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annotate OrthancServer/ServerJobs/SplitStudyJob.cpp @ 2998:0a52af0c66e7

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author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 11 Dec 2018 13:21:34 +0100
parents bbfd95a0c429
children 4e43e67f8ecf
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
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4 * Department, University Hospital of Liege, Belgium
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5 * Copyright (C) 2017-2018 Osimis S.A., Belgium
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6 *
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7 * This program is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License as
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9 * published by the Free Software Foundation, either version 3 of the
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10 * License, or (at your option) any later version.
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11 *
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12 * In addition, as a special exception, the copyright holders of this
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13 * program give permission to link the code of its release with the
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14 * OpenSSL project's "OpenSSL" library (or with modified versions of it
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15 * that use the same license as the "OpenSSL" library), and distribute
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16 * the linked executables. You must obey the GNU General Public License
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17 * in all respects for all of the code used other than "OpenSSL". If you
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18 * modify file(s) with this exception, you may extend this exception to
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19 * your version of the file(s), but you are not obligated to do so. If
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20 * you do not wish to do so, delete this exception statement from your
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21 * version. If you delete this exception statement from all source files
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22 * in the program, then also delete it here.
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23 *
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24 * This program is distributed in the hope that it will be useful, but
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25 * WITHOUT ANY WARRANTY; without even the implied warranty of
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26 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
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27 * General Public License for more details.
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28 *
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29 * You should have received a copy of the GNU General Public License
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30 * along with this program. If not, see <http://www.gnu.org/licenses/>.
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31 **/
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32
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34 #include "SplitStudyJob.h"
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35
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36 #include "../../Core/DicomParsing/FromDcmtkBridge.h"
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37 #include "../../Core/Logging.h"
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38 #include "../../Core/SerializationToolbox.h"
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39
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40 namespace Orthanc
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41 {
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42 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
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43 {
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44 if (allowedTags_.find(tag) == allowedTags_.end())
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45 {
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46 throw OrthancException(ErrorCode_ParameterOutOfRange,
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47 "Cannot modify the following tag while splitting a study "
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48 "(not in the patient/study modules): " +
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49 FromDcmtkBridge::GetTagName(tag, "") +
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50 " (" + tag.Format() + ")");
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51 }
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52 }
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53
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54
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55 void SplitStudyJob::Setup()
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56 {
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57 SetPermissive(false);
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58
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59 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
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60 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
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61 allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
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62 allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
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63 }
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64
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65
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66 bool SplitStudyJob::HandleInstance(const std::string& instance)
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67 {
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68 /**
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69 * Retrieve the DICOM instance to be modified
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70 **/
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71
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72 std::auto_ptr<ParsedDicomFile> modified;
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73
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74 try
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75 {
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76 ServerContext::DicomCacheLocker locker(context_, instance);
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77 modified.reset(locker.GetDicom().Clone(true));
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78 }
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79 catch (OrthancException&)
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80 {
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81 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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82 return false;
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83 }
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84
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85
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86 /**
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87 * Chose the target UIDs
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88 **/
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89
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90 assert(modified->GetHasher().HashStudy() == sourceStudy_);
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91
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92 std::string series = modified->GetHasher().HashSeries();
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93
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94 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series);
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95
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96 if (targetSeriesUid == seriesUidMap_.end())
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97 {
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98 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen
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99 }
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100
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101
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102 /**
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103 * Apply user-specified modifications
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104 **/
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105
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106 for (std::set<DicomTag>::const_iterator it = removals_.begin();
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107 it != removals_.end(); ++it)
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108 {
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109 modified->Remove(*it);
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110 }
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111
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112 for (Replacements::const_iterator it = replacements_.begin();
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113 it != replacements_.end(); ++it)
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114 {
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115 modified->ReplacePlainString(it->first, it->second);
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116 }
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117
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119 /**
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120 * Store the new instance into Orthanc
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121 **/
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122
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123 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
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124 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second);
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125
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126 if (targetStudy_.empty())
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127 {
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128 targetStudy_ = modified->GetHasher().HashStudy();
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129 }
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130
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131 DicomInstanceToStore toStore;
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132 toStore.SetOrigin(origin_);
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133 toStore.SetParsedDicomFile(*modified);
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134
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135 std::string modifiedInstance;
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136 if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success)
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137 {
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138 LOG(ERROR) << "Error while storing a modified instance " << instance;
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139 return false;
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140 }
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141
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142 return true;
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143 }
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144
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145
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146 bool SplitStudyJob::HandleTrailingStep()
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147 {
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148 if (!keepSource_)
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149 {
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150 const size_t n = GetInstancesCount();
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151
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152 for (size_t i = 0; i < n; i++)
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153 {
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154 Json::Value tmp;
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155 context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance);
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156 }
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157 }
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158
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159 return true;
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160 }
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161
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162
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163 SplitStudyJob::SplitStudyJob(ServerContext& context,
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164 const std::string& sourceStudy) :
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165 context_(context),
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166 keepSource_(false),
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167 sourceStudy_(sourceStudy),
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168 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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169 {
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170 Setup();
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171
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172 ResourceType type;
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173
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174 if (!context_.GetIndex().LookupResourceType(type, sourceStudy) ||
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175 type != ResourceType_Study)
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176 {
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177 throw OrthancException(ErrorCode_UnknownResource,
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178 "Cannot split unknown study " + sourceStudy);
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179 }
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180 }
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181
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182
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183 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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184 {
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185 if (IsStarted())
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186 {
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187 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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188 }
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189 else
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190 {
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191 origin_ = origin;
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192 }
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193 }
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194
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195
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196 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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197 {
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198 SetOrigin(DicomInstanceOrigin::FromRest(call));
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199 }
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200
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201
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202 void SplitStudyJob::AddSourceSeries(const std::string& series)
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203 {
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204 std::string parent;
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205
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206 if (IsStarted())
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207 {
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208 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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209 }
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210 else if (!context_.GetIndex().LookupParent(parent, series, ResourceType_Study) ||
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211 parent != sourceStudy_)
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212 {
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213 throw OrthancException(ErrorCode_UnknownResource,
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214 "This series does not belong to the study to be split: " + series);
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215 }
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diff changeset
216 else
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diff changeset
217 {
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218 // Generate a target SeriesInstanceUID for this series
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219 seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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220
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221 // Add all the instances of the series as to be processed
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222 std::list<std::string> instances;
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223 context_.GetIndex().GetChildren(instances, series);
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224
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225 for (std::list<std::string>::const_iterator
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226 it = instances.begin(); it != instances.end(); ++it)
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227 {
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diff changeset
228 AddInstance(*it);
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229 }
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230 }
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231 }
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diff changeset
232
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233
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diff changeset
234 void SplitStudyJob::SetKeepSource(bool keep)
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235 {
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diff changeset
236 if (IsStarted())
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diff changeset
237 {
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238 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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diff changeset
239 }
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diff changeset
240
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diff changeset
241 keepSource_ = keep;
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diff changeset
242 }
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diff changeset
243
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244
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2da68edacab6 unit testing of SplitStudyJob
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diff changeset
245 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
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246 const std::string& series) const
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247 {
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248 SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
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249
2da68edacab6 unit testing of SplitStudyJob
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250 if (found == seriesUidMap_.end())
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251 {
2da68edacab6 unit testing of SplitStudyJob
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252 return false;
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253 }
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diff changeset
254 else
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diff changeset
255 {
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diff changeset
256 uid = found->second;
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257 return true;
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258 }
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259 }
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260
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261
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262 void SplitStudyJob::Remove(const DicomTag& tag)
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263 {
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264 if (IsStarted())
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265 {
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266 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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267 }
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268
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269 CheckAllowedTag(tag);
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270 removals_.insert(tag);
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271 }
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272
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273
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274 void SplitStudyJob::Replace(const DicomTag& tag,
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275 const std::string& value)
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276 {
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277 if (IsStarted())
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278 {
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279 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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280 }
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281
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282 CheckAllowedTag(tag);
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283 replacements_[tag] = value;
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284 }
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285
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286
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287 bool SplitStudyJob::LookupReplacement(std::string& value,
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288 const DicomTag& tag) const
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289 {
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290 Replacements::const_iterator found = replacements_.find(tag);
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291
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292 if (found == replacements_.end())
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293 {
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294 return false;
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295 }
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296 else
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297 {
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298 value = found->second;
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299 return true;
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300 }
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301 }
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302
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303
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304 void SplitStudyJob::GetPublicContent(Json::Value& value)
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305 {
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306 SetOfInstancesJob::GetPublicContent(value);
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307
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308 if (!targetStudy_.empty())
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309 {
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310 value["TargetStudy"] = targetStudy_;
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311 }
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312
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313 value["TargetStudyUID"] = targetStudyUid_;
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314 }
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315
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316
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317 static const char* KEEP_SOURCE = "KeepSource";
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318 static const char* SOURCE_STUDY = "SourceStudy";
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319 static const char* TARGET_STUDY = "TargetStudy";
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320 static const char* TARGET_STUDY_UID = "TargetStudyUID";
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321 static const char* SERIES_UID_MAP = "SeriesUIDMap";
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322 static const char* ORIGIN = "Origin";
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323 static const char* REPLACEMENTS = "Replacements";
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324 static const char* REMOVALS = "Removals";
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325
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326
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327 SplitStudyJob::SplitStudyJob(ServerContext& context,
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328 const Json::Value& serialized) :
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329 SetOfInstancesJob(serialized), // (*)
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330 context_(context)
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331 {
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332 if (!HasTrailingStep())
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333 {
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334 // Should have been set by (*)
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335 throw OrthancException(ErrorCode_InternalError);
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336 }
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337
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338 Setup();
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339
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340 keepSource_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SOURCE);
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341 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
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342 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
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343 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
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344 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
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345 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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346 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
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347 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
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348 }
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349
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350
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351 bool SplitStudyJob::Serialize(Json::Value& target)
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352 {
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353 if (!SetOfInstancesJob::Serialize(target))
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354 {
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355 return false;
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356 }
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357 else
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358 {
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359 target[KEEP_SOURCE] = keepSource_;
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360 target[SOURCE_STUDY] = sourceStudy_;
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361 target[TARGET_STUDY] = targetStudy_;
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362 target[TARGET_STUDY_UID] = targetStudyUid_;
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363 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
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364 origin_.Serialize(target[ORIGIN]);
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365 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
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366 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
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367
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368 return true;
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369 }
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370 }
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371 }