Mercurial > hg > orthanc
annotate OrthancServer/ServerToolbox.cpp @ 2406:f0cfacd0c9b8
Orthanc framework: ORTHANC_SANDBOXED parameter
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 20 Sep 2017 16:28:27 +0200 |
parents | 96b3ec054b69 |
children | e4045b3c9772 |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
1900 | 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 Osimis, 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 |
234 | 42 #include <cassert> |
43 | |
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44 namespace Orthanc |
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45 { |
2120 | 46 namespace ServerToolbox |
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47 { |
2121 | 48 static const DicomTag patientIdentifiers[] = |
49 { | |
50 DICOM_TAG_PATIENT_ID, | |
51 DICOM_TAG_PATIENT_NAME, | |
52 DICOM_TAG_PATIENT_BIRTH_DATE | |
53 }; | |
54 | |
55 static const DicomTag studyIdentifiers[] = | |
56 { | |
57 DICOM_TAG_PATIENT_ID, | |
58 DICOM_TAG_PATIENT_NAME, | |
59 DICOM_TAG_PATIENT_BIRTH_DATE, | |
60 DICOM_TAG_STUDY_INSTANCE_UID, | |
61 DICOM_TAG_ACCESSION_NUMBER, | |
62 DICOM_TAG_STUDY_DESCRIPTION, | |
63 DICOM_TAG_STUDY_DATE | |
64 }; | |
65 | |
66 static const DicomTag seriesIdentifiers[] = | |
67 { | |
68 DICOM_TAG_SERIES_INSTANCE_UID | |
69 }; | |
70 | |
71 static const DicomTag instanceIdentifiers[] = | |
72 { | |
73 DICOM_TAG_SOP_INSTANCE_UID | |
74 }; | |
75 | |
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 assert(source.isObject()); |
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82 |
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83 target = Json::objectValue; |
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84 Json::Value::Members members = source.getMemberNames(); |
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85 |
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86 for (size_t i = 0; i < members.size(); i++) |
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87 { |
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88 const Json::Value& v = source[members[i]]; |
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89 const std::string& type = v["Type"].asString(); |
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90 |
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91 std::string name; |
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92 switch (format) |
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93 { |
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94 case DicomToJsonFormat_Human: |
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95 name = v["Name"].asString(); |
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96 break; |
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97 |
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98 case DicomToJsonFormat_Short: |
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99 name = members[i]; |
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100 break; |
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101 |
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102 default: |
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103 throw OrthancException(ErrorCode_ParameterOutOfRange); |
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104 } |
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105 |
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106 if (type == "String") |
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107 { |
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108 target[name] = v["Value"].asString(); |
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109 } |
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110 else if (type == "TooLong" || |
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111 type == "Null") |
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112 { |
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113 target[name] = Json::nullValue; |
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114 } |
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115 else if (type == "Sequence") |
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116 { |
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117 const Json::Value& array = v["Value"]; |
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118 assert(array.isArray()); |
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119 |
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120 Json::Value children = Json::arrayValue; |
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121 for (Json::Value::ArrayIndex i = 0; i < array.size(); i++) |
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122 { |
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123 Json::Value c; |
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124 SimplifyTags(c, array[i], format); |
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125 children.append(c); |
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126 } |
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127 |
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128 target[name] = children; |
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129 } |
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130 else |
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131 { |
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132 assert(0); |
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133 } |
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134 } |
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135 } |
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136 |
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137 |
2120 | 138 static void StoreMainDicomTagsInternal(IDatabaseWrapper& database, |
139 int64_t resource, | |
140 const DicomMap& tags) | |
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141 { |
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142 DicomArray flattened(tags); |
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143 |
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144 for (size_t i = 0; i < flattened.GetSize(); i++) |
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145 { |
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146 const DicomElement& element = flattened.GetElement(i); |
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147 const DicomTag& tag = element.GetTag(); |
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148 const DicomValue& value = element.GetValue(); |
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149 if (!value.IsNull() && |
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150 !value.IsBinary()) |
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151 { |
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152 database.SetMainDicomTag(resource, tag, element.GetValue().GetContent()); |
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153 } |
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154 } |
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155 } |
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156 |
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157 |
2123 | 158 static void StoreIdentifiers(IDatabaseWrapper& database, |
159 int64_t resource, | |
160 ResourceType level, | |
161 const DicomMap& map) | |
162 { | |
163 const DicomTag* tags; | |
164 size_t size; | |
165 | |
166 LoadIdentifiers(tags, size, level); | |
167 | |
168 for (size_t i = 0; i < size; i++) | |
169 { | |
170 const DicomValue* value = map.TestAndGetValue(tags[i]); | |
171 if (value != NULL && | |
172 !value->IsNull() && | |
173 !value->IsBinary()) | |
174 { | |
175 std::string s = NormalizeIdentifier(value->GetContent()); | |
176 database.SetIdentifierTag(resource, tags[i], s); | |
177 } | |
178 } | |
179 } | |
180 | |
181 | |
2120 | 182 void StoreMainDicomTags(IDatabaseWrapper& database, |
183 int64_t resource, | |
184 ResourceType level, | |
185 const DicomMap& dicomSummary) | |
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186 { |
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187 // WARNING: The database should be locked with a transaction! |
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188 |
2121 | 189 StoreIdentifiers(database, resource, level, dicomSummary); |
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190 |
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191 DicomMap tags; |
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192 |
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193 switch (level) |
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194 { |
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195 case ResourceType_Patient: |
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196 dicomSummary.ExtractPatientInformation(tags); |
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197 break; |
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198 |
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199 case ResourceType_Study: |
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200 // Duplicate the patient tags at the study level (new in Orthanc 0.9.5 - db v6) |
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201 dicomSummary.ExtractPatientInformation(tags); |
2120 | 202 StoreMainDicomTagsInternal(database, resource, tags); |
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203 |
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204 dicomSummary.ExtractStudyInformation(tags); |
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205 break; |
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206 |
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207 case ResourceType_Series: |
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208 dicomSummary.ExtractSeriesInformation(tags); |
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209 break; |
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210 |
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211 case ResourceType_Instance: |
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212 dicomSummary.ExtractInstanceInformation(tags); |
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213 break; |
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214 |
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215 default: |
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216 throw OrthancException(ErrorCode_InternalError); |
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217 } |
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218 |
2120 | 219 StoreMainDicomTagsInternal(database, resource, tags); |
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220 } |
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221 |
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222 |
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223 bool FindOneChildInstance(int64_t& result, |
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224 IDatabaseWrapper& database, |
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225 int64_t resource, |
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226 ResourceType type) |
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227 { |
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228 for (;;) |
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229 { |
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230 if (type == ResourceType_Instance) |
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231 { |
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232 result = resource; |
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233 return true; |
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234 } |
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235 |
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236 std::list<int64_t> children; |
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237 database.GetChildrenInternalId(children, resource); |
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238 if (children.empty()) |
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239 { |
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240 return false; |
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241 } |
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242 |
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243 resource = children.front(); |
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244 type = GetChildResourceType(type); |
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245 } |
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246 } |
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247 |
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248 |
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249 void ReconstructMainDicomTags(IDatabaseWrapper& database, |
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250 IStorageArea& storageArea, |
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251 ResourceType level) |
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252 { |
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253 // WARNING: The database should be locked with a transaction! |
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254 |
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255 // TODO: This function might consume much memory if level == |
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256 // ResourceType_Instance. To improve this, first download the |
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257 // list of studies, then remove the instances for each single |
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258 // study (check out OrthancRestApi::InvalidateTags for an |
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259 // example). Take this improvement into consideration for the |
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260 // next upgrade of the database schema. |
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261 |
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262 const char* plural = NULL; |
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263 |
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264 switch (level) |
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265 { |
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266 case ResourceType_Patient: |
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267 plural = "patients"; |
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268 break; |
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269 |
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270 case ResourceType_Study: |
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271 plural = "studies"; |
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272 break; |
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273 |
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274 case ResourceType_Series: |
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275 plural = "series"; |
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276 break; |
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277 |
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278 case ResourceType_Instance: |
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279 plural = "instances"; |
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280 break; |
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281 |
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282 default: |
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283 throw OrthancException(ErrorCode_InternalError); |
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284 } |
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285 |
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286 LOG(WARNING) << "Upgrade: Reconstructing the main DICOM tags of all the " << plural << "..."; |
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287 |
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288 std::list<std::string> resources; |
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289 database.GetAllPublicIds(resources, level); |
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290 |
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291 for (std::list<std::string>::const_iterator |
1847 | 292 it = resources.begin(); it != resources.end(); ++it) |
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293 { |
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294 // Locate the resource and one of its child instances |
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295 int64_t resource, instance; |
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296 ResourceType tmp; |
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297 |
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298 if (!database.LookupResource(resource, tmp, *it) || |
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299 tmp != level || |
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300 !FindOneChildInstance(instance, database, resource, level)) |
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301 { |
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302 LOG(ERROR) << "Cannot find an instance for " << EnumerationToString(level) |
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303 << " with identifier " << *it; |
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304 throw OrthancException(ErrorCode_InternalError); |
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305 } |
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306 |
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307 // Get the DICOM file attached to some instances in the resource |
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308 FileInfo attachment; |
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309 if (!database.LookupAttachment(attachment, instance, FileContentType_Dicom)) |
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310 { |
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311 LOG(ERROR) << "Cannot retrieve the DICOM file associated with instance " << database.GetPublicId(instance); |
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312 throw OrthancException(ErrorCode_InternalError); |
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313 } |
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314 |
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315 try |
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316 { |
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317 // Read and parse the content of the DICOM file |
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318 StorageAccessor accessor(storageArea); |
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319 |
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320 std::string content; |
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321 accessor.Read(content, attachment); |
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322 |
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323 ParsedDicomFile dicom(content); |
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324 |
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325 // Update the tags of this resource |
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326 DicomMap dicomSummary; |
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327 dicom.ExtractDicomSummary(dicomSummary); |
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328 |
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329 database.ClearMainDicomTags(resource); |
2120 | 330 StoreMainDicomTags(database, resource, level, dicomSummary); |
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331 } |
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332 catch (OrthancException&) |
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333 { |
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334 LOG(ERROR) << "Cannot decode the DICOM file with UUID " << attachment.GetUuid() |
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335 << " associated with instance " << database.GetPublicId(instance); |
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336 throw; |
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337 } |
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338 } |
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339 } |
2121 | 340 |
341 | |
342 void LoadIdentifiers(const DicomTag*& tags, | |
343 size_t& size, | |
344 ResourceType level) | |
345 { | |
346 switch (level) | |
347 { | |
348 case ResourceType_Patient: | |
349 tags = patientIdentifiers; | |
350 size = sizeof(patientIdentifiers) / sizeof(DicomTag); | |
351 break; | |
352 | |
353 case ResourceType_Study: | |
354 tags = studyIdentifiers; | |
355 size = sizeof(studyIdentifiers) / sizeof(DicomTag); | |
356 break; | |
357 | |
358 case ResourceType_Series: | |
359 tags = seriesIdentifiers; | |
360 size = sizeof(seriesIdentifiers) / sizeof(DicomTag); | |
361 break; | |
362 | |
363 case ResourceType_Instance: | |
364 tags = instanceIdentifiers; | |
365 size = sizeof(instanceIdentifiers) / sizeof(DicomTag); | |
366 break; | |
367 | |
368 default: | |
369 throw OrthancException(ErrorCode_ParameterOutOfRange); | |
370 } | |
371 } | |
372 | |
373 | |
374 std::string NormalizeIdentifier(const std::string& value) | |
375 { | |
376 std::string t; | |
377 t.reserve(value.size()); | |
378 | |
379 for (size_t i = 0; i < value.size(); i++) | |
380 { | |
381 if (value[i] == '%' || | |
382 value[i] == '_') | |
383 { | |
384 t.push_back(' '); // These characters might break wildcard queries in SQL | |
385 } | |
386 else if (isascii(value[i]) && | |
387 !iscntrl(value[i]) && | |
388 (!isspace(value[i]) || value[i] == ' ')) | |
389 { | |
390 t.push_back(value[i]); | |
391 } | |
392 } | |
393 | |
394 Toolbox::ToUpperCase(t); | |
395 | |
396 return Toolbox::StripSpaces(t); | |
397 } | |
398 | |
399 | |
400 bool IsIdentifier(const DicomTag& tag, | |
401 ResourceType level) | |
402 { | |
403 const DicomTag* tags; | |
404 size_t size; | |
405 | |
406 LoadIdentifiers(tags, size, level); | |
407 | |
408 for (size_t i = 0; i < size; i++) | |
409 { | |
410 if (tag == tags[i]) | |
411 { | |
412 return true; | |
413 } | |
414 } | |
415 | |
416 return false; | |
417 } | |
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418 |
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419 |
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420 void ReconstructResource(ServerContext& context, |
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421 const std::string& resource) |
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422 { |
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423 LOG(WARNING) << "Reconstructing resource " << resource; |
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424 |
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425 std::list<std::string> instances; |
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426 context.GetIndex().GetChildInstances(instances, resource); |
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427 |
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428 for (std::list<std::string>::const_iterator |
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429 it = instances.begin(); it != instances.end(); ++it) |
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430 { |
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431 ServerContext::DicomCacheLocker locker(context, *it); |
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432 |
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433 Json::Value dicomAsJson; |
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434 locker.GetDicom().ExtractDicomAsJson(dicomAsJson); |
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435 |
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436 std::string s = dicomAsJson.toStyledString(); |
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437 context.AddAttachment(*it, FileContentType_DicomAsJson, s.c_str(), s.size()); |
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438 |
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439 context.GetIndex().ReconstructInstance(locker.GetDicom()); |
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440 } |
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441 } |
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442 } |
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443 } |