Mercurial > hg > orthanc

annotate OrthancServer/OrthancRestApi/OrthancRestArchive.cpp @ 1315:0c735fed8953

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ZIP archives now display the accession number of the studies
author Sebastien Jodogne <s.jodogne@gmail.com>
date Thu, 12 Feb 2015 13:28:47 +0100
parents bba8a47922d1
children 02f5a3f5c0a0
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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/Uuid.h"
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40
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41 #include <glog/logging.h>
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42 #include <stdio.h>
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43
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44 #if defined(_MSC_VER)
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45 #define snprintf _snprintf
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46 #endif
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47
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48 static const uint64_t MEGA_BYTES = 1024 * 1024;
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49 static const uint64_t GIGA_BYTES = 1024 * 1024 * 1024;
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50
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51 namespace Orthanc
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52 {
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53 // Download of ZIP files ----------------------------------------------------
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54
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55 static std::string GetDirectoryNameInArchive(const Json::Value& resource,
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56 ResourceType resourceType)
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57 {
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58 std::string s;
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59 const Json::Value& tags = resource["MainDicomTags"];
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60
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61 switch (resourceType)
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62 {
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63 case ResourceType_Patient:
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64 {
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65 std::string p = tags["PatientID"].asString();
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66 std::string n = tags["PatientName"].asString();
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67 s = p + " " + n;
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68 break;
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69 }
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70
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71 case ResourceType_Study:
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72 {
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73 std::string p;
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74 if (tags.isMember("AccessionNumber"))
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75 {
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76 p = tags["AccessionNumber"].asString() + " ";
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77 }
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78
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79 s = p + tags["StudyDescription"].asString();
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80 break;
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81 }
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82
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83 case ResourceType_Series:
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84 {
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85 std::string d = tags["SeriesDescription"].asString();
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86 std::string m = tags["Modality"].asString();
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87 s = m + " " + d;
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88 break;
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89 }
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90
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91 default:
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92 throw OrthancException(ErrorCode_InternalError);
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93 }
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94
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95 // Get rid of special characters
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96 return Toolbox::ConvertToAscii(s);
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97 }
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98
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99 static bool CreateRootDirectoryInArchive(HierarchicalZipWriter& writer,
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100 ServerContext& context,
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101 const Json::Value& resource,
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102 ResourceType resourceType)
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103 {
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104 if (resourceType == ResourceType_Patient)
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105 {
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106 return true;
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107 }
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108
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109 ResourceType parentType = GetParentResourceType(resourceType);
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110 Json::Value parent;
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111
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112 switch (resourceType)
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113 {
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114 case ResourceType_Study:
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115 {
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116 if (!context.GetIndex().LookupResource(parent, resource["ParentPatient"].asString(), parentType))
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117 {
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118 return false;
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119 }
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120
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121 break;
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122 }
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123
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124 case ResourceType_Series:
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125 if (!context.GetIndex().LookupResource(parent, resource["ParentStudy"].asString(), parentType) ||
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126 !CreateRootDirectoryInArchive(writer, context, parent, parentType))
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127 {
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128 return false;
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129 }
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130 break;
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131
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132 default:
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133 throw OrthancException(ErrorCode_NotImplemented);
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134 }
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135
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136 writer.OpenDirectory(GetDirectoryNameInArchive(parent, parentType).c_str());
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137 return true;
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diff changeset
138 }
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diff changeset
139
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diff changeset
140 static bool ArchiveInstance(HierarchicalZipWriter& writer,
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diff changeset
141 ServerContext& context,
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diff changeset
142 const std::string& instancePublicId,
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diff changeset
143 const char* filename)
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diff changeset
144 {
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diff changeset
145 writer.OpenFile(filename);
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Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
146
5197fd35333c refactoring of OrthancRestApi
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diff changeset
147 std::string dicom;
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diff changeset
148 context.ReadFile(dicom, instancePublicId, FileContentType_Dicom);
5197fd35333c refactoring of OrthancRestApi
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diff changeset
149 writer.Write(dicom);
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diff changeset
150
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151 return true;
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152 }
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153
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154 static bool ArchiveInternal(HierarchicalZipWriter& writer,
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155 ServerContext& context,
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156 const std::string& publicId,
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157 ResourceType resourceType,
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158 bool isFirstLevel)
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159 {
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160 Json::Value resource;
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161 if (!context.GetIndex().LookupResource(resource, publicId, resourceType))
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162 {
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163 return false;
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164 }
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165
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166 if (isFirstLevel &&
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167 !CreateRootDirectoryInArchive(writer, context, resource, resourceType))
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168 {
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169 return false;
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170 }
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171
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172 writer.OpenDirectory(GetDirectoryNameInArchive(resource, resourceType).c_str());
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173
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174 switch (resourceType)
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175 {
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176 case ResourceType_Patient:
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177 for (Json::Value::ArrayIndex i = 0; i < resource["Studies"].size(); i++)
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178 {
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179 std::string studyId = resource["Studies"][i].asString();
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180 if (!ArchiveInternal(writer, context, studyId, ResourceType_Study, false))
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181 {
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182 return false;
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183 }
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184 }
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185 break;
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186
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187 case ResourceType_Study:
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188 for (Json::Value::ArrayIndex i = 0; i < resource["Series"].size(); i++)
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189 {
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190 std::string seriesId = resource["Series"][i].asString();
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191 if (!ArchiveInternal(writer, context, seriesId, ResourceType_Series, false))
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192 {
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193 return false;
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diff changeset
194 }
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195 }
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196 break;
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197
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198 case ResourceType_Series:
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199 {
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200 // Create a filename prefix, depending on the modality
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201 char format[16] = "%08d";
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202
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diff changeset
203 if (resource["MainDicomTags"].isMember("Modality"))
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diff changeset
204 {
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diff changeset
205 std::string modality = resource["MainDicomTags"]["Modality"].asString();
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diff changeset
206
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diff changeset
207 if (modality.size() == 1)
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diff changeset
208 {
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diff changeset
209 snprintf(format, sizeof(format) - 1, "%c%%07d", toupper(modality[0]));
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210 }
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parents:
diff changeset
211 else if (modality.size() >= 2)
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diff changeset
212 {
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diff changeset
213 snprintf(format, sizeof(format) - 1, "%c%c%%06d", toupper(modality[0]), toupper(modality[1]));
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214 }
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diff changeset
215 }
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parents:
diff changeset
216
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diff changeset
217 char filename[16];
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parents:
diff changeset
218
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diff changeset
219 for (Json::Value::ArrayIndex i = 0; i < resource["Instances"].size(); i++)
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diff changeset
220 {
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diff changeset
221 snprintf(filename, sizeof(filename) - 1, format, i);
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diff changeset
222
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diff changeset
223 std::string publicId = resource["Instances"][i].asString();
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diff changeset
224
5197fd35333c refactoring of OrthancRestApi
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diff changeset
225 // This was the implementation up to Orthanc 0.7.0:
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diff changeset
226 // std::string filename = instance["MainDicomTags"]["SOPInstanceUID"].asString() + ".dcm";
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parents:
diff changeset
227
5197fd35333c refactoring of OrthancRestApi
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diff changeset
228 if (!ArchiveInstance(writer, context, publicId, filename))
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parents:
diff changeset
229 {
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
230 return false;
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
231 }
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
232 }
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
233
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
234 break;
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parents:
diff changeset
235 }
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
236
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
237 default:
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
238 throw OrthancException(ErrorCode_InternalError);
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parents:
diff changeset
239 }
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parents:
diff changeset
240
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
241 writer.CloseDirectory();
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
242 return true;
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
243 }
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
244
1121
82567bac5e25 Creation of ZIP archives for media storage, with DICOMDIR
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parents: 976
diff changeset
245
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parents: 976
diff changeset
246 static bool IsZip64Required(ServerIndex& index,
82567bac5e25 Creation of ZIP archives for media storage, with DICOMDIR
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diff changeset
247 const std::string& id)
751
5197fd35333c refactoring of OrthancRestApi
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diff changeset
248 {
5197fd35333c refactoring of OrthancRestApi
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diff changeset
249 /**
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diff changeset
250 * Determine whether ZIP64 is required. Original ZIP format can
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
251 * store up to 2GB of data (some implementation supporting up to
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diff changeset
252 * 4GB of data), and up to 65535 files.
5197fd35333c refactoring of OrthancRestApi
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diff changeset
253 * https://en.wikipedia.org/wiki/Zip_(file_format)#ZIP64
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
254 **/
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
255
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
256 uint64_t uncompressedSize;
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
257 uint64_t compressedSize;
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
258 unsigned int countStudies;
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
259 unsigned int countSeries;
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
260 unsigned int countInstances;
1121
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diff changeset
261 index.GetStatistics(compressedSize, uncompressedSize,
82567bac5e25 Creation of ZIP archives for media storage, with DICOMDIR
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parents: 976
diff changeset
262 countStudies, countSeries, countInstances, id);
751
5197fd35333c refactoring of OrthancRestApi
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diff changeset
263 const bool isZip64 = (uncompressedSize >= 2 * GIGA_BYTES ||
5197fd35333c refactoring of OrthancRestApi
Sebastien Jodogne <s.jodogne@gmail.com>
parents:
diff changeset
264 countInstances >= 65535);
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
265
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
266 LOG(INFO) << "Creating a ZIP file with " << countInstances << " files of size "
5197fd35333c refactoring of OrthancRestApi
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parents:
diff changeset
267 << (uncompressedSize / MEGA_BYTES) << "MB using the "
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parents:
diff changeset
268 << (isZip64 ? "ZIP64" : "ZIP32") << " file format";
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parents:
diff changeset
269
1121
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diff changeset
270 return isZip64;
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diff changeset
271 }
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diff changeset
272
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diff changeset
273
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diff changeset
274 template <enum ResourceType resourceType>
82567bac5e25 Creation of ZIP archives for media storage, with DICOMDIR
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diff changeset
275 static void GetArchive(RestApiGetCall& call)
82567bac5e25 Creation of ZIP archives for media storage, with DICOMDIR
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parents: 976
diff changeset
276 {
82567bac5e25 Creation of ZIP archives for media storage, with DICOMDIR
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parents: 976
diff changeset
277 ServerContext& context = OrthancRestApi::GetContext(call);
82567bac5e25 Creation of ZIP archives for media storage, with DICOMDIR
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parents: 976
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278
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279 std::string id = call.GetUriComponent("id", "");
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280 bool isZip64 = IsZip64Required(context.GetIndex(), id);
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281
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282 // Create a RAII for the temporary file to manage the ZIP file
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283 Toolbox::TemporaryFile tmp;
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284
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285 {
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286 // Create a ZIP writer
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287 HierarchicalZipWriter writer(tmp.GetPath().c_str());
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288 writer.SetZip64(isZip64);
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289
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290 // Store the requested resource into the ZIP
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291 if (!ArchiveInternal(writer, context, id, resourceType, true))
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292 {
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293 return;
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294 }
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295 }
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296
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297 // Prepare the sending of the ZIP file
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298 FilesystemHttpSender sender(tmp.GetPath().c_str());
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299 sender.SetContentType("application/zip");
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300 sender.SetDownloadFilename(id + ".zip");
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301
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302 // Send the ZIP
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303 call.GetOutput().AnswerFile(sender);
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304
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305 // The temporary file is automatically removed thanks to the RAII
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306 }
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307
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308
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309 static void GetMediaArchive(RestApiGetCall& call)
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310 {
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311 ServerContext& context = OrthancRestApi::GetContext(call);
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312
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313 std::string id = call.GetUriComponent("id", "");
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314 bool isZip64 = IsZip64Required(context.GetIndex(), id);
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315
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316 // Create a RAII for the temporary file to manage the ZIP file
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317 Toolbox::TemporaryFile tmp;
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318
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319 {
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320 // Create a ZIP writer
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321 HierarchicalZipWriter writer(tmp.GetPath().c_str());
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322 writer.SetZip64(isZip64);
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323 writer.OpenDirectory("IMAGES");
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324
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325 // Create the DICOMDIR writer
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326 DicomDirWriter dicomDir;
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327
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328 // Retrieve the list of the instances
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329 std::list<std::string> instances;
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330 context.GetIndex().GetChildInstances(instances, id);
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331
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332 size_t pos = 0;
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333 for (std::list<std::string>::const_iterator
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334 it = instances.begin(); it != instances.end(); ++it, ++pos)
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335 {
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336 // "DICOM restricts the filenames on DICOM media to 8
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337 // characters (some systems wrongly use 8.3, but this does not
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338 // conform to the standard)."
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339 std::string filename = "IM" + boost::lexical_cast<std::string>(pos);
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340 writer.OpenFile(filename.c_str());
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341
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342 std::string dicom;
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343 context.ReadFile(dicom, *it, FileContentType_Dicom);
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344 writer.Write(dicom);
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345
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346 ParsedDicomFile parsed(dicom);
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347 dicomDir.Add("IMAGES", filename, parsed);
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348 }
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349
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350 // Add the DICOMDIR
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351 writer.CloseDirectory();
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352 writer.OpenFile("DICOMDIR");
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353 std::string s;
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354 dicomDir.Encode(s);
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355 writer.Write(s);
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356 }
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357
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358 // Prepare the sending of the ZIP file
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359 FilesystemHttpSender sender(tmp.GetPath().c_str());
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360 sender.SetContentType("application/zip");
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361 sender.SetDownloadFilename(id + ".zip");
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362
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363 // Send the ZIP
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364 call.GetOutput().AnswerFile(sender);
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365
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366 // The temporary file is automatically removed thanks to the RAII
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367 }
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368
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369
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370 void OrthancRestApi::RegisterArchive()
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371 {
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372 Register("/patients/{id}/archive", GetArchive<ResourceType_Patient>);
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373 Register("/studies/{id}/archive", GetArchive<ResourceType_Study>);
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374 Register("/series/{id}/archive", GetArchive<ResourceType_Series>);
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375
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376 Register("/patients/{id}/media", GetMediaArchive);
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377 Register("/studies/{id}/media", GetMediaArchive);
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378 Register("/series/{id}/media", GetMediaArchive);
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379 }
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380 }