Mercurial > hg > orthanc
annotate OrthancServer/OrthancRestApi/OrthancRestArchive.cpp @ 1774:784a6b92d2f1
start of refactoring the creation of archives
author | Sebastien Jodogne <s.jodogne@gmail.com> |
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date | Thu, 12 Nov 2015 17:49:04 +0100 |
parents | 76ed4cf74bb5 |
children | 1861e410a9d7 |
rev | line source |
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1 /** |
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2 * Orthanc - A Lightweight, RESTful DICOM Store |
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3 * Copyright (C) 2012-2015 Sebastien Jodogne, Medical Physics |
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4 * Department, University Hospital of Liege, Belgium |
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5 * |
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6 * This program is free software: you can redistribute it and/or |
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7 * modify it under the terms of the GNU General Public License as |
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8 * published by the Free Software Foundation, either version 3 of the |
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9 * License, or (at your option) any later version. |
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10 * |
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11 * In addition, as a special exception, the copyright holders of this |
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12 * program give permission to link the code of its release with the |
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13 * OpenSSL project's "OpenSSL" library (or with modified versions of it |
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14 * that use the same license as the "OpenSSL" library), and distribute |
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15 * the linked executables. You must obey the GNU General Public License |
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16 * in all respects for all of the code used other than "OpenSSL". If you |
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17 * modify file(s) with this exception, you may extend this exception to |
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18 * your version of the file(s), but you are not obligated to do so. If |
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19 * you do not wish to do so, delete this exception statement from your |
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20 * version. If you delete this exception statement from all source files |
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21 * in the program, then also delete it here. |
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22 * |
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23 * This program is distributed in the hope that it will be useful, but |
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24 * WITHOUT ANY WARRANTY; without even the implied warranty of |
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25 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU |
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26 * General Public License for more details. |
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27 * |
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28 * You should have received a copy of the GNU General Public License |
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29 * along with this program. If not, see <http://www.gnu.org/licenses/>. |
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30 **/ |
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31 |
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32 |
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33 #include "../PrecompiledHeadersServer.h" |
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34 #include "OrthancRestApi.h" |
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35 |
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36 #include "../DicomDirWriter.h" |
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37 #include "../../Core/Compression/HierarchicalZipWriter.h" |
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38 #include "../../Core/HttpServer/FilesystemHttpSender.h" |
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39 #include "../../Core/Logging.h" |
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40 #include "../../Core/Uuid.h" |
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41 #include "../ServerContext.h" |
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42 |
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43 #include <stdio.h> |
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44 |
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45 #if defined(_MSC_VER) |
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46 #define snprintf _snprintf |
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47 #endif |
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48 |
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49 static const uint64_t MEGA_BYTES = 1024 * 1024; |
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50 static const uint64_t GIGA_BYTES = 1024 * 1024 * 1024; |
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51 |
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52 namespace Orthanc |
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53 { |
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54 // Download of ZIP files ---------------------------------------------------- |
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55 |
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56 static std::string GetDirectoryNameInArchive(const Json::Value& resource, |
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57 ResourceType resourceType) |
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58 { |
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59 std::string s; |
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60 const Json::Value& tags = resource["MainDicomTags"]; |
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61 |
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62 switch (resourceType) |
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63 { |
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64 case ResourceType_Patient: |
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65 { |
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66 std::string p = tags["PatientID"].asString(); |
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67 std::string n = tags["PatientName"].asString(); |
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68 s = p + " " + n; |
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69 break; |
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70 } |
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71 |
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72 case ResourceType_Study: |
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73 { |
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74 std::string p; |
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75 if (tags.isMember("AccessionNumber")) |
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76 { |
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77 p = tags["AccessionNumber"].asString() + " "; |
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78 } |
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79 |
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80 s = p + tags["StudyDescription"].asString(); |
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81 break; |
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82 } |
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83 |
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84 case ResourceType_Series: |
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85 { |
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86 std::string d = tags["SeriesDescription"].asString(); |
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87 std::string m = tags["Modality"].asString(); |
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88 s = m + " " + d; |
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89 break; |
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90 } |
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91 |
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92 default: |
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93 throw OrthancException(ErrorCode_InternalError); |
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94 } |
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95 |
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96 // Get rid of special characters |
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97 return Toolbox::ConvertToAscii(s); |
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98 } |
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99 |
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100 static bool CreateRootDirectoryInArchive(HierarchicalZipWriter& writer, |
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101 ServerContext& context, |
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102 const Json::Value& resource, |
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103 ResourceType resourceType) |
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104 { |
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105 if (resourceType == ResourceType_Patient) |
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106 { |
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107 return true; |
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108 } |
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109 |
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110 ResourceType parentType = GetParentResourceType(resourceType); |
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111 Json::Value parent; |
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112 |
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113 switch (resourceType) |
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114 { |
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115 case ResourceType_Study: |
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116 { |
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117 if (!context.GetIndex().LookupResource(parent, resource["ParentPatient"].asString(), parentType)) |
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118 { |
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119 return false; |
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120 } |
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121 |
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122 break; |
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123 } |
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124 |
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125 case ResourceType_Series: |
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126 if (!context.GetIndex().LookupResource(parent, resource["ParentStudy"].asString(), parentType) || |
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127 !CreateRootDirectoryInArchive(writer, context, parent, parentType)) |
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128 { |
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129 return false; |
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130 } |
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131 break; |
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132 |
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133 default: |
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134 throw OrthancException(ErrorCode_NotImplemented); |
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135 } |
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136 |
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137 writer.OpenDirectory(GetDirectoryNameInArchive(parent, parentType).c_str()); |
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138 return true; |
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139 } |
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140 |
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141 static bool ArchiveInstance(HierarchicalZipWriter& writer, |
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142 ServerContext& context, |
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143 const std::string& instancePublicId, |
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144 const char* filename) |
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145 { |
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146 writer.OpenFile(filename); |
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147 |
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148 std::string dicom; |
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149 context.ReadFile(dicom, instancePublicId, FileContentType_Dicom); |
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150 writer.Write(dicom); |
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151 |
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152 return true; |
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153 } |
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154 |
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155 static bool ArchiveInternal(HierarchicalZipWriter& writer, |
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156 ServerContext& context, |
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157 const std::string& publicId, |
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158 ResourceType resourceType, |
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159 bool isFirstLevel) |
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160 { |
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161 Json::Value resource; |
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162 if (!context.GetIndex().LookupResource(resource, publicId, resourceType)) |
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163 { |
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164 return false; |
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165 } |
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166 |
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167 if (isFirstLevel && |
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168 !CreateRootDirectoryInArchive(writer, context, resource, resourceType)) |
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169 { |
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170 return false; |
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171 } |
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172 |
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173 writer.OpenDirectory(GetDirectoryNameInArchive(resource, resourceType).c_str()); |
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174 |
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175 switch (resourceType) |
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176 { |
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177 case ResourceType_Patient: |
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178 for (Json::Value::ArrayIndex i = 0; i < resource["Studies"].size(); i++) |
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179 { |
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180 std::string studyId = resource["Studies"][i].asString(); |
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181 if (!ArchiveInternal(writer, context, studyId, ResourceType_Study, false)) |
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182 { |
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183 return false; |
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184 } |
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185 } |
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186 break; |
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187 |
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188 case ResourceType_Study: |
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189 for (Json::Value::ArrayIndex i = 0; i < resource["Series"].size(); i++) |
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190 { |
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191 std::string seriesId = resource["Series"][i].asString(); |
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192 if (!ArchiveInternal(writer, context, seriesId, ResourceType_Series, false)) |
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193 { |
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194 return false; |
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195 } |
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196 } |
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197 break; |
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198 |
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199 case ResourceType_Series: |
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200 { |
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201 // Create a filename prefix, depending on the modality |
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202 char format[24] = "%08d.dcm"; |
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203 |
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204 if (resource["MainDicomTags"].isMember("Modality")) |
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205 { |
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206 std::string modality = resource["MainDicomTags"]["Modality"].asString(); |
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207 |
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208 if (modality.size() == 1) |
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209 { |
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210 snprintf(format, sizeof(format) - 1, "%c%%07d.dcm", toupper(modality[0])); |
751
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211 } |
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212 else if (modality.size() >= 2) |
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213 { |
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214 snprintf(format, sizeof(format) - 1, "%c%c%%06d.dcm", toupper(modality[0]), toupper(modality[1])); |
751
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215 } |
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216 } |
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217 |
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218 char filename[24]; |
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219 |
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220 for (Json::Value::ArrayIndex i = 0; i < resource["Instances"].size(); i++) |
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221 { |
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222 snprintf(filename, sizeof(filename) - 1, format, i); |
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223 |
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224 std::string publicId = resource["Instances"][i].asString(); |
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225 |
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226 // This was the implementation up to Orthanc 0.7.0: |
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227 // std::string filename = instance["MainDicomTags"]["SOPInstanceUID"].asString() + ".dcm"; |
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228 |
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229 if (!ArchiveInstance(writer, context, publicId, filename)) |
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230 { |
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231 return false; |
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232 } |
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233 } |
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234 |
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235 break; |
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236 } |
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237 |
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238 default: |
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239 throw OrthancException(ErrorCode_InternalError); |
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240 } |
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241 |
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242 writer.CloseDirectory(); |
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243 return true; |
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244 } |
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245 |
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246 |
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247 static bool IsZip64Required(uint64_t uncompressedSize, |
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248 unsigned int countInstances) |
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249 { |
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250 static const uint64_t SAFETY_MARGIN = 64 * MEGA_BYTES; |
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251 |
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252 /** |
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253 * Determine whether ZIP64 is required. Original ZIP format can |
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254 * store up to 2GB of data (some implementation supporting up to |
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255 * 4GB of data), and up to 65535 files. |
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256 * https://en.wikipedia.org/wiki/Zip_(file_format)#ZIP64 |
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257 **/ |
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258 |
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259 const bool isZip64 = (uncompressedSize >= 2 * GIGA_BYTES - SAFETY_MARGIN || |
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260 countInstances >= 65535); |
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261 |
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262 LOG(INFO) << "Creating a ZIP file with " << countInstances << " files of size " |
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263 << (uncompressedSize / MEGA_BYTES) << "MB using the " |
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264 << (isZip64 ? "ZIP64" : "ZIP32") << " file format"; |
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265 |
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266 return isZip64; |
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267 } |
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268 |
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269 |
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270 static bool IsZip64Required(ServerIndex& index, |
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271 const std::string& id) |
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272 { |
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273 uint64_t uncompressedSize; |
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274 uint64_t compressedSize; |
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275 unsigned int countStudies; |
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276 unsigned int countSeries; |
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277 unsigned int countInstances; |
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278 |
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279 index.GetStatistics(compressedSize, uncompressedSize, |
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280 countStudies, countSeries, countInstances, id); |
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281 |
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282 return IsZip64Required(uncompressedSize, countInstances); |
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283 } |
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284 |
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285 |
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286 template <enum ResourceType resourceType> |
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287 static void GetArchive(RestApiGetCall& call) |
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288 { |
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289 ServerContext& context = OrthancRestApi::GetContext(call); |
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290 |
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291 std::string id = call.GetUriComponent("id", ""); |
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292 bool isZip64 = IsZip64Required(context.GetIndex(), id); |
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293 |
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294 // Create a RAII for the temporary file to manage the ZIP file |
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295 Toolbox::TemporaryFile tmp; |
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296 |
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297 { |
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298 // Create a ZIP writer |
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299 HierarchicalZipWriter writer(tmp.GetPath().c_str()); |
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300 writer.SetZip64(isZip64); |
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301 |
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302 // Store the requested resource into the ZIP |
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303 if (!ArchiveInternal(writer, context, id, resourceType, true)) |
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304 { |
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305 return; |
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306 } |
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307 } |
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308 |
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309 // Prepare the sending of the ZIP file |
1522 | 310 FilesystemHttpSender sender(tmp.GetPath()); |
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311 sender.SetContentType("application/zip"); |
1522 | 312 sender.SetContentFilename(id + ".zip"); |
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313 |
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314 // Send the ZIP |
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315 call.GetOutput().AnswerStream(sender); |
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316 |
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317 // The temporary file is automatically removed thanks to the RAII |
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318 } |
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319 |
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320 |
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321 static void GetMediaArchive(RestApiGetCall& call) |
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322 { |
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323 ServerContext& context = OrthancRestApi::GetContext(call); |
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324 |
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325 std::string id = call.GetUriComponent("id", ""); |
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326 bool isZip64 = IsZip64Required(context.GetIndex(), id); |
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327 |
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328 // Create a RAII for the temporary file to manage the ZIP file |
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329 Toolbox::TemporaryFile tmp; |
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330 |
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331 { |
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332 // Create a ZIP writer |
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333 HierarchicalZipWriter writer(tmp.GetPath().c_str()); |
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334 writer.SetZip64(isZip64); |
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335 writer.OpenDirectory("IMAGES"); |
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336 |
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337 // Create the DICOMDIR writer |
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338 DicomDirWriter dicomDir; |
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339 |
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340 // Retrieve the list of the instances |
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341 std::list<std::string> instances; |
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342 context.GetIndex().GetChildInstances(instances, id); |
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343 |
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344 size_t pos = 0; |
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345 for (std::list<std::string>::const_iterator |
1303 | 346 it = instances.begin(); it != instances.end(); ++it, ++pos) |
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347 { |
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348 // "DICOM restricts the filenames on DICOM media to 8 |
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349 // characters (some systems wrongly use 8.3, but this does not |
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350 // conform to the standard)." |
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351 std::string filename = "IM" + boost::lexical_cast<std::string>(pos); |
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352 writer.OpenFile(filename.c_str()); |
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353 |
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354 std::string dicom; |
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355 context.ReadFile(dicom, *it, FileContentType_Dicom); |
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356 writer.Write(dicom); |
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357 |
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358 ParsedDicomFile parsed(dicom); |
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359 dicomDir.Add("IMAGES", filename, parsed); |
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360 } |
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361 |
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362 // Add the DICOMDIR |
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363 writer.CloseDirectory(); |
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364 writer.OpenFile("DICOMDIR"); |
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365 std::string s; |
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366 dicomDir.Encode(s); |
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367 writer.Write(s); |
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368 } |
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369 |
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370 // Prepare the sending of the ZIP file |
1522 | 371 FilesystemHttpSender sender(tmp.GetPath()); |
1121
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372 sender.SetContentType("application/zip"); |
1522 | 373 sender.SetContentFilename(id + ".zip"); |
1121
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374 |
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375 // Send the ZIP |
1519
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376 call.GetOutput().AnswerStream(sender); |
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377 |
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378 // The temporary file is automatically removed thanks to the RAII |
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379 } |
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380 |
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381 |
1774
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382 |
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383 |
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384 namespace |
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385 { |
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386 class Resource |
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387 { |
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388 private: |
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389 ResourceType level_; |
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390 std::string patient_; |
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391 std::string study_; |
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392 std::string series_; |
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393 std::string instance_; |
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394 |
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395 static void GoToParent(ServerIndex& index, |
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396 std::string& current) |
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397 { |
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398 std::string tmp; |
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399 |
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400 if (index.LookupParent(tmp, current)) |
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401 { |
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402 current = tmp; |
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403 } |
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404 else |
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405 { |
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406 throw OrthancException(ErrorCode_UnknownResource); |
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407 } |
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408 } |
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409 |
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410 |
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411 public: |
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412 Resource(ServerIndex& index, |
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413 const std::string& publicId) |
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414 { |
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415 if (!index.LookupResourceType(level_, publicId)) |
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416 { |
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417 throw OrthancException(ErrorCode_UnknownResource); |
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418 } |
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419 |
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420 std::string current = publicId;; |
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421 switch (level_) // Do not add "break" below! |
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422 { |
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423 case ResourceType_Instance: |
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424 instance_ = current; |
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425 GoToParent(index, current); |
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426 |
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427 case ResourceType_Series: |
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428 series_ = current; |
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429 GoToParent(index, current); |
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430 |
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431 case ResourceType_Study: |
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432 study_ = current; |
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433 GoToParent(index, current); |
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434 |
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435 case ResourceType_Patient: |
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436 patient_ = current; |
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437 break; |
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438 |
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439 default: |
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440 throw OrthancException(ErrorCode_InternalError); |
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441 } |
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442 } |
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443 |
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444 ResourceType GetLevel() const |
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445 { |
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446 return level_; |
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447 } |
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448 |
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449 const std::string& GetIdentifier(ResourceType level) const |
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450 { |
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451 // Some sanity check to ensure enumerations are not altered |
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452 assert(ResourceType_Patient < ResourceType_Study); |
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453 assert(ResourceType_Study < ResourceType_Series); |
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454 assert(ResourceType_Series < ResourceType_Instance); |
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455 |
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456 if (level > level_) |
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457 { |
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458 throw OrthancException(ErrorCode_InternalError); |
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459 } |
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460 |
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461 switch (level) |
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462 { |
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463 case ResourceType_Patient: |
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464 return patient_; |
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465 |
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466 case ResourceType_Study: |
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467 return study_; |
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468 |
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469 case ResourceType_Series: |
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470 return series_; |
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471 |
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472 case ResourceType_Instance: |
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473 return instance_; |
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474 |
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475 default: |
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476 throw OrthancException(ErrorCode_InternalError); |
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477 } |
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478 } |
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479 }; |
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480 |
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481 |
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482 class ArchiveIndex |
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483 { |
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484 private: |
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485 typedef std::map<std::string, ArchiveIndex*> Resources; |
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486 |
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487 ServerIndex& index_; |
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488 ResourceType level_; |
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489 Resources resources_; |
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490 |
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491 void AddResourceToExpand(const std::string& id) |
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492 { |
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493 resources_[id] = NULL; |
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494 } |
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495 |
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496 public: |
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497 ArchiveIndex(ServerIndex& index, |
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498 ResourceType level) : |
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499 index_(index), |
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500 level_(level) |
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501 { |
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502 } |
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503 |
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504 ~ArchiveIndex() |
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505 { |
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506 for (Resources::iterator it = resources_.begin(); |
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507 it != resources_.end(); ++it) |
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508 { |
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509 delete it->second; |
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510 } |
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511 } |
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512 |
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513 void Add(const Resource& resource) |
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514 { |
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515 const std::string& id = resource.GetIdentifier(level_); |
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516 Resources::iterator previous = resources_.find(id); |
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517 |
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518 if (resource.GetLevel() == level_) |
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519 { |
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520 // Mark this resource for further expansion |
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521 if (previous != resources_.end()) |
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522 { |
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523 delete previous->second; |
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524 } |
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525 |
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526 resources_[id] = NULL; |
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527 } |
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528 else if (previous == resources_.end()) |
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529 { |
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530 // This is the first time we meet this resource |
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531 std::auto_ptr<ArchiveIndex> child(new ArchiveIndex(index_, GetChildResourceType(level_))); |
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532 child->Add(resource); |
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533 resources_[id] = child.release(); |
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534 } |
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535 else if (previous->second != NULL) |
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536 { |
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537 previous->second->Add(resource); |
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538 } |
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539 else |
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540 { |
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541 // Nothing to do: This item is marked for further expansion |
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542 } |
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543 } |
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544 |
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545 |
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546 void Expand() |
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547 { |
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548 if (level_ == ResourceType_Instance) |
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549 { |
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550 return; |
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551 } |
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552 |
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553 for (Resources::iterator it = resources_.begin(); |
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554 it != resources_.end(); ++it) |
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555 { |
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556 if (it->second == NULL) |
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557 { |
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558 std::list<std::string> children; |
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559 index_.GetChildren(children, it->first); |
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560 |
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561 std::auto_ptr<ArchiveIndex> child(new ArchiveIndex(index_, GetChildResourceType(level_))); |
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562 |
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563 for (std::list<std::string>::const_iterator |
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564 it2 = children.begin(); it2 != children.end(); ++it2) |
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565 { |
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566 child->AddResourceToExpand(*it2); |
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567 } |
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568 |
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569 it->second = child.release(); |
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570 } |
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571 |
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572 assert(it->second != NULL); |
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573 it->second->Expand(); |
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574 } |
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575 } |
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576 |
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577 |
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578 void ComputeStatistics(uint64_t& totalSize, |
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579 unsigned int& totalInstances) |
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580 { |
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581 for (Resources::iterator it = resources_.begin(); |
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582 it != resources_.end(); ++it) |
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583 { |
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584 if (level_ == ResourceType_Instance) |
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585 { |
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586 FileInfo dicom; |
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587 if (index_.LookupAttachment(dicom, it->first, FileContentType_Dicom)) |
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588 { |
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589 totalSize += dicom.GetUncompressedSize(); |
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590 totalInstances ++; |
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591 } |
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592 } |
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593 else |
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594 { |
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595 if (it->second == NULL) |
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596 { |
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597 // The method "Expand" was not called |
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598 throw OrthancException(ErrorCode_InternalError); |
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599 } |
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600 |
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601 it->second->ComputeStatistics(totalSize, totalInstances); |
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602 } |
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603 } |
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604 } |
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605 |
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606 |
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607 void Print(std::ostream& o, |
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608 const std::string& indent = "") const |
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609 { |
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610 for (Resources::const_iterator it = resources_.begin(); |
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611 it != resources_.end(); ++it) |
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612 { |
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613 o << indent << it->first << std::endl; |
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614 if (it->second == NULL) |
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615 { |
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616 if (level_ != ResourceType_Instance) |
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617 { |
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618 o << indent << " *" << std::endl; |
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619 } |
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620 } |
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621 else |
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622 { |
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623 it->second->Print(o, indent + " "); |
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624 } |
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625 } |
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626 } |
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627 }; |
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628 } |
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629 |
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630 |
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631 static void CreateBatchArchive(RestApiPostCall& call) |
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632 { |
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633 ServerIndex& index = OrthancRestApi::GetIndex(call); |
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634 |
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635 Json::Value resources; |
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636 if (call.ParseJsonRequest(resources) && |
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637 resources.type() == Json::arrayValue) |
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638 { |
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639 ArchiveIndex archive(index, ResourceType_Patient); // root |
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640 |
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641 for (Json::Value::ArrayIndex i = 0; i < resources.size(); i++) |
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642 { |
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643 if (resources[i].type() != Json::stringValue) |
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644 { |
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645 return; // Bad request |
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646 } |
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647 |
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648 Resource resource(index, resources[i].asString()); |
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649 archive.Add(resource); |
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650 } |
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651 |
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652 archive.Expand(); |
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653 |
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654 archive.Print(std::cout); |
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655 |
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656 uint64_t totalSize = 0; |
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657 unsigned int totalInstances = 0; |
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658 archive.ComputeStatistics(totalSize, totalInstances); |
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|
659 |
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660 std::cout << totalSize << " " << totalInstances << std::endl; |
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661 } |
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662 } |
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|
663 |
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|
664 |
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665 |
751
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666 void OrthancRestApi::RegisterArchive() |
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|
667 { |
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668 Register("/patients/{id}/archive", GetArchive<ResourceType_Patient>); |
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669 Register("/studies/{id}/archive", GetArchive<ResourceType_Study>); |
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670 Register("/series/{id}/archive", GetArchive<ResourceType_Series>); |
1121
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|
671 |
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672 Register("/patients/{id}/media", GetMediaArchive); |
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673 Register("/studies/{id}/media", GetMediaArchive); |
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|
674 Register("/series/{id}/media", GetMediaArchive); |
1774
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|
675 |
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|
676 Register("/tools/archive", CreateBatchArchive); |
751
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|
677 } |
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678 } |