Mercurial > hg > orthanc

annotate OrthancServer/Sources/ServerToolbox.cpp @ 4792:434843934307 storage-cache

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Added a StorageCache in the StorageAccessor
author Alain Mazy <am@osimis.io>
date Thu, 30 Sep 2021 12:14:19 +0200
parents 66109d24d26e
children 70d2a97ca8cb 7053502fbf97
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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/FileStorage/StorageCache.h"
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40 #include "../../OrthancFramework/Sources/Logging.h"
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41 #include "../../OrthancFramework/Sources/OrthancException.h"
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42 #include "Database/IDatabaseWrapper.h"
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43 #include "Database/ResourcesContent.h"
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44 #include "OrthancConfiguration.h"
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45 #include "ServerContext.h"
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46
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47 #include <cassert>
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48
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49 namespace Orthanc
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50 {
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51 static const DicomTag PATIENT_IDENTIFIERS[] =
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52 {
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53 DICOM_TAG_PATIENT_ID,
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54 DICOM_TAG_PATIENT_NAME,
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55 DICOM_TAG_PATIENT_BIRTH_DATE
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56 };
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57
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58 static const DicomTag STUDY_IDENTIFIERS[] =
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59 {
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60 DICOM_TAG_PATIENT_ID,
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61 DICOM_TAG_PATIENT_NAME,
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62 DICOM_TAG_PATIENT_BIRTH_DATE,
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63 DICOM_TAG_STUDY_INSTANCE_UID,
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64 DICOM_TAG_ACCESSION_NUMBER,
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65 DICOM_TAG_STUDY_DESCRIPTION,
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66 DICOM_TAG_STUDY_DATE
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67 };
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68
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69 static const DicomTag SERIES_IDENTIFIERS[] =
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70 {
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71 DICOM_TAG_SERIES_INSTANCE_UID
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72 };
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73
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74 static const DicomTag INSTANCE_IDENTIFIERS[] =
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75 {
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76 DICOM_TAG_SOP_INSTANCE_UID
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77 };
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78
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79
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80 namespace ServerToolbox
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81 {
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82 bool FindOneChildInstance(int64_t& result,
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83 IDatabaseWrapper::ITransaction& transaction,
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84 int64_t resource,
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85 ResourceType type)
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86 {
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87 for (;;)
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88 {
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89 if (type == ResourceType_Instance)
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90 {
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91 result = resource;
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92 return true;
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93 }
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94
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95 std::list<int64_t> children;
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96 transaction.GetChildrenInternalId(children, resource);
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97 if (children.empty())
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98 {
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99 return false;
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100 }
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101
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102 resource = children.front();
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103 type = GetChildResourceType(type);
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104 }
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105 }
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106
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107
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108 void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction,
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109 IStorageArea& storageArea,
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110 ResourceType level)
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111 {
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112 // WARNING: The database should be locked with a transaction!
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113
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114 // TODO: This function might consume much memory if level ==
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115 // ResourceType_Instance. To improve this, first download the
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116 // list of studies, then remove the instances for each single
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117 // study (check out OrthancRestApi::InvalidateTags for an
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118 // example). Take this improvement into consideration for the
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119 // next upgrade of the database schema.
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120
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121 const char* plural = NULL;
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122
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123 switch (level)
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124 {
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125 case ResourceType_Patient:
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126 plural = "patients";
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127 break;
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128
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129 case ResourceType_Study:
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130 plural = "studies";
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131 break;
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132
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133 case ResourceType_Series:
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134 plural = "series";
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135 break;
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136
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137 case ResourceType_Instance:
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138 plural = "instances";
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139 break;
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140
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141 default:
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142 throw OrthancException(ErrorCode_InternalError);
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143 }
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144
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145 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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146
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147 std::list<std::string> resources;
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148 transaction.GetAllPublicIds(resources, level);
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149
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150 for (std::list<std::string>::const_iterator
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151 it = resources.begin(); it != resources.end(); ++it)
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152 {
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153 // Locate the resource and one of its child instances
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154 int64_t resource, instance;
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155 ResourceType tmp;
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156
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157 if (!transaction.LookupResource(resource, tmp, *it) ||
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158 tmp != level ||
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159 !FindOneChildInstance(instance, transaction, resource, level))
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160 {
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161 throw OrthancException(ErrorCode_InternalError,
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162 "Cannot find an instance for " +
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163 std::string(EnumerationToString(level)) +
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164 " with identifier " + *it);
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165 }
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166
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167 // Get the DICOM file attached to some instances in the resource
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168 FileInfo attachment;
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169 int64_t revision;
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170 if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom))
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171 {
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172 throw OrthancException(ErrorCode_InternalError,
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173 "Cannot retrieve the DICOM file associated with instance " +
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174 transaction.GetPublicId(instance));
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175 }
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176
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177 try
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178 {
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179 // Read and parse the content of the DICOM file
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180 StorageCache cache; // we create a temporary cache for this operation (required by the StorageAccessor)
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181 StorageAccessor accessor(storageArea, cache);
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182
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183 std::string content;
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184 accessor.Read(content, attachment);
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185
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186 ParsedDicomFile dicom(content);
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187
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188 // Update the tags of this resource
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189 DicomMap dicomSummary;
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190 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom);
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191
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192 transaction.ClearMainDicomTags(resource);
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683d572424b6 IDatabaseWrapper::SetResourcesContent
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193
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194 ResourcesContent tags(false /* prevent the setting of metadata */);
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195 tags.AddResource(resource, level, dicomSummary);
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196 transaction.SetResourcesContent(tags);
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197 }
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198 catch (OrthancException&)
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199 {
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200 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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201 << " associated with instance " << transaction.GetPublicId(instance);
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202 throw;
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203 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
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204 }
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parents:
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205 }
2121
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206
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207
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208 void LoadIdentifiers(const DicomTag*& tags,
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209 size_t& size,
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210 ResourceType level)
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211 {
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212 switch (level)
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213 {
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214 case ResourceType_Patient:
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215 tags = PATIENT_IDENTIFIERS;
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216 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
2121
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217 break;
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218
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219 case ResourceType_Study:
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220 tags = STUDY_IDENTIFIERS;
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221 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
2121
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diff changeset
222 break;
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223
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diff changeset
224 case ResourceType_Series:
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225 tags = SERIES_IDENTIFIERS;
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226 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
2121
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227 break;
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228
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229 case ResourceType_Instance:
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230 tags = INSTANCE_IDENTIFIERS;
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diff changeset
231 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
2121
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diff changeset
232 break;
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233
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234 default:
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235 throw OrthancException(ErrorCode_ParameterOutOfRange);
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236 }
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237 }
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238
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239
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240 std::string NormalizeIdentifier(const std::string& value)
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241 {
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242 std::string t;
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243 t.reserve(value.size());
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244
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diff changeset
245 for (size_t i = 0; i < value.size(); i++)
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246 {
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247 if (value[i] == '%' ||
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248 value[i] == '_')
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249 {
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250 t.push_back(' '); // These characters might break wildcard queries in SQL
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251 }
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252 else if (isascii(value[i]) &&
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253 !iscntrl(value[i]) &&
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254 (!isspace(value[i]) || value[i] == ' '))
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255 {
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diff changeset
256 t.push_back(value[i]);
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257 }
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diff changeset
258 }
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diff changeset
259
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diff changeset
260 Toolbox::ToUpperCase(t);
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261
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262 return Toolbox::StripSpaces(t);
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diff changeset
263 }
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diff changeset
264
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diff changeset
265
7e8889bc95c6 refactoring
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266 bool IsIdentifier(const DicomTag& tag,
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267 ResourceType level)
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268 {
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269 const DicomTag* tags;
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270 size_t size;
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271
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272 LoadIdentifiers(tags, size, level);
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273
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274 for (size_t i = 0; i < size; i++)
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275 {
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276 if (tag == tags[i])
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277 {
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278 return true;
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279 }
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280 }
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281
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282 return false;
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283 }
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284
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285
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286 void ReconstructResource(ServerContext& context,
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287 const std::string& resource)
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288 {
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289 LOG(WARNING) << "Reconstructing resource " << resource;
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290
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291 std::list<std::string> instances;
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292 context.GetIndex().GetChildInstances(instances, resource);
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293
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294 for (std::list<std::string>::const_iterator
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295 it = instances.begin(); it != instances.end(); ++it)
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296 {
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297 ServerContext::DicomCacheLocker locker(context, *it);
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298
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299 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext"
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300 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */,
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301 -1 /* dummy revision */, "" /* dummy MD5 */);
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302
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303 context.GetIndex().ReconstructInstance(locker.GetDicom());
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304 }
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305 }
213
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306 }
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307 }