Mercurial > hg > orthanc
annotate OrthancServer/OrthancRestApi/OrthancRestArchive.cpp @ 2246:596528620416
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author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Wed, 04 Jan 2017 17:01:02 +0100 |
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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 "OrthancRestApi.h" |
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36 |
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37 #include "../DicomDirWriter.h" |
1775 | 38 #include "../../Core/FileStorage/StorageAccessor.h" |
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39 #include "../../Core/Compression/HierarchicalZipWriter.h" |
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40 #include "../../Core/HttpServer/FilesystemHttpSender.h" |
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41 #include "../../Core/Logging.h" |
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43 #include "../ServerContext.h" |
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44 |
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45 #include <stdio.h> |
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46 |
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47 #if defined(_MSC_VER) |
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48 #define snprintf _snprintf |
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49 #endif |
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50 |
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51 static const uint64_t MEGA_BYTES = 1024 * 1024; |
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52 static const uint64_t GIGA_BYTES = 1024 * 1024 * 1024; |
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53 |
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54 namespace Orthanc |
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55 { |
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56 // Download of ZIP files ---------------------------------------------------- |
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57 |
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58 static bool IsZip64Required(uint64_t uncompressedSize, |
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59 unsigned int countInstances) |
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60 { |
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61 static const uint64_t SAFETY_MARGIN = 64 * MEGA_BYTES; |
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62 |
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63 /** |
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64 * Determine whether ZIP64 is required. Original ZIP format can |
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65 * store up to 2GB of data (some implementation supporting up to |
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66 * 4GB of data), and up to 65535 files. |
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67 * https://en.wikipedia.org/wiki/Zip_(file_format)#ZIP64 |
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68 **/ |
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69 |
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70 const bool isZip64 = (uncompressedSize >= 2 * GIGA_BYTES - SAFETY_MARGIN || |
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71 countInstances >= 65535); |
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72 |
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73 LOG(INFO) << "Creating a ZIP file with " << countInstances << " files of size " |
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74 << (uncompressedSize / MEGA_BYTES) << "MB using the " |
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75 << (isZip64 ? "ZIP64" : "ZIP32") << " file format"; |
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76 |
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77 return isZip64; |
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78 } |
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79 |
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80 |
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81 namespace |
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82 { |
1776 | 83 class ResourceIdentifiers |
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84 { |
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85 private: |
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86 ResourceType level_; |
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87 std::string patient_; |
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88 std::string study_; |
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89 std::string series_; |
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90 std::string instance_; |
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91 |
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92 static void GoToParent(ServerIndex& index, |
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93 std::string& current) |
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94 { |
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95 std::string tmp; |
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96 |
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97 if (index.LookupParent(tmp, current)) |
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98 { |
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99 current = tmp; |
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100 } |
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101 else |
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102 { |
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103 throw OrthancException(ErrorCode_UnknownResource); |
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104 } |
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105 } |
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106 |
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107 |
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108 public: |
1776 | 109 ResourceIdentifiers(ServerIndex& index, |
110 const std::string& publicId) | |
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111 { |
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112 if (!index.LookupResourceType(level_, publicId)) |
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113 { |
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114 throw OrthancException(ErrorCode_UnknownResource); |
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115 } |
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116 |
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117 std::string current = publicId;; |
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118 switch (level_) // Do not add "break" below! |
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119 { |
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120 case ResourceType_Instance: |
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121 instance_ = current; |
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122 GoToParent(index, current); |
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123 |
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124 case ResourceType_Series: |
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125 series_ = current; |
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126 GoToParent(index, current); |
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127 |
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128 case ResourceType_Study: |
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129 study_ = current; |
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130 GoToParent(index, current); |
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131 |
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132 case ResourceType_Patient: |
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133 patient_ = current; |
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134 break; |
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135 |
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136 default: |
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137 throw OrthancException(ErrorCode_InternalError); |
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138 } |
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139 } |
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140 |
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141 ResourceType GetLevel() const |
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142 { |
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143 return level_; |
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144 } |
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145 |
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146 const std::string& GetIdentifier(ResourceType level) const |
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147 { |
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148 // Some sanity check to ensure enumerations are not altered |
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149 assert(ResourceType_Patient < ResourceType_Study); |
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150 assert(ResourceType_Study < ResourceType_Series); |
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151 assert(ResourceType_Series < ResourceType_Instance); |
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152 |
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153 if (level > level_) |
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154 { |
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155 throw OrthancException(ErrorCode_InternalError); |
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156 } |
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157 |
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158 switch (level) |
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159 { |
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160 case ResourceType_Patient: |
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161 return patient_; |
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162 |
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163 case ResourceType_Study: |
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164 return study_; |
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165 |
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166 case ResourceType_Series: |
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167 return series_; |
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168 |
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169 case ResourceType_Instance: |
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170 return instance_; |
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171 |
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172 default: |
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173 throw OrthancException(ErrorCode_InternalError); |
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174 } |
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175 } |
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176 }; |
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177 |
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178 |
1775 | 179 class IArchiveVisitor : public boost::noncopyable |
180 { | |
181 public: | |
182 virtual ~IArchiveVisitor() | |
183 { | |
184 } | |
185 | |
186 virtual void Open(ResourceType level, | |
187 const std::string& publicId) = 0; | |
188 | |
189 virtual void Close() = 0; | |
190 | |
191 virtual void AddInstance(const std::string& instanceId, | |
192 const FileInfo& dicom) = 0; | |
193 }; | |
194 | |
195 | |
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196 class ArchiveIndex |
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197 { |
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198 private: |
1775 | 199 struct Instance |
200 { | |
201 std::string id_; | |
202 FileInfo dicom_; | |
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203 |
1775 | 204 Instance(const std::string& id, |
205 const FileInfo& dicom) : | |
206 id_(id), dicom_(dicom) | |
207 { | |
208 } | |
209 }; | |
210 | |
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211 // A "NULL" value for ArchiveIndex indicates a non-expanded node |
1775 | 212 typedef std::map<std::string, ArchiveIndex*> Resources; |
213 | |
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214 ResourceType level_; |
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215 Resources resources_; // Only at patient/study/series level |
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216 std::list<Instance> instances_; // Only at instance level |
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217 |
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218 |
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219 void AddResourceToExpand(ServerIndex& index, |
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220 const std::string& id) |
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221 { |
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222 if (level_ == ResourceType_Instance) |
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223 { |
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224 FileInfo tmp; |
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225 if (index.LookupAttachment(tmp, id, FileContentType_Dicom)) |
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226 { |
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227 instances_.push_back(Instance(id, tmp)); |
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228 } |
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229 } |
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230 else |
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231 { |
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232 resources_[id] = NULL; |
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233 } |
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234 } |
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235 |
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236 |
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237 public: |
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238 ArchiveIndex(ResourceType level) : |
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239 level_(level) |
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240 { |
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241 } |
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242 |
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243 ~ArchiveIndex() |
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244 { |
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245 for (Resources::iterator it = resources_.begin(); |
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246 it != resources_.end(); ++it) |
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247 { |
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248 delete it->second; |
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249 } |
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250 } |
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251 |
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252 |
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253 void Add(ServerIndex& index, |
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254 const ResourceIdentifiers& resource) |
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255 { |
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256 const std::string& id = resource.GetIdentifier(level_); |
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257 Resources::iterator previous = resources_.find(id); |
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258 |
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259 if (level_ == ResourceType_Instance) |
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260 { |
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261 AddResourceToExpand(index, id); |
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262 } |
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263 else if (resource.GetLevel() == level_) |
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264 { |
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265 // Mark this resource for further expansion |
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266 if (previous != resources_.end()) |
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267 { |
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268 delete previous->second; |
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269 } |
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270 |
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271 resources_[id] = NULL; |
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272 } |
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273 else if (previous == resources_.end()) |
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274 { |
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275 // This is the first time we meet this resource |
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276 std::auto_ptr<ArchiveIndex> child(new ArchiveIndex(GetChildResourceType(level_))); |
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277 child->Add(index, resource); |
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278 resources_[id] = child.release(); |
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279 } |
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280 else if (previous->second != NULL) |
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281 { |
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282 previous->second->Add(index, resource); |
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283 } |
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284 else |
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285 { |
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286 // Nothing to do: This item is marked for further expansion |
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287 } |
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288 } |
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289 |
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290 |
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291 void Expand(ServerIndex& index) |
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292 { |
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293 if (level_ == ResourceType_Instance) |
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294 { |
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295 // Expanding an instance node makes no sense |
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296 return; |
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297 } |
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298 |
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299 for (Resources::iterator it = resources_.begin(); |
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300 it != resources_.end(); ++it) |
1775 | 301 { |
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302 if (it->second == NULL) |
1775 | 303 { |
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304 // This is resource is marked for expansion |
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305 std::list<std::string> children; |
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306 index.GetChildren(children, it->first); |
1775 | 307 |
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308 std::auto_ptr<ArchiveIndex> child(new ArchiveIndex(GetChildResourceType(level_))); |
1775 | 309 |
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310 for (std::list<std::string>::const_iterator |
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311 it2 = children.begin(); it2 != children.end(); ++it2) |
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312 { |
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313 child->AddResourceToExpand(index, *it2); |
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314 } |
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315 |
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316 it->second = child.release(); |
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317 } |
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318 |
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319 assert(it->second != NULL); |
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320 it->second->Expand(index); |
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321 } |
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322 } |
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323 |
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324 |
1775 | 325 void Apply(IArchiveVisitor& visitor) const |
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326 { |
1775 | 327 if (level_ == ResourceType_Instance) |
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328 { |
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329 for (std::list<Instance>::const_iterator |
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330 it = instances_.begin(); it != instances_.end(); ++it) |
1775 | 331 { |
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332 visitor.AddInstance(it->id_, it->dicom_); |
1775 | 333 } |
334 } | |
335 else | |
336 { | |
337 for (Resources::const_iterator it = resources_.begin(); | |
338 it != resources_.end(); ++it) | |
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339 { |
1775 | 340 assert(it->second != NULL); // There must have been a call to "Expand()" |
341 visitor.Open(level_, it->first); | |
342 it->second->Apply(visitor); | |
343 visitor.Close(); | |
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344 } |
1775 | 345 } |
346 } | |
347 }; | |
348 | |
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349 |
1775 | 350 class StatisticsVisitor : public IArchiveVisitor |
351 { | |
352 private: | |
353 uint64_t size_; | |
354 unsigned int instances_; | |
355 | |
356 public: | |
357 StatisticsVisitor() : size_(0), instances_(0) | |
358 { | |
359 } | |
360 | |
361 uint64_t GetUncompressedSize() const | |
362 { | |
363 return size_; | |
364 } | |
365 | |
366 unsigned int GetInstancesCount() const | |
367 { | |
368 return instances_; | |
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369 } |
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370 |
1775 | 371 virtual void Open(ResourceType level, |
372 const std::string& publicId) | |
373 { | |
374 } | |
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375 |
1775 | 376 virtual void Close() |
377 { | |
378 } | |
379 | |
380 virtual void AddInstance(const std::string& instanceId, | |
381 const FileInfo& dicom) | |
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382 { |
1775 | 383 instances_ ++; |
384 size_ += dicom.GetUncompressedSize(); | |
385 } | |
386 }; | |
387 | |
388 | |
389 class PrintVisitor : public IArchiveVisitor | |
390 { | |
391 private: | |
392 std::ostream& out_; | |
393 std::string indent_; | |
394 | |
395 public: | |
396 PrintVisitor(std::ostream& out) : out_(out) | |
397 { | |
398 } | |
399 | |
400 virtual void Open(ResourceType level, | |
401 const std::string& publicId) | |
402 { | |
403 switch (level) | |
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404 { |
1775 | 405 case ResourceType_Patient: indent_ = ""; break; |
406 case ResourceType_Study: indent_ = " "; break; | |
407 case ResourceType_Series: indent_ = " "; break; | |
408 default: | |
409 throw OrthancException(ErrorCode_InternalError); | |
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410 } |
1775 | 411 |
412 out_ << indent_ << publicId << std::endl; | |
413 } | |
414 | |
415 virtual void Close() | |
416 { | |
417 } | |
418 | |
419 virtual void AddInstance(const std::string& instanceId, | |
420 const FileInfo& dicom) | |
421 { | |
422 out_ << " " << instanceId << std::endl; | |
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423 } |
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424 }; |
1778
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425 |
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426 |
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427 class ArchiveWriterVisitor : public IArchiveVisitor |
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428 { |
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429 private: |
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430 HierarchicalZipWriter& writer_; |
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431 ServerContext& context_; |
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432 char instanceFormat_[24]; |
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433 unsigned int countInstances_; |
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434 |
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435 static std::string GetTag(const DicomMap& tags, |
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436 const DicomTag& tag) |
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437 { |
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438 const DicomValue* v = tags.TestAndGetValue(tag); |
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439 if (v != NULL && |
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440 !v->IsBinary() && |
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441 !v->IsNull()) |
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442 { |
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443 return v->GetContent(); |
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444 } |
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445 else |
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446 { |
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447 return ""; |
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448 } |
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449 } |
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450 |
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451 public: |
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452 ArchiveWriterVisitor(HierarchicalZipWriter& writer, |
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453 ServerContext& context) : |
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454 writer_(writer), |
1847 | 455 context_(context), |
456 countInstances_(0) | |
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457 { |
1847 | 458 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%%08d.dcm"); |
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459 } |
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460 |
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461 virtual void Open(ResourceType level, |
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462 const std::string& publicId) |
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463 { |
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464 std::string path; |
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465 |
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466 DicomMap tags; |
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467 if (context_.GetIndex().GetMainDicomTags(tags, publicId, level, level)) |
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468 { |
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469 switch (level) |
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470 { |
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471 case ResourceType_Patient: |
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472 path = GetTag(tags, DICOM_TAG_PATIENT_ID) + " " + GetTag(tags, DICOM_TAG_PATIENT_NAME); |
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473 break; |
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474 |
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475 case ResourceType_Study: |
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476 path = GetTag(tags, DICOM_TAG_ACCESSION_NUMBER) + " " + GetTag(tags, DICOM_TAG_STUDY_DESCRIPTION); |
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477 break; |
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478 |
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479 case ResourceType_Series: |
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480 { |
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481 std::string modality = GetTag(tags, DICOM_TAG_MODALITY); |
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482 path = modality + " " + GetTag(tags, DICOM_TAG_SERIES_DESCRIPTION); |
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483 |
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484 if (modality.size() == 0) |
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485 { |
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486 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%%08d.dcm"); |
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487 } |
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488 else if (modality.size() == 1) |
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489 { |
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490 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%c%%07d.dcm", |
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491 toupper(modality[0])); |
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492 } |
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493 else if (modality.size() >= 2) |
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494 { |
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495 snprintf(instanceFormat_, sizeof(instanceFormat_) - 1, "%c%c%%06d.dcm", |
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496 toupper(modality[0]), toupper(modality[1])); |
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497 } |
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498 |
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499 countInstances_ = 0; |
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500 |
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501 break; |
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502 } |
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503 |
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504 default: |
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505 throw OrthancException(ErrorCode_InternalError); |
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506 } |
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507 } |
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508 |
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509 path = Toolbox::StripSpaces(Toolbox::ConvertToAscii(path)); |
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510 |
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511 if (path.empty()) |
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512 { |
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513 path = std::string("Unknown ") + EnumerationToString(level); |
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514 } |
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515 |
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516 writer_.OpenDirectory(path.c_str()); |
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517 } |
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518 |
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519 virtual void Close() |
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520 { |
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521 writer_.CloseDirectory(); |
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522 } |
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523 |
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524 virtual void AddInstance(const std::string& instanceId, |
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525 const FileInfo& dicom) |
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526 { |
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527 std::string content; |
2128
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528 context_.ReadAttachment(content, dicom); |
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529 |
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530 char filename[24]; |
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531 snprintf(filename, sizeof(filename) - 1, instanceFormat_, countInstances_); |
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532 countInstances_ ++; |
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533 |
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534 writer_.OpenFile(filename); |
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535 writer_.Write(content); |
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536 } |
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537 |
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538 static void Apply(RestApiOutput& output, |
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539 ServerContext& context, |
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540 ArchiveIndex& archive, |
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541 const std::string& filename) |
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542 { |
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543 archive.Expand(context.GetIndex()); |
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544 |
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545 StatisticsVisitor stats; |
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546 archive.Apply(stats); |
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547 |
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548 const bool isZip64 = IsZip64Required(stats.GetUncompressedSize(), stats.GetInstancesCount()); |
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549 |
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550 // Create a RAII for the temporary file to manage the ZIP file |
2140 | 551 TemporaryFile tmp; |
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552 |
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553 { |
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554 // Create a ZIP writer |
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555 HierarchicalZipWriter writer(tmp.GetPath().c_str()); |
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556 writer.SetZip64(isZip64); |
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557 |
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558 ArchiveWriterVisitor v(writer, context); |
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559 archive.Apply(v); |
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560 } |
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561 |
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562 // Prepare the sending of the ZIP file |
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563 FilesystemHttpSender sender(tmp.GetPath()); |
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564 sender.SetContentType("application/zip"); |
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565 sender.SetContentFilename(filename); |
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566 |
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567 // Send the ZIP |
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568 output.AnswerStream(sender); |
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569 |
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570 // The temporary file is automatically removed thanks to the RAII |
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571 } |
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572 }; |
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573 |
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574 |
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575 class MediaWriterVisitor : public IArchiveVisitor |
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576 { |
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577 private: |
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578 HierarchicalZipWriter& writer_; |
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579 DicomDirWriter dicomDir_; |
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580 ServerContext& context_; |
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581 unsigned int countInstances_; |
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582 |
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583 public: |
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584 MediaWriterVisitor(HierarchicalZipWriter& writer, |
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585 ServerContext& context) : |
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586 writer_(writer), |
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587 context_(context), |
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588 countInstances_(0) |
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589 { |
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590 } |
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591 |
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592 void EncodeDicomDir(std::string& result) |
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593 { |
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594 dicomDir_.Encode(result); |
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595 } |
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596 |
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597 virtual void Open(ResourceType level, |
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598 const std::string& publicId) |
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599 { |
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600 } |
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601 |
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602 virtual void Close() |
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603 { |
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604 } |
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605 |
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606 virtual void AddInstance(const std::string& instanceId, |
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607 const FileInfo& dicom) |
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608 { |
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609 // "DICOM restricts the filenames on DICOM media to 8 |
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610 // characters (some systems wrongly use 8.3, but this does not |
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611 // conform to the standard)." |
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612 std::string filename = "IM" + boost::lexical_cast<std::string>(countInstances_); |
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613 writer_.OpenFile(filename.c_str()); |
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614 |
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615 std::string content; |
2128
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616 context_.ReadAttachment(content, dicom); |
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617 writer_.Write(content); |
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618 |
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619 ParsedDicomFile parsed(content); |
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620 dicomDir_.Add("IMAGES", filename, parsed); |
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621 |
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622 countInstances_ ++; |
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623 } |
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624 |
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625 static void Apply(RestApiOutput& output, |
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626 ServerContext& context, |
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627 ArchiveIndex& archive, |
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628 const std::string& filename) |
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629 { |
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630 archive.Expand(context.GetIndex()); |
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631 |
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632 StatisticsVisitor stats; |
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633 archive.Apply(stats); |
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634 |
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635 const bool isZip64 = IsZip64Required(stats.GetUncompressedSize(), stats.GetInstancesCount()); |
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636 |
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637 // Create a RAII for the temporary file to manage the ZIP file |
2140 | 638 TemporaryFile tmp; |
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639 |
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640 { |
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641 // Create a ZIP writer |
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642 HierarchicalZipWriter writer(tmp.GetPath().c_str()); |
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643 writer.SetZip64(isZip64); |
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644 writer.OpenDirectory("IMAGES"); |
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645 |
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646 // Create the DICOMDIR writer |
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647 DicomDirWriter dicomDir; |
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648 |
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649 MediaWriterVisitor v(writer, context); |
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650 archive.Apply(v); |
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651 |
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652 // Add the DICOMDIR |
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653 writer.CloseDirectory(); |
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654 writer.OpenFile("DICOMDIR"); |
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655 std::string s; |
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656 v.EncodeDicomDir(s); |
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657 writer.Write(s); |
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658 } |
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659 |
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660 // Prepare the sending of the ZIP file |
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661 FilesystemHttpSender sender(tmp.GetPath()); |
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662 sender.SetContentType("application/zip"); |
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663 sender.SetContentFilename(filename); |
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664 |
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665 // Send the ZIP |
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666 output.AnswerStream(sender); |
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667 |
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668 // The temporary file is automatically removed thanks to the RAII |
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669 } |
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670 }; |
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671 } |
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672 |
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673 |
1778
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674 static bool AddResourcesOfInterest(ArchiveIndex& archive, |
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675 RestApiPostCall& call) |
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676 { |
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677 ServerIndex& index = OrthancRestApi::GetIndex(call); |
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678 |
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679 Json::Value resources; |
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680 if (call.ParseJsonRequest(resources) && |
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681 resources.type() == Json::arrayValue) |
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682 { |
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683 for (Json::Value::ArrayIndex i = 0; i < resources.size(); i++) |
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684 { |
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685 if (resources[i].type() != Json::stringValue) |
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686 { |
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687 return false; // Bad request |
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688 } |
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689 |
1776 | 690 ResourceIdentifiers resource(index, resources[i].asString()); |
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691 archive.Add(index, resource); |
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692 } |
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693 |
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694 return true; |
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695 } |
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696 else |
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697 { |
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698 return false; |
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699 } |
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700 } |
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701 |
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702 |
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703 static void CreateBatchArchive(RestApiPostCall& call) |
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704 { |
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705 ArchiveIndex archive(ResourceType_Patient); // root |
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706 |
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707 if (AddResourcesOfInterest(archive, call)) |
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708 { |
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709 ArchiveWriterVisitor::Apply(call.GetOutput(), |
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710 OrthancRestApi::GetContext(call), |
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711 archive, |
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712 "Archive.zip"); |
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713 } |
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714 } |
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715 |
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716 |
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717 static void CreateBatchMedia(RestApiPostCall& call) |
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718 { |
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719 ArchiveIndex archive(ResourceType_Patient); // root |
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720 |
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721 if (AddResourcesOfInterest(archive, call)) |
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722 { |
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723 MediaWriterVisitor::Apply(call.GetOutput(), |
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724 OrthancRestApi::GetContext(call), |
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725 archive, |
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726 "Archive.zip"); |
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727 } |
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728 } |
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729 |
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730 |
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731 static void CreateArchive(RestApiGetCall& call) |
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732 { |
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733 ServerIndex& index = OrthancRestApi::GetIndex(call); |
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734 |
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735 std::string id = call.GetUriComponent("id", ""); |
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736 ResourceIdentifiers resource(index, id); |
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737 |
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738 ArchiveIndex archive(ResourceType_Patient); // root |
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739 archive.Add(OrthancRestApi::GetIndex(call), resource); |
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740 |
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741 ArchiveWriterVisitor::Apply(call.GetOutput(), |
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742 OrthancRestApi::GetContext(call), |
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743 archive, |
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744 id + ".zip"); |
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745 } |
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746 |
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747 |
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748 static void CreateMedia(RestApiGetCall& call) |
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749 { |
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750 ServerIndex& index = OrthancRestApi::GetIndex(call); |
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751 |
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752 std::string id = call.GetUriComponent("id", ""); |
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753 ResourceIdentifiers resource(index, id); |
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754 |
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755 ArchiveIndex archive(ResourceType_Patient); // root |
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756 archive.Add(OrthancRestApi::GetIndex(call), resource); |
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757 |
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758 MediaWriterVisitor::Apply(call.GetOutput(), |
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759 OrthancRestApi::GetContext(call), |
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760 archive, |
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761 id + ".zip"); |
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762 } |
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763 |
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764 |
751
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765 void OrthancRestApi::RegisterArchive() |
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766 { |
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767 Register("/patients/{id}/archive", CreateArchive); |
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768 Register("/studies/{id}/archive", CreateArchive); |
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769 Register("/series/{id}/archive", CreateArchive); |
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|
770 |
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771 Register("/patients/{id}/media", CreateMedia); |
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772 Register("/studies/{id}/media", CreateMedia); |
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773 Register("/series/{id}/media", CreateMedia); |
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774 |
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775 Register("/tools/create-archive", CreateBatchArchive); |
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776 Register("/tools/create-media", CreateBatchMedia); |
751
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777 } |
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778 } |