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annotate OrthancServer/Sources/ServerToolbox.cpp @ 5410:16cbfefa15e9

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Solved a deadlock related to the Job Engine events and plugins
author Alain Mazy <am@osimis.io>
date Tue, 07 Nov 2023 12:52:37 +0100
parents 28f0e38e4082
children 48b8dae6dc77
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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) 2021-2023 Sebastien Jodogne, ICTEAM UCLouvain, Belgium
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7 *
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8 * This program is free software: you can redistribute it and/or
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9 * modify it under the terms of the GNU General Public License as
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10 * published by the Free Software Foundation, either version 3 of the
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11 * License, or (at your option) any later version.
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12 *
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13 * This program is distributed in the hope that it will be useful, but
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14 * WITHOUT ANY WARRANTY; without even the implied warranty of
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15 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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16 * General Public License for more details.
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17 *
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18 * You should have received a copy of the GNU General Public License
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19 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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20 **/
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22
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23 #include "PrecompiledHeadersServer.h"
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24 #include "ServerToolbox.h"
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25
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26 #include "../../OrthancFramework/Sources/DicomParsing/ParsedDicomFile.h"
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27 #include "../../OrthancFramework/Sources/FileStorage/StorageAccessor.h"
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28 #include "../../OrthancFramework/Sources/FileStorage/StorageCache.h"
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29 #include "../../OrthancFramework/Sources/Logging.h"
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30 #include "../../OrthancFramework/Sources/OrthancException.h"
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31 #include "Database/IDatabaseWrapper.h"
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32 #include "Database/ResourcesContent.h"
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33 #include "OrthancConfiguration.h"
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34 #include "ServerContext.h"
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35
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36 #include <cassert>
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37
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38 namespace Orthanc
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39 {
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40 static const DicomTag PATIENT_IDENTIFIERS[] =
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41 {
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42 DICOM_TAG_PATIENT_ID,
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43 DICOM_TAG_PATIENT_NAME,
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44 DICOM_TAG_PATIENT_BIRTH_DATE
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45 };
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46
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47 static const DicomTag STUDY_IDENTIFIERS[] =
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48 {
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49 DICOM_TAG_PATIENT_ID,
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50 DICOM_TAG_PATIENT_NAME,
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51 DICOM_TAG_PATIENT_BIRTH_DATE,
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52 DICOM_TAG_STUDY_INSTANCE_UID,
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53 DICOM_TAG_ACCESSION_NUMBER,
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54 DICOM_TAG_STUDY_DESCRIPTION,
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55 DICOM_TAG_STUDY_DATE
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56 };
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57
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58 static const DicomTag SERIES_IDENTIFIERS[] =
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59 {
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60 DICOM_TAG_SERIES_INSTANCE_UID
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61 };
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62
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63 static const DicomTag INSTANCE_IDENTIFIERS[] =
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64 {
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65 DICOM_TAG_SOP_INSTANCE_UID
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66 };
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67
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68
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69 namespace ServerToolbox
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70 {
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71 bool FindOneChildInstance(int64_t& result,
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72 IDatabaseWrapper::ITransaction& transaction,
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73 int64_t resource,
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74 ResourceType type)
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75 {
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76 for (;;)
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77 {
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78 if (type == ResourceType_Instance)
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79 {
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80 result = resource;
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81 return true;
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82 }
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83
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84 std::list<int64_t> children;
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85 transaction.GetChildrenInternalId(children, resource);
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86 if (children.empty())
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87 {
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88 return false;
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89 }
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90
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91 resource = children.front();
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92 type = GetChildResourceType(type);
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93 }
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94 }
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95
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96
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97 void ReconstructMainDicomTags(IDatabaseWrapper::ITransaction& transaction,
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98 IStorageArea& storageArea,
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99 ResourceType level)
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100 {
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101 // WARNING: The database should be locked with a transaction!
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102
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103 // TODO: This function might consume much memory if level ==
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104 // ResourceType_Instance. To improve this, first download the
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105 // list of studies, then remove the instances for each single
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106 // study (check out OrthancRestApi::InvalidateTags for an
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107 // example). Take this improvement into consideration for the
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108 // next upgrade of the database schema.
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109
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110 const char* plural = Orthanc::GetResourceTypeText(level, true, true);
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111
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112 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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113
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114 std::list<std::string> resources;
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115 transaction.GetAllPublicIds(resources, level);
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116
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117 for (std::list<std::string>::const_iterator
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118 it = resources.begin(); it != resources.end(); ++it)
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119 {
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120 // Locate the resource and one of its child instances
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121 int64_t resource, instance;
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122 ResourceType tmp;
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123
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124 if (!transaction.LookupResource(resource, tmp, *it) ||
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125 tmp != level ||
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126 !FindOneChildInstance(instance, transaction, resource, level))
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127 {
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128 throw OrthancException(ErrorCode_InternalError,
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129 "Cannot find an instance for " +
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130 std::string(EnumerationToString(level)) +
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131 " with identifier " + *it);
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132 }
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133
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134 // Get the DICOM file attached to some instances in the resource
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135 FileInfo attachment;
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136 int64_t revision;
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137 if (!transaction.LookupAttachment(attachment, revision, instance, FileContentType_Dicom))
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138 {
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139 throw OrthancException(ErrorCode_InternalError,
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140 "Cannot retrieve the DICOM file associated with instance " +
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141 transaction.GetPublicId(instance));
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142 }
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143
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144 try
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145 {
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146 // Read and parse the content of the DICOM file
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147 StorageAccessor accessor(storageArea); // no cache
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148
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149 std::string content;
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150 accessor.Read(content, attachment);
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151
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152 ParsedDicomFile dicom(content);
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153
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154 // Update the tags of this resource
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155 DicomMap dicomSummary;
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156 OrthancConfiguration::DefaultExtractDicomSummary(dicomSummary, dicom);
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157
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158 transaction.ClearMainDicomTags(resource);
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159
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160 ResourcesContent tags(false /* prevent the setting of metadata */);
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161 tags.AddResource(resource, level, dicomSummary);
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162 transaction.SetResourcesContent(tags);
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163
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164 transaction.DeleteMetadata(resource, MetadataType_MainDicomTagsSignature);
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165 transaction.SetMetadata(resource, MetadataType_MainDicomTagsSignature, DicomMap::GetMainDicomTagsSignature(level), 0);
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166 }
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167 catch (OrthancException&)
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168 {
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169 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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170 << " associated with instance " << transaction.GetPublicId(instance);
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171 throw;
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172 }
213
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173 }
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174 }
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175
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176
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177 void LoadIdentifiers(const DicomTag*& tags,
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178 size_t& size,
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179 ResourceType level)
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180 {
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181 switch (level)
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182 {
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183 case ResourceType_Patient:
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184 tags = PATIENT_IDENTIFIERS;
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185 size = sizeof(PATIENT_IDENTIFIERS) / sizeof(DicomTag);
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186 break;
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187
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188 case ResourceType_Study:
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189 tags = STUDY_IDENTIFIERS;
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190 size = sizeof(STUDY_IDENTIFIERS) / sizeof(DicomTag);
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191 break;
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192
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193 case ResourceType_Series:
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194 tags = SERIES_IDENTIFIERS;
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195 size = sizeof(SERIES_IDENTIFIERS) / sizeof(DicomTag);
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196 break;
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197
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198 case ResourceType_Instance:
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199 tags = INSTANCE_IDENTIFIERS;
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200 size = sizeof(INSTANCE_IDENTIFIERS) / sizeof(DicomTag);
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201 break;
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202
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203 default:
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204 throw OrthancException(ErrorCode_ParameterOutOfRange);
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205 }
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206 }
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207
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208
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209 std::string NormalizeIdentifier(const std::string& value)
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210 {
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211 std::string t;
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212 t.reserve(value.size());
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213
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214 #if 0
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215 // 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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216 // and seems functional: I could run the integration tests with both SQLite and PG + the DicomWeb tests with PG.
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217 // However, it can not go into production because NormalizeIdentifier is used both at ingest time and at search time;
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218 // 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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219 // systems, running the Housekeeper to rebuild the indexes might take months ...
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220 // We keep it here because it might be handy once we refactor the DicomIdentifier searches in the future.
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221 for (size_t i = 0; i < value.size(); i++)
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222 {
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223 if (value[i] == '%' ||
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224 value[i] == '_')
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225 {
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226 t.push_back(' '); // These characters might break wildcard queries in SQL
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227 }
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228 else if (//isascii(value[i]) &&
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229 !iscntrl(value[i]) &&
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230 (!isspace(value[i]) || value[i] == ' '))
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231 {
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232 t.push_back(value[i]);
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233 }
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234 }
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235
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236 //Toolbox::ToUpperCase(t);
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237 t = Toolbox::ToUpperCaseWithAccents(t);
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238 #else
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239 for (size_t i = 0; i < value.size(); i++)
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240 {
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241 if (value[i] == '%' ||
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242 value[i] == '_')
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243 {
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244 t.push_back(' '); // These characters might break wildcard queries in SQL
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245 }
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246 else if (isascii(value[i]) &&
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247 !iscntrl(value[i]) &&
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248 (!isspace(value[i]) || value[i] == ' '))
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249 {
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250 t.push_back(value[i]);
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251 }
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252 }
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253
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254 Toolbox::ToUpperCase(t);
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255 #endif
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256
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257 return Toolbox::StripSpaces(t);
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258 }
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259
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260
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261 bool IsIdentifier(const DicomTag& tag,
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262 ResourceType level)
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263 {
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264 const DicomTag* tags;
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265 size_t size;
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266
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267 LoadIdentifiers(tags, size, level);
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268
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269 for (size_t i = 0; i < size; i++)
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270 {
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271 if (tag == tags[i])
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272 {
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273 return true;
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274 }
7e8889bc95c6 refactoring
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275 }
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276
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277 return false;
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278 }
2209
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279
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Sebastien Jodogne <s.jodogne@gmail.com>
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280
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diff changeset
281 void ReconstructResource(ServerContext& context,
4988
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
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282 const std::string& resource,
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
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283 bool reconstructFiles)
2209
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284 {
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285 LOG(WARNING) << "Reconstructing resource " << resource;
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286
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diff changeset
287 std::list<std::string> instances;
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
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288 context.GetIndex().GetChildInstances(instances, resource);
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289
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diff changeset
290 for (std::list<std::string>::const_iterator
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diff changeset
291 it = instances.begin(); it != instances.end(); ++it)
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diff changeset
292 {
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diff changeset
293 ServerContext::DicomCacheLocker locker(context, *it);
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294
4498
7b99e8bb8246 IStorageArea::HasReadRange()
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295 // Delay the reconstruction of DICOM-as-JSON to its next access through "ServerContext"
4640
66109d24d26e "ETag" headers for metadata and attachments now allow strong comparison (MD5 is included)
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parents: 4627
diff changeset
296 context.GetIndex().DeleteAttachment(*it, FileContentType_DicomAsJson, false /* no revision */,
66109d24d26e "ETag" headers for metadata and attachments now allow strong comparison (MD5 is included)
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 4627
diff changeset
297 -1 /* dummy revision */, "" /* dummy MD5 */);
4498
7b99e8bb8246 IStorageArea::HasReadRange()
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diff changeset
298
2209
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diff changeset
299 context.GetIndex().ReconstructInstance(locker.GetDicom());
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diff changeset
300
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
301 if (reconstructFiles)
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diff changeset
302 {
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
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diff changeset
303 std::string resultPublicId; // ignored
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Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
304 std::unique_ptr<DicomInstanceToStore> dicomInstancetoStore(DicomInstanceToStore::CreateFromParsedDicomFile(locker.GetDicom()));
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Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
305
5224
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Alain Mazy <am@osimis.io>
parents: 5185
diff changeset
306 // TODO: TranscodeAndStore and specifically ServerIndex::Store have been "poluted" by the isReconstruct parameter
feba2b0e91bc Fix a crash in /tools/reconstruct triggered by the Housekeeper plugin when only changing the StorageCompression.
Alain Mazy <am@osimis.io>
parents: 5185
diff changeset
307 // we should very likely refactor it
4988
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parents: 4934
diff changeset
308 context.TranscodeAndStore(resultPublicId, dicomInstancetoStore.get(), StoreInstanceMode_OverwriteDuplicate, true);
8fba26292a9f Housekeeper plugin: finalizing + integration tests ok
Alain Mazy <am@osimis.io>
parents: 4934
diff changeset
309 }
2209
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diff changeset
310 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
311 }
5244
72dfa0ac84eb lookup for labels in orthanc explorer
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parents: 5224
diff changeset
312
72dfa0ac84eb lookup for labels in orthanc explorer
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parents: 5224
diff changeset
313
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
314 bool IsValidLabel(const std::string& label)
72dfa0ac84eb lookup for labels in orthanc explorer
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parents: 5224
diff changeset
315 {
72dfa0ac84eb lookup for labels in orthanc explorer
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parents: 5224
diff changeset
316 if (label.empty())
72dfa0ac84eb lookup for labels in orthanc explorer
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parents: 5224
diff changeset
317 {
72dfa0ac84eb lookup for labels in orthanc explorer
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parents: 5224
diff changeset
318 return false;
72dfa0ac84eb lookup for labels in orthanc explorer
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parents: 5224
diff changeset
319 }
5247
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
320
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
321 if (label.size() > 64)
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
322 {
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
323 // 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
324 // column of undefined length as a primary key
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
325 return false;
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
326 }
5244
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 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
329 {
5250
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parents: 5247
diff changeset
330 if (!(label[i] == '_' ||
5244
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
331 label[i] == '-' ||
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
332 (label[i] >= 'a' && label[i] <= 'z') ||
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
333 (label[i] >= 'A' && label[i] <= 'Z') ||
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
334 (label[i] >= '0' && label[i] <= '9')))
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
335 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
336 return false;
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
337 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
338 }
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 return true;
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
341 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
342
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
343
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
344 void CheckValidLabel(const std::string& label)
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
345 {
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
346 if (!IsValidLabel(label))
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 throw OrthancException(ErrorCode_ParameterOutOfRange,
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
349 "A label must be a non-empty, alphanumeric string, "
5250
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5247
diff changeset
350 "possibly with '_' or '-' characters, "
5247
eb2684260c19 support labels for mysql
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5244
diff changeset
351 "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
352 }
72dfa0ac84eb lookup for labels in orthanc explorer
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 5224
diff changeset
353 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
354 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
355 }