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annotate OrthancServer/Sources/ServerToolbox.cpp @ 4831:7053502fbf97

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added copyright UCLouvain
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 25 Nov 2021 19:01:11 +0100
parents 434843934307
children 2e71a08eea15 43e613a7756b
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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) 2017-2021 Osimis S.A., Belgium
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6 * Copyright (C) 2021-2021 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU General Public License as
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10 * published by the Free Software Foundation, either version 3 of the
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11 * License, or (at your option) any later version.
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12 *
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13 * In addition, as a special exception, the copyright holders of this
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14 * program give permission to link the code of its release with the
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15 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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16 * that use the same license as the "OpenSSL" library), and distribute
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17 * the linked executables. You must obey the GNU General Public License
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18 * in all respects for all of the code used other than "OpenSSL". If you
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19 * modify file(s) with this exception, you may extend this exception to
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20 * your version of the file(s), but you are not obligated to do so. If
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21 * you do not wish to do so, delete this exception statement from your
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22 * version. If you delete this exception statement from all source files
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23 * in the program, then also delete it here.
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24 *
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25 * This program is distributed in the hope that it will be useful, but
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26 * WITHOUT ANY WARRANTY; without even the implied warranty of
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27 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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28 * General Public License for more details.
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29 *
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30 * You should have received a copy of the GNU General Public License
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31 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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32 **/
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34
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35 #include "PrecompiledHeadersServer.h"
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36 #include "ServerToolbox.h"
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37
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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/FileStorage/StorageCache.h"
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41 #include "../../OrthancFramework/Sources/Logging.h"
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42 #include "../../OrthancFramework/Sources/OrthancException.h"
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43 #include "Database/IDatabaseWrapper.h"
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44 #include "Database/ResourcesContent.h"
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45 #include "OrthancConfiguration.h"
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46 #include "ServerContext.h"
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47
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48 #include <cassert>
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49
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50 namespace Orthanc
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51 {
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52 static const DicomTag PATIENT_IDENTIFIERS[] =
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53 {
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54 DICOM_TAG_PATIENT_ID,
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55 DICOM_TAG_PATIENT_NAME,
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56 DICOM_TAG_PATIENT_BIRTH_DATE
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57 };
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58
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59 static const DicomTag STUDY_IDENTIFIERS[] =
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60 {
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61 DICOM_TAG_PATIENT_ID,
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62 DICOM_TAG_PATIENT_NAME,
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63 DICOM_TAG_PATIENT_BIRTH_DATE,
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64 DICOM_TAG_STUDY_INSTANCE_UID,
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65 DICOM_TAG_ACCESSION_NUMBER,
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66 DICOM_TAG_STUDY_DESCRIPTION,
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67 DICOM_TAG_STUDY_DATE
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68 };
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69
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70 static const DicomTag SERIES_IDENTIFIERS[] =
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71 {
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72 DICOM_TAG_SERIES_INSTANCE_UID
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73 };
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74
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75 static const DicomTag INSTANCE_IDENTIFIERS[] =
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76 {
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77 DICOM_TAG_SOP_INSTANCE_UID
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78 };
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79
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80
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81 namespace ServerToolbox
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82 {
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83 bool FindOneChildInstance(int64_t& result,
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84 IDatabaseWrapper::ITransaction& transaction,
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85 int64_t resource,
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86 ResourceType type)
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87 {
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88 for (;;)
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89 {
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90 if (type == ResourceType_Instance)
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91 {
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92 result = resource;
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93 return true;
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94 }
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95
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96 std::list<int64_t> children;
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97 transaction.GetChildrenInternalId(children, resource);
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98 if (children.empty())
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99 {
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100 return false;
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101 }
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102
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103 resource = children.front();
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104 type = GetChildResourceType(type);
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105 }
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106 }
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107
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108
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109 void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction,
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110 IStorageArea& storageArea,
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111 ResourceType level)
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112 {
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113 // WARNING: The database should be locked with a transaction!
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114
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115 // TODO: This function might consume much memory if level ==
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116 // ResourceType_Instance. To improve this, first download the
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117 // list of studies, then remove the instances for each single
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118 // study (check out OrthancRestApi::InvalidateTags for an
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119 // example). Take this improvement into consideration for the
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120 // next upgrade of the database schema.
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121
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122 const char* plural = NULL;
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123
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124 switch (level)
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125 {
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126 case ResourceType_Patient:
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127 plural = "patients";
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128 break;
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129
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130 case ResourceType_Study:
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131 plural = "studies";
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132 break;
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133
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134 case ResourceType_Series:
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135 plural = "series";
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136 break;
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137
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138 case ResourceType_Instance:
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139 plural = "instances";
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140 break;
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141
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142 default:
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143 throw OrthancException(ErrorCode_InternalError);
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144 }
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145
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146 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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147
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148 std::list<std::string> resources;
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149 transaction.GetAllPublicIds(resources, level);
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150
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151 for (std::list<std::string>::const_iterator
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152 it = resources.begin(); it != resources.end(); ++it)
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153 {
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154 // Locate the resource and one of its child instances
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155 int64_t resource, instance;
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156 ResourceType tmp;
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157
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158 if (!transaction.LookupResource(resource, tmp, *it) ||
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159 tmp != level ||
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160 !FindOneChildInstance(instance, transaction, resource, level))
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161 {
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162 throw OrthancException(ErrorCode_InternalError,
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163 "Cannot find an instance for " +
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164 std::string(EnumerationToString(level)) +
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165 " with identifier " + *it);
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166 }
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167
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168 // Get the DICOM file attached to some instances in the resource
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169 FileInfo attachment;
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170 int64_t revision;
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171 if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom))
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172 {
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173 throw OrthancException(ErrorCode_InternalError,
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174 "Cannot retrieve the DICOM file associated with instance " +
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175 transaction.GetPublicId(instance));
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176 }
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177
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178 try
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179 {
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180 // Read and parse the content of the DICOM file
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181 StorageCache cache; // we create a temporary cache for this operation (required by the StorageAccessor)
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182 StorageAccessor accessor(storageArea, cache);
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183
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184 std::string content;
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185 accessor.Read(content, attachment);
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186
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187 ParsedDicomFile dicom(content);
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188
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189 // Update the tags of this resource
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190 DicomMap dicomSummary;
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191 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom);
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192
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193 transaction.ClearMainDicomTags(resource);
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194
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195 ResourcesContent tags(false /* prevent the setting of metadata */);
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196 tags.AddResource(resource, level, dicomSummary);
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197 transaction.SetResourcesContent(tags);
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198 }
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199 catch (OrthancException&)
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200 {
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201 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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202 << " associated with instance " << transaction.GetPublicId(instance);
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203 throw;
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204 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
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205 }
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parents:
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206 }
2121
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207
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208
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209 void LoadIdentifiers(const DicomTag*& tags,
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210 size_t& size,
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211 ResourceType level)
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212 {
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213 switch (level)
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214 {
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215 case ResourceType_Patient:
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216 tags = PATIENT_IDENTIFIERS;
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217 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
2121
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218 break;
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219
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220 case ResourceType_Study:
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221 tags = STUDY_IDENTIFIERS;
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222 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
2121
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223 break;
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224
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225 case ResourceType_Series:
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226 tags = SERIES_IDENTIFIERS;
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diff changeset
227 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
2121
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228 break;
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229
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230 case ResourceType_Instance:
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231 tags = INSTANCE_IDENTIFIERS;
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diff changeset
232 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
2121
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233 break;
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234
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235 default:
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236 throw OrthancException(ErrorCode_ParameterOutOfRange);
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237 }
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diff changeset
238 }
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diff changeset
239
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240
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241 std::string NormalizeIdentifier(const std::string& value)
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242 {
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diff changeset
243 std::string t;
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244 t.reserve(value.size());
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245
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diff changeset
246 for (size_t i = 0; i < value.size(); i++)
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247 {
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248 if (value[i] == '%' ||
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249 value[i] == '_')
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250 {
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251 t.push_back(' '); // These characters might break wildcard queries in SQL
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252 }
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253 else if (isascii(value[i]) &&
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254 !iscntrl(value[i]) &&
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255 (!isspace(value[i]) || value[i] == ' '))
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diff changeset
256 {
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diff changeset
257 t.push_back(value[i]);
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diff changeset
258 }
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diff changeset
259 }
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diff changeset
260
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diff changeset
261 Toolbox::ToUpperCase(t);
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262
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263 return Toolbox::StripSpaces(t);
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diff changeset
264 }
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diff changeset
265
7e8889bc95c6 refactoring
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parents: 2120
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266
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267 bool IsIdentifier(const DicomTag& tag,
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268 ResourceType level)
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269 {
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270 const DicomTag* tags;
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271 size_t size;
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272
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273 LoadIdentifiers(tags, size, level);
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274
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275 for (size_t i = 0; i < size; i++)
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276 {
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277 if (tag == tags[i])
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278 {
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279 return true;
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280 }
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281 }
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282
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283 return false;
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284 }
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285
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286
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287 void ReconstructResource(ServerContext& context,
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288 const std::string& resource)
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289 {
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290 LOG(WARNING) << "Reconstructing resource " << resource;
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291
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292 std::list<std::string> instances;
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293 context.GetIndex().GetChildInstances(instances, resource);
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294
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295 for (std::list<std::string>::const_iterator
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296 it = instances.begin(); it != instances.end(); ++it)
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297 {
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298 ServerContext::DicomCacheLocker locker(context, *it);
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299
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300 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext"
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301 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */,
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302 -1 /* dummy revision */, "" /* dummy MD5 */);
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303
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304 context.GetIndex().ReconstructInstance(locker.GetDicom());
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305 }
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306 }
213
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307 }
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308 }