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annotate OrthancServer/Sources/ServerToolbox.cpp @ 4741:a6b7c29f5118 openssl-3.x

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compiler warning about openssl license
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 06 Jul 2021 09:52:15 +0200
parents f0038043fb97
children 70d2a97ca8cb
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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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20
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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/Logging.h"
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28 #include "../../OrthancFramework/Sources/OrthancException.h"
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29 #include "Database/IDatabaseWrapper.h"
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30 #include "Database/ResourcesContent.h"
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31 #include "OrthancConfiguration.h"
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32 #include "ServerContext.h"
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33
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34 #include <cassert>
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35
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36 namespace Orthanc
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37 {
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38 static const DicomTag PATIENT_IDENTIFIERS[] =
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39 {
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40 DICOM_TAG_PATIENT_ID,
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41 DICOM_TAG_PATIENT_NAME,
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42 DICOM_TAG_PATIENT_BIRTH_DATE
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43 };
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44
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45 static const DicomTag STUDY_IDENTIFIERS[] =
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46 {
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47 DICOM_TAG_PATIENT_ID,
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48 DICOM_TAG_PATIENT_NAME,
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49 DICOM_TAG_PATIENT_BIRTH_DATE,
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50 DICOM_TAG_STUDY_INSTANCE_UID,
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51 DICOM_TAG_ACCESSION_NUMBER,
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52 DICOM_TAG_STUDY_DESCRIPTION,
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53 DICOM_TAG_STUDY_DATE
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54 };
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55
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56 static const DicomTag SERIES_IDENTIFIERS[] =
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57 {
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58 DICOM_TAG_SERIES_INSTANCE_UID
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59 };
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60
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61 static const DicomTag INSTANCE_IDENTIFIERS[] =
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62 {
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63 DICOM_TAG_SOP_INSTANCE_UID
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64 };
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65
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66
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67 namespace ServerToolbox
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68 {
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69 bool FindOneChildInstance(int64_t& result,
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70 IDatabaseWrapper::ITransaction& transaction,
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71 int64_t resource,
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72 ResourceType type)
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73 {
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74 for (;;)
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75 {
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76 if (type == ResourceType_Instance)
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77 {
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78 result = resource;
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79 return true;
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80 }
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81
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82 std::list<int64_t> children;
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83 transaction.GetChildrenInternalId(children, resource);
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84 if (children.empty())
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85 {
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86 return false;
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87 }
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88
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89 resource = children.front();
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90 type = GetChildResourceType(type);
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91 }
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92 }
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93
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94
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95 void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction,
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96 IStorageArea& storageArea,
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97 ResourceType level)
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98 {
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99 // WARNING: The database should be locked with a transaction!
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100
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101 // TODO: This function might consume much memory if level ==
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102 // ResourceType_Instance. To improve this, first download the
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103 // list of studies, then remove the instances for each single
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104 // study (check out OrthancRestApi::InvalidateTags for an
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105 // example). Take this improvement into consideration for the
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106 // next upgrade of the database schema.
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107
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108 const char* plural = NULL;
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109
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110 switch (level)
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111 {
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112 case ResourceType_Patient:
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113 plural = "patients";
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114 break;
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115
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116 case ResourceType_Study:
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117 plural = "studies";
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118 break;
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119
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120 case ResourceType_Series:
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121 plural = "series";
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122 break;
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123
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124 case ResourceType_Instance:
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125 plural = "instances";
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126 break;
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127
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128 default:
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129 throw OrthancException(ErrorCode_InternalError);
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130 }
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131
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132 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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133
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134 std::list<std::string> resources;
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135 transaction.GetAllPublicIds(resources, level);
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136
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137 for (std::list<std::string>::const_iterator
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138 it = resources.begin(); it != resources.end(); ++it)
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139 {
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140 // Locate the resource and one of its child instances
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141 int64_t resource, instance;
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142 ResourceType tmp;
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143
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144 if (!transaction.LookupResource(resource, tmp, *it) ||
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145 tmp != level ||
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146 !FindOneChildInstance(instance, transaction, resource, level))
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147 {
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148 throw OrthancException(ErrorCode_InternalError,
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149 "Cannot find an instance for " +
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150 std::string(EnumerationToString(level)) +
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151 " with identifier " + *it);
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152 }
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153
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154 // Get the DICOM file attached to some instances in the resource
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155 FileInfo attachment;
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156 int64_t revision;
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157 if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom))
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158 {
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159 throw OrthancException(ErrorCode_InternalError,
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160 "Cannot retrieve the DICOM file associated with instance " +
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161 transaction.GetPublicId(instance));
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162 }
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163
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164 try
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165 {
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166 // Read and parse the content of the DICOM file
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167 StorageAccessor accessor(storageArea);
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168
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169 std::string content;
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170 accessor.Read(content, attachment);
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171
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172 ParsedDicomFile dicom(content);
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173
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174 // Update the tags of this resource
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175 DicomMap dicomSummary;
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176 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom);
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177
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178 transaction.ClearMainDicomTags(resource);
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179
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180 ResourcesContent tags(false /* prevent the setting of metadata */);
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181 tags.AddResource(resource, level, dicomSummary);
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182 transaction.SetResourcesContent(tags);
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183 }
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184 catch (OrthancException&)
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185 {
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186 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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187 << " associated with instance " << transaction.GetPublicId(instance);
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188 throw;
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189 }
213
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190 }
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191 }
2121
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192
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193
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194 void LoadIdentifiers(const DicomTag*& tags,
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195 size_t& size,
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196 ResourceType level)
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197 {
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198 switch (level)
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199 {
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200 case ResourceType_Patient:
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201 tags = PATIENT_IDENTIFIERS;
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202 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
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203 break;
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204
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205 case ResourceType_Study:
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206 tags = STUDY_IDENTIFIERS;
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207 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
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208 break;
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209
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210 case ResourceType_Series:
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211 tags = SERIES_IDENTIFIERS;
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212 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
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213 break;
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214
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215 case ResourceType_Instance:
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216 tags = INSTANCE_IDENTIFIERS;
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217 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
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218 break;
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219
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220 default:
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221 throw OrthancException(ErrorCode_ParameterOutOfRange);
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222 }
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223 }
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224
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225
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226 std::string NormalizeIdentifier(const std::string& value)
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227 {
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228 std::string t;
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229 t.reserve(value.size());
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230
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231 for (size_t i = 0; i < value.size(); i++)
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232 {
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233 if (value[i] == '%' ||
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234 value[i] == '_')
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235 {
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236 t.push_back(' '); // These characters might break wildcard queries in SQL
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237 }
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238 else if (isascii(value[i]) &&
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239 !iscntrl(value[i]) &&
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240 (!isspace(value[i]) || value[i] == ' '))
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241 {
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242 t.push_back(value[i]);
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243 }
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244 }
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245
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246 Toolbox::ToUpperCase(t);
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247
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248 return Toolbox::StripSpaces(t);
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249 }
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250
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251
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252 bool IsIdentifier(const DicomTag& tag,
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253 ResourceType level)
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254 {
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255 const DicomTag* tags;
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256 size_t size;
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257
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258 LoadIdentifiers(tags, size, level);
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259
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260 for (size_t i = 0; i < size; i++)
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261 {
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262 if (tag == tags[i])
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263 {
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264 return true;
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265 }
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266 }
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267
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268 return false;
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269 }
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271
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272 void ReconstructResource(ServerContext& context,
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273 const std::string& resource)
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274 {
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275 LOG(WARNING) << "Reconstructing resource " << resource;
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276
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277 std::list<std::string> instances;
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278 context.GetIndex().GetChildInstances(instances, resource);
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279
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280 for (std::list<std::string>::const_iterator
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281 it = instances.begin(); it != instances.end(); ++it)
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282 {
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283 ServerContext::DicomCacheLocker locker(context, *it);
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284
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285 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext"
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286 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */,
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287 -1 /* dummy revision */, "" /* dummy MD5 */);
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288
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289 context.GetIndex().ReconstructInstance(locker.GetDicom());
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290 }
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291 }
213
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292 }
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293 }