Mercurial > hg > orthanc

annotate OrthancServer/Sources/ServerToolbox.cpp @ 4819:70d2a97ca8cb openssl-3.x

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integration mainline->openssl-3.x
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 25 Nov 2021 13:12:32 +0100
parents f0038043fb97 434843934307
children 2e71a08eea15
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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 * This program is distributed in the hope that it will be useful, but
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13 * WITHOUT ANY WARRANTY; without even the implied warranty of
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14 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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15 * General Public License for more details.
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16 *
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17 * You should have received a copy of the GNU General Public License
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18 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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19 **/
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21
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22 #include "PrecompiledHeadersServer.h"
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23 #include "ServerToolbox.h"
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24
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25 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h"
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26 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h"
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27 #include "../../OrthancFramework/Sources/FileStorage/StorageCache.h"
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28 #include "../../OrthancFramework/Sources/Logging.h"
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29 #include "../../OrthancFramework/Sources/OrthancException.h"
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30 #include "Database/IDatabaseWrapper.h"
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31 #include "Database/ResourcesContent.h"
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32 #include "OrthancConfiguration.h"
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33 #include "ServerContext.h"
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34
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35 #include <cassert>
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36
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37 namespace Orthanc
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38 {
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39 static const DicomTag PATIENT_IDENTIFIERS[] =
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40 {
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41 DICOM_TAG_PATIENT_ID,
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42 DICOM_TAG_PATIENT_NAME,
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43 DICOM_TAG_PATIENT_BIRTH_DATE
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44 };
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45
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46 static const DicomTag STUDY_IDENTIFIERS[] =
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47 {
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48 DICOM_TAG_PATIENT_ID,
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49 DICOM_TAG_PATIENT_NAME,
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50 DICOM_TAG_PATIENT_BIRTH_DATE,
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51 DICOM_TAG_STUDY_INSTANCE_UID,
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52 DICOM_TAG_ACCESSION_NUMBER,
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53 DICOM_TAG_STUDY_DESCRIPTION,
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54 DICOM_TAG_STUDY_DATE
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55 };
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56
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57 static const DicomTag SERIES_IDENTIFIERS[] =
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58 {
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59 DICOM_TAG_SERIES_INSTANCE_UID
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60 };
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61
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62 static const DicomTag INSTANCE_IDENTIFIERS[] =
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63 {
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64 DICOM_TAG_SOP_INSTANCE_UID
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65 };
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66
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67
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68 namespace ServerToolbox
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69 {
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70 bool FindOneChildInstance(int64_t& result,
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71 IDatabaseWrapper::ITransaction& transaction,
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72 int64_t resource,
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73 ResourceType type)
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74 {
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75 for (;;)
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76 {
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77 if (type == ResourceType_Instance)
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78 {
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79 result = resource;
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80 return true;
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81 }
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82
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83 std::list<int64_t> children;
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84 transaction.GetChildrenInternalId(children, resource);
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85 if (children.empty())
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86 {
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87 return false;
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88 }
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89
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90 resource = children.front();
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91 type = GetChildResourceType(type);
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92 }
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93 }
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94
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95
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96 void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction,
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97 IStorageArea& storageArea,
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98 ResourceType level)
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99 {
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100 // WARNING: The database should be locked with a transaction!
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101
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102 // TODO: This function might consume much memory if level ==
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103 // ResourceType_Instance. To improve this, first download the
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104 // list of studies, then remove the instances for each single
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105 // study (check out OrthancRestApi::InvalidateTags for an
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106 // example). Take this improvement into consideration for the
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107 // next upgrade of the database schema.
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108
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109 const char* plural = NULL;
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110
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111 switch (level)
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112 {
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113 case ResourceType_Patient:
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114 plural = "patients";
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115 break;
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116
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117 case ResourceType_Study:
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118 plural = "studies";
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119 break;
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120
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121 case ResourceType_Series:
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122 plural = "series";
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123 break;
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124
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125 case ResourceType_Instance:
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126 plural = "instances";
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127 break;
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128
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129 default:
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130 throw OrthancException(ErrorCode_InternalError);
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131 }
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132
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133 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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134
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135 std::list<std::string> resources;
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136 transaction.GetAllPublicIds(resources, level);
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137
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138 for (std::list<std::string>::const_iterator
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139 it = resources.begin(); it != resources.end(); ++it)
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140 {
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141 // Locate the resource and one of its child instances
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142 int64_t resource, instance;
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143 ResourceType tmp;
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144
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145 if (!transaction.LookupResource(resource, tmp, *it) ||
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146 tmp != level ||
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147 !FindOneChildInstance(instance, transaction, resource, level))
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148 {
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149 throw OrthancException(ErrorCode_InternalError,
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150 "Cannot find an instance for " +
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151 std::string(EnumerationToString(level)) +
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152 " with identifier " + *it);
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153 }
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154
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155 // Get the DICOM file attached to some instances in the resource
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156 FileInfo attachment;
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157 int64_t revision;
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158 if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom))
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159 {
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160 throw OrthancException(ErrorCode_InternalError,
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161 "Cannot retrieve the DICOM file associated with instance " +
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162 transaction.GetPublicId(instance));
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163 }
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164
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165 try
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166 {
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167 // Read and parse the content of the DICOM file
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168 StorageCache cache; // we create a temporary cache for this operation (required by the StorageAccessor)
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169 StorageAccessor accessor(storageArea, cache);
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170
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171 std::string content;
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172 accessor.Read(content, attachment);
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173
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174 ParsedDicomFile dicom(content);
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175
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176 // Update the tags of this resource
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177 DicomMap dicomSummary;
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178 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom);
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179
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180 transaction.ClearMainDicomTags(resource);
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181
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182 ResourcesContent tags(false /* prevent the setting of metadata */);
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183 tags.AddResource(resource, level, dicomSummary);
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184 transaction.SetResourcesContent(tags);
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185 }
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186 catch (OrthancException&)
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187 {
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188 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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189 << " associated with instance " << transaction.GetPublicId(instance);
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190 throw;
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191 }
213
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192 }
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193 }
2121
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194
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195
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196 void LoadIdentifiers(const DicomTag*& tags,
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197 size_t& size,
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198 ResourceType level)
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199 {
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200 switch (level)
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201 {
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202 case ResourceType_Patient:
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203 tags = PATIENT_IDENTIFIERS;
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204 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
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205 break;
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206
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207 case ResourceType_Study:
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208 tags = STUDY_IDENTIFIERS;
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209 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
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210 break;
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211
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212 case ResourceType_Series:
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213 tags = SERIES_IDENTIFIERS;
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214 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
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215 break;
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216
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217 case ResourceType_Instance:
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218 tags = INSTANCE_IDENTIFIERS;
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219 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
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220 break;
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221
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222 default:
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223 throw OrthancException(ErrorCode_ParameterOutOfRange);
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224 }
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225 }
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226
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227
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228 std::string NormalizeIdentifier(const std::string& value)
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229 {
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230 std::string t;
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231 t.reserve(value.size());
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232
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233 for (size_t i = 0; i < value.size(); i++)
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234 {
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235 if (value[i] == '%' ||
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236 value[i] == '_')
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237 {
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238 t.push_back(' '); // These characters might break wildcard queries in SQL
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239 }
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240 else if (isascii(value[i]) &&
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241 !iscntrl(value[i]) &&
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242 (!isspace(value[i]) || value[i] == ' '))
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243 {
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244 t.push_back(value[i]);
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245 }
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246 }
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247
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248 Toolbox::ToUpperCase(t);
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249
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250 return Toolbox::StripSpaces(t);
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251 }
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252
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253
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254 bool IsIdentifier(const DicomTag& tag,
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255 ResourceType level)
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256 {
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257 const DicomTag* tags;
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258 size_t size;
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259
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260 LoadIdentifiers(tags, size, level);
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261
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262 for (size_t i = 0; i < size; i++)
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263 {
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264 if (tag == tags[i])
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265 {
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266 return true;
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267 }
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268 }
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269
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270 return false;
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271 }
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272
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273
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274 void ReconstructResource(ServerContext& context,
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275 const std::string& resource)
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276 {
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277 LOG(WARNING) << "Reconstructing resource " << resource;
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278
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279 std::list<std::string> instances;
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280 context.GetIndex().GetChildInstances(instances, resource);
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281
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282 for (std::list<std::string>::const_iterator
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283 it = instances.begin(); it != instances.end(); ++it)
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284 {
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285 ServerContext::DicomCacheLocker locker(context, *it);
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286
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287 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext"
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288 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */,
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289 -1 /* dummy revision */, "" /* dummy MD5 */);
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290
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291 context.GetIndex().ReconstructInstance(locker.GetDicom());
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292 }
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293 }
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294 }
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295 }