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annotate OrthancServer/Sources/ServerToolbox.cpp @ 4627:f7d5372b59b3 db-changes

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 20 Apr 2021 15:11:59 +0200
parents 95ffe3b6ef7c
children 66109d24d26e
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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 *
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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/DicomParsing/ParsedDicomFile.h"
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38 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h"
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39 #include "../../OrthancFramework/Sources/Logging.h"
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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
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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 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
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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 {
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160 throw OrthancException(ErrorCode_InternalError,
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161 "Cannot find an instance for " +
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162 std::string(EnumerationToString(level)) +
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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 {
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171 throw OrthancException(ErrorCode_InternalError,
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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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parents:
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202 }
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parents:
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203 }
2121
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204
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205
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206 void LoadIdentifiers(const DicomTag*& tags,
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207 size_t& size,
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208 ResourceType level)
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209 {
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210 switch (level)
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211 {
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212 case ResourceType_Patient:
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213 tags = PATIENT_IDENTIFIERS;
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214 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
2121
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215 break;
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216
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217 case ResourceType_Study:
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218 tags = STUDY_IDENTIFIERS;
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219 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
2121
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220 break;
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221
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222 case ResourceType_Series:
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223 tags = SERIES_IDENTIFIERS;
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224 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
2121
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225 break;
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226
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227 case ResourceType_Instance:
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228 tags = INSTANCE_IDENTIFIERS;
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229 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
2121
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230 break;
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231
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232 default:
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233 throw OrthancException(ErrorCode_ParameterOutOfRange);
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234 }
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235 }
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236
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237
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238 std::string NormalizeIdentifier(const std::string& value)
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239 {
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240 std::string t;
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241 t.reserve(value.size());
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242
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243 for (size_t i = 0; i < value.size(); i++)
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244 {
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245 if (value[i] == '%' ||
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246 value[i] == '_')
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247 {
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248 t.push_back(' '); // These characters might break wildcard queries in SQL
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249 }
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250 else if (isascii(value[i]) &&
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251 !iscntrl(value[i]) &&
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252 (!isspace(value[i]) || value[i] == ' '))
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253 {
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254 t.push_back(value[i]);
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255 }
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256 }
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257
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258 Toolbox::ToUpperCase(t);
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259
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260 return Toolbox::StripSpaces(t);
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261 }
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262
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263
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264 bool IsIdentifier(const DicomTag& tag,
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265 ResourceType level)
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266 {
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267 const DicomTag* tags;
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268 size_t size;
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269
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270 LoadIdentifiers(tags, size, level);
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271
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272 for (size_t i = 0; i < size; i++)
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273 {
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274 if (tag == tags[i])
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275 {
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276 return true;
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277 }
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278 }
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279
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280 return false;
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281 }
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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(
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299 *it, FileContentType_DicomAsJson, false /* no revision */, -1 /* dummy revision */);
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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 }