Mercurial > hg > orthanc

annotate OrthancServer/ServerToolbox.cpp @ 3058:6faf575ba9cc db-changes

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refactoring: class ISqlLookupFormatter to be used in orthanc-databases
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 21 Dec 2018 17:07:58 +0100
parents 5da6d1063d8f
children ce272138f15e
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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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) 2017-2018 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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32
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33
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34 #include "PrecompiledHeadersServer.h"
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35 #include "ServerToolbox.h"
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36
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37 #include "../Core/DicomFormat/DicomArray.h"
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38 #include "../Core/FileStorage/StorageAccessor.h"
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39 #include "../Core/Logging.h"
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40 #include "../Core/OrthancException.h"
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41
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42 #include <cassert>
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43
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44 namespace Orthanc
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45 {
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46 namespace ServerToolbox
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47 {
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48 static const DicomTag patientIdentifiers[] =
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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 };
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54
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55 static const DicomTag studyIdentifiers[] =
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56 {
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57 DICOM_TAG_PATIENT_ID,
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58 DICOM_TAG_PATIENT_NAME,
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59 DICOM_TAG_PATIENT_BIRTH_DATE,
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60 DICOM_TAG_STUDY_INSTANCE_UID,
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61 DICOM_TAG_ACCESSION_NUMBER,
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62 DICOM_TAG_STUDY_DESCRIPTION,
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63 DICOM_TAG_STUDY_DATE
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64 };
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65
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66 static const DicomTag seriesIdentifiers[] =
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67 {
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68 DICOM_TAG_SERIES_INSTANCE_UID
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69 };
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70
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71 static const DicomTag instanceIdentifiers[] =
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72 {
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73 DICOM_TAG_SOP_INSTANCE_UID
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74 };
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75
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76
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77 void SimplifyTags(Json::Value& target,
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78 const Json::Value& source,
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79 DicomToJsonFormat format)
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80 {
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81 if (!source.isObject())
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82 {
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83 throw Orthanc::OrthancException(Orthanc::ErrorCode_BadFileFormat);
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84 }
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85
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86 target = Json::objectValue;
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87 Json::Value::Members members = source.getMemberNames();
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88
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89 for (size_t i = 0; i < members.size(); i++)
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90 {
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91 const Json::Value& v = source[members[i]];
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92 const std::string& type = v["Type"].asString();
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93
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94 std::string name;
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95 switch (format)
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96 {
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97 case DicomToJsonFormat_Human:
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98 name = v["Name"].asString();
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99 break;
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100
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101 case DicomToJsonFormat_Short:
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102 name = members[i];
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103 break;
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104
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105 default:
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106 throw OrthancException(ErrorCode_ParameterOutOfRange);
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107 }
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108
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109 if (type == "String")
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110 {
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111 target[name] = v["Value"].asString();
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112 }
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113 else if (type == "TooLong" ||
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114 type == "Null")
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115 {
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116 target[name] = Json::nullValue;
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117 }
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118 else if (type == "Sequence")
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119 {
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120 const Json::Value& array = v["Value"];
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121 assert(array.isArray());
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122
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123 Json::Value children = Json::arrayValue;
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124 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++)
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125 {
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126 Json::Value c;
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127 SimplifyTags(c, array[i], format);
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128 children.append(c);
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129 }
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130
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131 target[name] = children;
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132 }
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133 else
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134 {
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135 assert(0);
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136 }
213
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137 }
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138 }
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139
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140
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141 static void StoreMainDicomTagsInternal(IDatabaseWrapper& database,
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142 int64_t resource,
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143 const DicomMap& tags)
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144 {
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145 DicomArray flattened(tags);
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146
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147 for (size_t i = 0; i < flattened.GetSize(); i++)
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148 {
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149 const DicomElement& element = flattened.GetElement(i);
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150 const DicomTag& tag = element.GetTag();
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151 const DicomValue& value = element.GetValue();
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152 if (!value.IsNull() &&
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153 !value.IsBinary())
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154 {
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155 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent());
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156 }
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157 }
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158 }
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159
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160
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161 static void StoreIdentifiers(IDatabaseWrapper& database,
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162 int64_t resource,
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163 ResourceType level,
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164 const DicomMap& map)
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165 {
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166 const DicomTag* tags;
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167 size_t size;
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168
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169 LoadIdentifiers(tags, size, level);
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170
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171 for (size_t i = 0; i < size; i++)
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172 {
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173 // The identifiers tags are a subset of the main DICOM tags
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174 assert(DicomMap::IsMainDicomTag(tags[i]));
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175
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176 const DicomValue* value = map.TestAndGetValue(tags[i]);
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177 if (value != NULL &&
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178 !value->IsNull() &&
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179 !value->IsBinary())
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180 {
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181 std::string s = NormalizeIdentifier(value->GetContent());
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182 database.SetIdentifierTag(resource, tags[i], s);
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183 }
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184 }
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185 }
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186
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187
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188 void StoreMainDicomTags(IDatabaseWrapper& database,
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189 int64_t resource,
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190 ResourceType level,
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191 const DicomMap& dicomSummary)
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192 {
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193 // WARNING: The database should be locked with a transaction!
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194
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195 StoreIdentifiers(database, resource, level, dicomSummary);
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196
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197 DicomMap tags;
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198
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199 switch (level)
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200 {
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201 case ResourceType_Patient:
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202 dicomSummary.ExtractPatientInformation(tags);
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203 break;
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204
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205 case ResourceType_Study:
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206 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6)
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207 dicomSummary.ExtractPatientInformation(tags);
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208 StoreMainDicomTagsInternal(database, resource, tags);
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209
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210 dicomSummary.ExtractStudyInformation(tags);
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211 break;
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212
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213 case ResourceType_Series:
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214 dicomSummary.ExtractSeriesInformation(tags);
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215 break;
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216
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217 case ResourceType_Instance:
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218 dicomSummary.ExtractInstanceInformation(tags);
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219 break;
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220
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221 default:
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222 throw OrthancException(ErrorCode_InternalError);
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223 }
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224
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225 StoreMainDicomTagsInternal(database, resource, tags);
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226 }
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227
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228
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229 bool FindOneChildInstance(int64_t& result,
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230 IDatabaseWrapper& database,
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231 int64_t resource,
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232 ResourceType type)
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233 {
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234 for (;;)
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235 {
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236 if (type == ResourceType_Instance)
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237 {
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238 result = resource;
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239 return true;
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240 }
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241
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242 std::list<int64_t> children;
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243 database.GetChildrenInternalId(children, resource);
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244 if (children.empty())
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245 {
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246 return false;
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247 }
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248
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249 resource = children.front();
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250 type = GetChildResourceType(type);
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251 }
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252 }
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253
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254
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255 void ReconstructMainDicomTags(IDatabaseWrapper& database,
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256 IStorageArea& storageArea,
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257 ResourceType level)
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258 {
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259 // WARNING: The database should be locked with a transaction!
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260
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261 // TODO: This function might consume much memory if level ==
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262 // ResourceType_Instance. To improve this, first download the
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263 // list of studies, then remove the instances for each single
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264 // study (check out OrthancRestApi::InvalidateTags for an
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265 // example). Take this improvement into consideration for the
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266 // next upgrade of the database schema.
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267
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268 const char* plural = NULL;
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269
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270 switch (level)
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271 {
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272 case ResourceType_Patient:
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273 plural = "patients";
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diff changeset
274 break;
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275
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276 case ResourceType_Study:
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277 plural = "studies";
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278 break;
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279
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280 case ResourceType_Series:
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281 plural = "series";
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282 break;
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283
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284 case ResourceType_Instance:
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285 plural = "instances";
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286 break;
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287
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288 default:
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289 throw OrthancException(ErrorCode_InternalError);
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290 }
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291
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292 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "...";
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293
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294 std::list<std::string> resources;
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295 database.GetAllPublicIds(resources, level);
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296
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297 for (std::list<std::string>::const_iterator
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298 it = resources.begin(); it != resources.end(); ++it)
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299 {
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300 // Locate the resource and one of its child instances
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301 int64_t resource, instance;
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302 ResourceType tmp;
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303
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304 if (!database.LookupResource(resource, tmp, *it) ||
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305 tmp != level ||
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306 !FindOneChildInstance(instance, database, resource, level))
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307 {
2955
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308 throw OrthancException(ErrorCode_InternalError,
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309 "Cannot find an instance for " +
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310 std::string(EnumerationToString(level)) +
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311 " with identifier " + *it);
1668
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312 }
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313
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314 // Get the DICOM file attached to some instances in the resource
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315 FileInfo attachment;
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316 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom))
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317 {
2955
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318 throw OrthancException(ErrorCode_InternalError,
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319 "Cannot retrieve the DICOM file associated with instance " +
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320 database.GetPublicId(instance));
1668
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321 }
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322
1870
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323 try
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324 {
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325 // Read and parse the content of the DICOM file
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326 StorageAccessor accessor(storageArea);
1673
0bbcfd9695e5 UpgradeDatabase in the sample plugin
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327
1870
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328 std::string content;
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329 accessor.Read(content, attachment);
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330
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331 ParsedDicomFile dicom(content);
1668
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332
1870
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333 // Update the tags of this resource
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334 DicomMap dicomSummary;
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
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335 dicom.ExtractDicomSummary(dicomSummary);
1668
de1413733c97 reconstructing main dicom tags
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336
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337 database.ClearMainDicomTags(resource);
2120
4b02ec79728a refactoring
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diff changeset
338 StoreMainDicomTags(database, resource, level, dicomSummary);
1870
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339 }
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diff changeset
340 catch (OrthancException&)
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341 {
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diff changeset
342 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid()
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diff changeset
343 << " associated with instance " << database.GetPublicId(instance);
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344 throw;
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diff changeset
345 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
diff changeset
346 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
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parents:
diff changeset
347 }
2121
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diff changeset
348
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diff changeset
349
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diff changeset
350 void LoadIdentifiers(const DicomTag*& tags,
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351 size_t& size,
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diff changeset
352 ResourceType level)
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diff changeset
353 {
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diff changeset
354 switch (level)
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diff changeset
355 {
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parents: 2120
diff changeset
356 case ResourceType_Patient:
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357 tags = patientIdentifiers;
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diff changeset
358 size = sizeof(patientIdentifiers) / sizeof(DicomTag);
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diff changeset
359 break;
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parents: 2120
diff changeset
360
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parents: 2120
diff changeset
361 case ResourceType_Study:
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
362 tags = studyIdentifiers;
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parents: 2120
diff changeset
363 size = sizeof(studyIdentifiers) / sizeof(DicomTag);
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
364 break;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
365
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parents: 2120
diff changeset
366 case ResourceType_Series:
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
367 tags = seriesIdentifiers;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
368 size = sizeof(seriesIdentifiers) / sizeof(DicomTag);
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parents: 2120
diff changeset
369 break;
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parents: 2120
diff changeset
370
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
371 case ResourceType_Instance:
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
372 tags = instanceIdentifiers;
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parents: 2120
diff changeset
373 size = sizeof(instanceIdentifiers) / sizeof(DicomTag);
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
374 break;
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
375
7e8889bc95c6 refactoring
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diff changeset
376 default:
7e8889bc95c6 refactoring
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diff changeset
377 throw OrthancException(ErrorCode_ParameterOutOfRange);
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parents: 2120
diff changeset
378 }
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
379 }
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
380
7e8889bc95c6 refactoring
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diff changeset
381
7e8889bc95c6 refactoring
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diff changeset
382 std::string NormalizeIdentifier(const std::string& value)
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diff changeset
383 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
384 std::string t;
7e8889bc95c6 refactoring
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diff changeset
385 t.reserve(value.size());
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parents: 2120
diff changeset
386
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
387 for (size_t i = 0; i < value.size(); i++)
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
388 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
389 if (value[i] == '%' ||
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
390 value[i] == '_')
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
391 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
392 t.push_back(' '); // These characters might break wildcard queries in SQL
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
393 }
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
394 else if (isascii(value[i]) &&
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
395 !iscntrl(value[i]) &&
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
396 (!isspace(value[i]) || value[i] == ' '))
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
397 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
398 t.push_back(value[i]);
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
399 }
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
400 }
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
401
7e8889bc95c6 refactoring
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diff changeset
402 Toolbox::ToUpperCase(t);
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
403
7e8889bc95c6 refactoring
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diff changeset
404 return Toolbox::StripSpaces(t);
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
405 }
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
406
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
407
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
408 bool IsIdentifier(const DicomTag& tag,
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
409 ResourceType level)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
410 {
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
411 const DicomTag* tags;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
412 size_t size;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
413
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
414 LoadIdentifiers(tags, size, level);
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
415
7e8889bc95c6 refactoring
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parents: 2120
diff changeset
416 for (size_t i = 0; i < size; i++)
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
diff changeset
417 {
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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418 if (tag == tags[i])
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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419 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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420 return true;
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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421 }
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422 }
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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423
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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424 return false;
7e8889bc95c6 refactoring
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2120
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425 }
2209
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
426
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
427
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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428 void ReconstructResource(ServerContext& context,
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
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429 const std::string& resource)
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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430 {
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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431 LOG(WARNING) << "Reconstructing resource " << resource;
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
432
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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433 std::list<std::string> instances;
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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434 context.GetIndex().GetChildInstances(instances, resource);
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
435
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
436 for (std::list<std::string>::const_iterator
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
437 it = instances.begin(); it != instances.end(); ++it)
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
438 {
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
439 ServerContext::DicomCacheLocker locker(context, *it);
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
440
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Sebastien Jodogne <s.jodogne@gmail.com>
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441 Json::Value dicomAsJson;
2409
e4045b3c9772 ignore-length argument if retrieving DICOM tags
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2380
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442 locker.GetDicom().DatasetToJson(dicomAsJson);
2209
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diff changeset
443
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
444 std::string s = dicomAsJson.toStyledString();
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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445 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size());
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
446
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Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
447 context.GetIndex().ReconstructInstance(locker.GetDicom());
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
diff changeset
448 }
e3fd5bc429a2 URI to reconstruct the main DICOM tags, the JSON summary and the metadata
Sebastien Jodogne <s.jodogne@gmail.com>
parents: 2129
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449 }
213
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
450 }
4ce7fdcc8879 access to tags, simplified-tags and file of an instance
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
451 }