schema. |
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119 |
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120 const char* plural = NULL; |
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121 |
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122 switch (level) |
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123 { |
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124 case ResourceType_Patient: |
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125 plural = "patients"; |
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126 break; |
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127 |
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128 case ResourceType_Study: |
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129 plural = "studies"; |
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130 break; |
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131 |
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132 case ResourceType_Series: |
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133 plural = "series"; |
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134 break; |
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135 |
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136 case ResourceType_Instance: |
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137 plural = "instances"; |
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138 break; |
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139 |
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140 default: |
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141 throw OrthancException(ErrorCode_InternalError); |
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142 } |
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143 |
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144 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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145 |
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146 std::list<std::string> resources; |
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147 transaction.GetAllPublicIds(resources, level); |
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148 |
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149 for (std::list<std::string>::const_iterator |
1847 | 150 it = resources.begin(); it != resources.end(); ++it) |
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151 { |
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152 // Locate the resource and one of its child instances |
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153 int64_t resource, instance; |
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154 ResourceType tmp; |
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155 |
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156 if (!transaction.LookupResource(resource, tmp, *it) || |
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157 tmp != level || |
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158 !FindOneChildInstance(instance, transaction, resource, level)) |
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159 { |
2955 | 160 throw OrthancException(ErrorCode_InternalError, |
161 "Cannot find an instance for " + | |
162 std::string(EnumerationToString(level)) + | |
163 " with identifier " + *it); | |
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164 } |
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165 |
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166 // Get the DICOM file attached to some instances in the resource |
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167 FileInfo attachment; |
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168 int64_t revision; |
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169 if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom)) |
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170 { |
2955 | 171 throw OrthancException(ErrorCode_InternalError, |
172 "Cannot retrieve the DICOM file associated with instance " + | |
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173 transaction.GetPublicId(instance)); |
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174 } |
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175 |
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176 try |
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177 { |
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178 // Read and parse the content of the DICOM file |
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179 StorageAccessor accessor(storageArea); |
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180 |
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181 std::string content; |
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182 accessor.Read(content, attachment); |
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183 |
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184 ParsedDicomFile dicom(content); |
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185 |
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186 // Update the tags of this resource |
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187 DicomMap dicomSummary; |
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188 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom); |
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189 |
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190 transaction.ClearMainDicomTags(resource); |
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191 |
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192 ResourcesContent tags(false /* prevent the setting of metadata */); |
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193 tags.AddResource(resource, level, dicomSummary); |
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194 transaction.SetResourcesContent(tags); |
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195 } |
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196 catch (OrthancException&) |
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197 { |
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198 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() |
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199 << " associated with instance " << transaction.GetPublicId(instance); |
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200 throw; |
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201 } |
213
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202 } |
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203 } |
2121 | 204 |
205 | |
206 void LoadIdentifiers(const DicomTag*& tags, | |
207 size_t& size, | |
208 ResourceType level) | |
209 { | |
210 switch (level) | |
211 { | |
212 case ResourceType_Patient: | |
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213 tags = PATIENT_IDENTIFIERS; |
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214 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 215 break; |
216 | |
217 case ResourceType_Study: | |
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218 tags = STUDY_IDENTIFIERS; |
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219 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 220 break; |
221 | |
222 case ResourceType_Series: | |
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223 tags = SERIES_IDENTIFIERS; |
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224 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 225 break; |
226 | |
227 case ResourceType_Instance: | |
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228 tags = INSTANCE_IDENTIFIERS; |
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229 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag); |
2121 | 230 break; |
231 | |
232 default: | |
233 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
234 } | |
235 } | |
236 | |
237 | |
238 std::string NormalizeIdentifier(const std::string& value) | |
239 { | |
240 std::string t; | |
241 t.reserve(value.size()); | |
242 | |
243 for (size_t i = 0; i < value.size(); i++) | |
244 { | |
245 if (value[i] == '%' || | |
246 value[i] == '_') | |
247 { | |
248 t.push_back(' '); // These characters might break wildcard queries in SQL | |
249 } | |
250 else if (isascii(value[i]) && | |
251 !iscntrl(value[i]) && | |
252 (!isspace(value[i]) || value[i] == ' ')) | |
253 { | |
254 t.push_back(value[i]); | |
255 } | |
256 } | |
257 | |
258 Toolbox::ToUpperCase(t); | |
259 | |
260 return Toolbox::StripSpaces(t); | |
261 } | |
262 | |
263 | |
264 bool IsIdentifier(const DicomTag& tag, | |
265 ResourceType level) | |
266 { | |
267 const DicomTag* tags; | |
268 size_t size; | |
269 | |
270 LoadIdentifiers(tags, size, level); | |
271 | |
272 for (size_t i = 0; i < size; i++) | |
273 { | |
274 if (tag == tags[i]) | |
275 { | |
276 return true; | |
277 } | |
278 } | |
279 | |
280 return false; | |
281 } | |
2209
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282 |
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283 |
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284 void ReconstructResource(ServerContext& context, |
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285 const std::string& resource) |
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286 { |
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287 LOG(WARNING) << "Reconstructing resource " << resource; |
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288 |
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289 std::list<std::string> instances; |
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290 context.GetIndex().GetChildInstances(instances, resource); |
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291 |
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292 for (std::list<std::string>::const_iterator |
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293 it = instances.begin(); it != instances.end(); ++it) |
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294 { |
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295 ServerContext::DicomCacheLocker locker(context, *it); |
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296 |
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297 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext" |
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298 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */, |
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299 -1 /* dummy revision */, "" /* dummy MD5 */); |
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300 |
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301 context.GetIndex().ReconstructInstance(locker.GetDicom()); |
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302 } |
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303 } |
213
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304 } |
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305 } |