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annotate OrthancServer/Sources/ServerToolbox.cpp @ 5640:f7adfb22e20e

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updated copyright, as Orthanc Team now replaces Osimis
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 30 May 2024 21:19:57 +0200
parents c1ed59a5bdc2
children
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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) 2017-2023 Osimis S.A., Belgium
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6 * Copyright (C) 2024-2024 Orthanc Team SRL, Belgium
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7 * Copyright (C) 2021-2024 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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8 *
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9 * This program is free software: you can redistribute it and/or
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10 * modify it under the terms of the GNU General Public License as
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11 * published by the Free Software Foundation, either version 3 of the
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12 * License, or (at your option) any later version.
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13 *
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14 * This program is distributed in the hope that it will be useful, but
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15 * WITHOUT ANY WARRANTY; without even the implied warranty of
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16 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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17 * General Public License for more details.
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18 *
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19 * You should have received a copy of the GNU General Public License
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20 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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21 **/
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22
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23
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24 #include "PrecompiledHeadersServer.h"
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25 #include "ServerToolbox.h"
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26
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27 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h"
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28 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h"
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29 #include "../../OrthancFramework/Sources/FileStorage/StorageCache.h"
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30 #include "../../OrthancFramework/Sources/Logging.h"
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31 #include "../../OrthancFramework/Sources/OrthancException.h"
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32 #include "Database/IDatabaseWrapper.h"
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33 #include "Database/ResourcesContent.h"
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34 #include "OrthancConfiguration.h"
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35 #include "ServerContext.h"
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36
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37 #include <cassert>
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38
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39 namespace Orthanc
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40 {
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41 static const DicomTag PATIENT_IDENTIFIERS[] =
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42 {
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43 DICOM_TAG_PATIENT_ID,
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44 DICOM_TAG_PATIENT_NAME,
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45 DICOM_TAG_PATIENT_BIRTH_DATE
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46 };
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47
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48 static const DicomTag STUDY_IDENTIFIERS[] =
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49 {
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50 DICOM_TAG_PATIENT_ID,
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51 DICOM_TAG_PATIENT_NAME,
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52 DICOM_TAG_PATIENT_BIRTH_DATE,
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53 DICOM_TAG_STUDY_INSTANCE_UID,
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54 DICOM_TAG_ACCESSION_NUMBER,
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55 DICOM_TAG_STUDY_DESCRIPTION,
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56 DICOM_TAG_STUDY_DATE
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57 };
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58
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59 static const DicomTag SERIES_IDENTIFIERS[] =
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60 {
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61 DICOM_TAG_SERIES_INSTANCE_UID
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62 };
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63
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64 static const DicomTag INSTANCE_IDENTIFIERS[] =
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65 {
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66 DICOM_TAG_SOP_INSTANCE_UID
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67 };
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68
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69
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70 namespace ServerToolbox
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71 {
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72 bool FindOneChildInstance(int64_t& result,
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73 IDatabaseWrapper::ITransaction& transaction,
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74 int64_t resource,
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75 ResourceType type)
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76 {
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77 for (;;)
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78 {
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79 if (type == ResourceType_Instance)
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80 {
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81 result = resource;
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82 return true;
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83 }
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84
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85 std::list<int64_t> children;
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86 transaction.GetChildrenInternalId(children, resource);
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87 if (children.empty())
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88 {
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89 return false;
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90 }
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91
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92 resource = children.front();
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93 type = GetChildResourceType(type);
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94 }
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95 }
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96
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97
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98 void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction,
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99 IStorageArea& storageArea,
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100 ResourceType level)
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101 {
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102 // WARNING: The database should be locked with a transaction!
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103
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104 // TODO: This function might consume much memory if level ==
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105 // ResourceType_Instance. To improve this, first download the
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106 // list of studies, then remove the instances for each single
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107 // study (check out OrthancRestApi::InvalidateTags for an
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108 // example). Take this improvement into consideration for the
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109 // next upgrade of the database schema.
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110
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111 const char* plural = Orthanc::GetResourceTypeText(level, true, true);
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112
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113 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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114
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115 std::list<std::string> resources;
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116 transaction.GetAllPublicIds(resources, level);
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117
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118 for (std::list<std::string>::const_iterator
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119 it = resources.begin(); it != resources.end(); ++it)
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120 {
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121 // Locate the resource and one of its child instances
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122 int64_t resource, instance;
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123 ResourceType tmp;
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124
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125 if (!transaction.LookupResource(resource, tmp, *it) ||
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126 tmp != level ||
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127 !FindOneChildInstance(instance, transaction, resource, level))
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128 {
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129 throw OrthancException(ErrorCode_InternalError,
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130 "Cannot find an instance for " +
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131 std::string(EnumerationToString(level)) +
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132 " with identifier " + *it);
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133 }
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134
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135 // Get the DICOM file attached to some instances in the resource
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136 FileInfo attachment;
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137 int64_t revision;
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138 if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom))
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139 {
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140 throw OrthancException(ErrorCode_InternalError,
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141 "Cannot retrieve the DICOM file associated with instance " +
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142 transaction.GetPublicId(instance));
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143 }
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144
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145 try
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146 {
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147 // Read and parse the content of the DICOM file
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148 StorageAccessor accessor(storageArea); // no cache
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149
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150 std::string content;
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151 accessor.Read(content, attachment);
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152
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153 ParsedDicomFile dicom(content);
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154
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155 // Update the tags of this resource
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156 DicomMap dicomSummary;
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157 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom);
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158
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159 transaction.ClearMainDicomTags(resource);
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160
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161 ResourcesContent tags(false /* prevent the setting of metadata */);
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162 tags.AddResource(resource, level, dicomSummary);
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163 transaction.SetResourcesContent(tags);
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164
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165 transaction.DeleteMetadata(resource, MetadataType_MainDicomTagsSignature);
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166 transaction.SetMetadata(resource, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(level), 0);
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167 }
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168 catch (OrthancException&)
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169 {
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170 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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171 << " associated with instance " << transaction.GetPublicId(instance);
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172 throw;
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173 }
213
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174 }
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175 }
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176
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177
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178 void LoadIdentifiers(const DicomTag*& tags,
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179 size_t& size,
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180 ResourceType level)
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181 {
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182 switch (level)
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183 {
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184 case ResourceType_Patient:
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185 tags = PATIENT_IDENTIFIERS;
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186 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
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187 break;
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188
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189 case ResourceType_Study:
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190 tags = STUDY_IDENTIFIERS;
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191 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
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192 break;
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193
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194 case ResourceType_Series:
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195 tags = SERIES_IDENTIFIERS;
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196 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
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197 break;
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198
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199 case ResourceType_Instance:
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200 tags = INSTANCE_IDENTIFIERS;
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201 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
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202 break;
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203
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204 default:
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205 throw OrthancException(ErrorCode_ParameterOutOfRange);
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206 }
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207 }
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208
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209
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210 std::string NormalizeIdentifier(const std::string& value)
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211 {
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212 std::string t;
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213 t.reserve(value.size());
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214
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215 #if 0
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216 // This version solves some indexing issue (https://discourse.orthanc-server.org/t/postgress-index-effectively-disabled-when-searching-for-greek-names/3371)
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217 // and seems functional: I could run the integration tests with both SQLite and PG + the DicomWeb tests with PG.
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218 // However, it can not go into production because NormalizeIdentifier is used both at ingest time and at search time;
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219 // therefore, if we change it while we have an already populated DB, the searches won't work anymore and, on very large
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220 // systems, running the Housekeeper to rebuild the indexes might take months ...
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221 // We keep it here because it might be handy once we refactor the DicomIdentifier searches in the future.
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222 for (size_t i = 0; i < value.size(); i++)
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223 {
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224 if (value[i] == '%' ||
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225 value[i] == '_')
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226 {
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227 t.push_back(' '); // These characters might break wildcard queries in SQL
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228 }
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229 else if (//isascii(value[i]) &&
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230 !iscntrl(value[i]) &&
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231 (!isspace(value[i]) || value[i] == ' '))
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232 {
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233 t.push_back(value[i]);
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234 }
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235 }
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236
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237 //Toolbox::ToUpperCase(t);
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238 t = Toolbox::ToUpperCaseWithAccents(t);
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239 #else
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240 for (size_t i = 0; i < value.size(); i++)
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241 {
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242 if (value[i] == '%' ||
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243 value[i] == '_')
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244 {
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245 t.push_back(' '); // These characters might break wildcard queries in SQL
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246 }
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247 else if (isascii(value[i]) &&
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248 !iscntrl(value[i]) &&
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249 (!isspace(value[i]) || value[i] == ' '))
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250 {
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251 t.push_back(value[i]);
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252 }
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253 }
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254
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255 Toolbox::ToUpperCase(t);
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256 #endif
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257
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258 return Toolbox::StripSpaces(t);
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259 }
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260
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261
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262 bool IsIdentifier(const DicomTag& tag,
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263 ResourceType level)
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264 {
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265 const DicomTag* tags;
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266 size_t size;
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267
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268 LoadIdentifiers(tags, size, level);
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269
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270 for (size_t i = 0; i < size; i++)
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271 {
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272 if (tag == tags[i])
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273 {
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274 return true;
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275 }
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276 }
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277
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278 return false;
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279 }
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280
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281
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282 void ReconstructResource(ServerContext& context,
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283 const std::string& resource,
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284 bool reconstructFiles,
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285 bool limitToThisLevelDicomTags,
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286 ResourceType limitToLevel)
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287 {
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288 LOG(WARNING) << "Reconstructing resource " << resource;
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289
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290 std::list<std::string> instances;
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291 context.GetIndex().GetChildInstances(instances, resource);
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292
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293
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294 if (limitToThisLevelDicomTags && instances.size() > 0) // in this case, we only need to rebuild one instance !
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295 {
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296 ServerContext::DicomCacheLocker locker(context, instances.front());
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297 context.GetIndex().ReconstructInstance(locker.GetDicom(), true, limitToLevel);
c1ed59a5bdc2 new LimitToThisLevelMainDicomTags reconstruct mode + * Housekeeper plugin: Added an option LimitMainDicomTagsReconstructLevel
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298 }
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299 else
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300 {
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301 for (std::list<std::string>::const_iterator
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302 it = instances.begin(); it != instances.end(); ++it)
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303 {
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diff changeset
304 ServerContext::DicomCacheLocker locker(context, *it);
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305
5558
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306 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext"
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diff changeset
307 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */,
c1ed59a5bdc2 new LimitToThisLevelMainDicomTags reconstruct mode + * Housekeeper plugin: Added an option LimitMainDicomTagsReconstructLevel
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parents: 5485
diff changeset
308 -1 /* dummy revision */, "" /* dummy MD5 */);
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diff changeset
309
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diff changeset
310 context.GetIndex().ReconstructInstance(locker.GetDicom(), false, ResourceType_Instance /* dummy */);
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Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
311
5558
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diff changeset
312 if (reconstructFiles)
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diff changeset
313 {
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diff changeset
314 std::string resultPublicId; // ignored
c1ed59a5bdc2 new LimitToThisLevelMainDicomTags reconstruct mode + * Housekeeper plugin: Added an option LimitMainDicomTagsReconstructLevel
Alain Mazy <am@orthanc.team>
parents: 5485
diff changeset
315 std::unique_ptr<DicomInstanceToStore> dicomInstancetoStore(DicomInstanceToStore::CreateFromParsedDicomFile(locker.GetDicom()));
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Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
316
5558
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diff changeset
317 // TODO: TranscodeAndStore and specifically ServerIndex::Store have been "poluted" by the isReconstruct parameter
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diff changeset
318 // we should very likely refactor it
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parents: 5485
diff changeset
319 context.TranscodeAndStore(resultPublicId, dicomInstancetoStore.get(), StoreInstanceMode_OverwriteDuplicate, true);
c1ed59a5bdc2 new LimitToThisLevelMainDicomTags reconstruct mode + * Housekeeper plugin: Added an option LimitMainDicomTagsReconstructLevel
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320 }
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Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
321 }
2209
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diff changeset
322 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
323 }
5244
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
324
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
325
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
326 bool IsValidLabel(const std::string& label)
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
327 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
328 if (label.empty())
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
329 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
330 return false;
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
331 }
5247
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
332
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
333 if (label.size() > 64)
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
334 {
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
335 // This limitation is for MySQL, which cannot use a TEXT
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
336 // column of undefined length as a primary key
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
337 return false;
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
338 }
5244
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
339
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
340 for (size_t i = 0; i < label.size(); i++)
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
341 {
5250
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parents: 5247
diff changeset
342 if (!(label[i] == '_' ||
5244
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
343 label[i] == '-' ||
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
344 (label[i] >= 'a' && label[i] <= 'z') ||
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
345 (label[i] >= 'A' && label[i] <= 'Z') ||
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
346 (label[i] >= '0' && label[i] <= '9')))
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
347 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
348 return false;
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
349 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
350 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
351
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
352 return true;
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
353 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
354
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
355
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
356 void CheckValidLabel(const std::string& label)
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
357 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
358 if (!IsValidLabel(label))
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
359 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
360 throw OrthancException(ErrorCode_ParameterOutOfRange,
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
361 "A label must be a non-empty, alphanumeric string, "
5250
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parents: 5247
diff changeset
362 "possibly with '_' or '-' characters, "
5247
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
363 "with maximum 64 characters, but got: " + label);
5244
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
364 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
365 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
366 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
367 }