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annotate OrthancServer/ServerJobs/SplitStudyJob.cpp @ 3493:c465c6ee2bfb

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author Benjamin Golinvaux <bgo@osimis.io>
date Mon, 19 Aug 2019 10:18:04 +0200
parents beeeb6096f27
children 69e49fc044f8
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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) 2017-2019 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 #include "../ServerContext.h"
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40
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41
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42 namespace Orthanc
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43 {
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44 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
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45 {
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46 if (allowedTags_.find(tag) == allowedTags_.end())
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47 {
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48 throw OrthancException(ErrorCode_ParameterOutOfRange,
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49 "Cannot modify the following tag while splitting a study "
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50 "(not in the patient/study modules): " +
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51 FromDcmtkBridge::GetTagName(tag, "") +
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52 " (" + tag.Format() + ")");
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53 }
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54 }
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56
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57 void SplitStudyJob::Setup()
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58 {
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59 SetPermissive(false);
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60
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61 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
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62 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
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63 allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
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64 allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
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65 }
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67
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68 bool SplitStudyJob::HandleInstance(const std::string& instance)
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69 {
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70 /**
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71 * Retrieve the DICOM instance to be modified
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72 **/
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73
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74 std::auto_ptr<ParsedDicomFile> modified;
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75
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76 try
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77 {
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78 ServerContext::DicomCacheLocker locker(context_, instance);
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79 modified.reset(locker.GetDicom().Clone(true));
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80 }
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81 catch (OrthancException&)
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82 {
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83 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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84 return false;
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85 }
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86
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87
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88 /**
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89 * Chose the target UIDs
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90 **/
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91
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92 assert(modified->GetHasher().HashStudy() == sourceStudy_);
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93
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94 std::string series = modified->GetHasher().HashSeries();
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95
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96 SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series);
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97
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98 if (targetSeriesUid == seriesUidMap_.end())
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99 {
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100 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen
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101 }
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103
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104 /**
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105 * Apply user-specified modifications
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106 **/
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107
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108 for (std::set<DicomTag>::const_iterator it = removals_.begin();
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109 it != removals_.end(); ++it)
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110 {
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111 modified->Remove(*it);
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112 }
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113
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114 for (Replacements::const_iterator it = replacements_.begin();
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115 it != replacements_.end(); ++it)
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116 {
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117 modified->ReplacePlainString(it->first, it->second);
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118 }
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119
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120
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121 /**
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122 * Store the new instance into Orthanc
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123 **/
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124
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125 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
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126 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second);
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127
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128 if (targetStudy_.empty())
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129 {
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130 targetStudy_ = modified->GetHasher().HashStudy();
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131 }
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132
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133 DicomInstanceToStore toStore;
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134 toStore.SetOrigin(origin_);
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135 toStore.SetParsedDicomFile(*modified);
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136
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137 std::string modifiedInstance;
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138 if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success)
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139 {
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140 LOG(ERROR) << "Error while storing a modified instance " << instance;
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141 return false;
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142 }
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143
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144 return true;
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145 }
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146
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147
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148 bool SplitStudyJob::HandleTrailingStep()
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149 {
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150 if (!keepSource_)
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151 {
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152 const size_t n = GetInstancesCount();
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153
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154 for (size_t i = 0; i < n; i++)
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155 {
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156 Json::Value tmp;
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157 context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance);
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158 }
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159 }
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160
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161 return true;
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162 }
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163
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164
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165 SplitStudyJob::SplitStudyJob(ServerContext& context,
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166 const std::string& sourceStudy) :
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167 context_(context),
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168 keepSource_(false),
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169 sourceStudy_(sourceStudy),
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170 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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171 {
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172 Setup();
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173
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174 ResourceType type;
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175
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176 if (!context_.GetIndex().LookupResourceType(type, sourceStudy) ||
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177 type != ResourceType_Study)
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178 {
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179 throw OrthancException(ErrorCode_UnknownResource,
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180 "Cannot split unknown study " + sourceStudy);
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181 }
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182 }
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183
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184
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185 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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186 {
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187 if (IsStarted())
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188 {
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189 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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190 }
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191 else
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192 {
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193 origin_ = origin;
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194 }
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195 }
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196
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197
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198 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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199 {
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200 SetOrigin(DicomInstanceOrigin::FromRest(call));
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201 }
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202
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203
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204 void SplitStudyJob::AddSourceSeries(const std::string& series)
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205 {
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206 std::string parent;
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207
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208 if (IsStarted())
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209 {
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210 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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211 }
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212 else if (!context_.GetIndex().LookupParent(parent, series, ResourceType_Study) ||
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213 parent != sourceStudy_)
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214 {
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215 throw OrthancException(ErrorCode_UnknownResource,
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216 "This series does not belong to the study to be split: " + series);
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217 }
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218 else
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219 {
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220 // Generate a target SeriesInstanceUID for this series
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221 seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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222
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223 // Add all the instances of the series as to be processed
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224 std::list<std::string> instances;
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225 context_.GetIndex().GetChildren(instances, series);
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226
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227 for (std::list<std::string>::const_iterator
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228 it = instances.begin(); it != instances.end(); ++it)
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229 {
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diff changeset
230 AddInstance(*it);
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231 }
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232 }
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233 }
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234
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235
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236 void SplitStudyJob::SetKeepSource(bool keep)
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237 {
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238 if (IsStarted())
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239 {
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240 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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241 }
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242
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243 keepSource_ = keep;
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diff changeset
244 }
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245
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246
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2da68edacab6 unit testing of SplitStudyJob
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247 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
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248 const std::string& series) const
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249 {
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250 SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
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251
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252 if (found == seriesUidMap_.end())
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253 {
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254 return false;
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255 }
2da68edacab6 unit testing of SplitStudyJob
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256 else
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257 {
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258 uid = found->second;
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259 return true;
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260 }
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261 }
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262
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263
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264 void SplitStudyJob::Remove(const DicomTag& tag)
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265 {
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266 if (IsStarted())
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267 {
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268 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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269 }
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270
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271 CheckAllowedTag(tag);
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272 removals_.insert(tag);
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273 }
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274
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275
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276 void SplitStudyJob::Replace(const DicomTag& tag,
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277 const std::string& value)
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278 {
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279 if (IsStarted())
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280 {
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281 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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282 }
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283
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284 CheckAllowedTag(tag);
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285 replacements_[tag] = value;
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286 }
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287
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288
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289 bool SplitStudyJob::LookupReplacement(std::string& value,
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290 const DicomTag& tag) const
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291 {
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292 Replacements::const_iterator found = replacements_.find(tag);
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293
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294 if (found == replacements_.end())
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295 {
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296 return false;
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297 }
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298 else
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299 {
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300 value = found->second;
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301 return true;
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302 }
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303 }
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304
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305
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306 void SplitStudyJob::GetPublicContent(Json::Value& value)
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307 {
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308 SetOfInstancesJob::GetPublicContent(value);
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309
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310 if (!targetStudy_.empty())
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311 {
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312 value["TargetStudy"] = targetStudy_;
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313 }
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314
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315 value["TargetStudyUID"] = targetStudyUid_;
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316 }
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317
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318
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319 static const char* KEEP_SOURCE = "KeepSource";
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320 static const char* SOURCE_STUDY = "SourceStudy";
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321 static const char* TARGET_STUDY = "TargetStudy";
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322 static const char* TARGET_STUDY_UID = "TargetStudyUID";
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323 static const char* SERIES_UID_MAP = "SeriesUIDMap";
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324 static const char* ORIGIN = "Origin";
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325 static const char* REPLACEMENTS = "Replacements";
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326 static const char* REMOVALS = "Removals";
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327
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328
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329 SplitStudyJob::SplitStudyJob(ServerContext& context,
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330 const Json::Value& serialized) :
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331 SetOfInstancesJob(serialized), // (*)
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332 context_(context)
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333 {
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334 if (!HasTrailingStep())
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335 {
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336 // Should have been set by (*)
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337 throw OrthancException(ErrorCode_InternalError);
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338 }
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339
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diff changeset
340 Setup();
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341
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342 keepSource_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SOURCE);
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343 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
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344 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
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345 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
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346 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
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347 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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348 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
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349 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
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350 }
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351
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352
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353 bool SplitStudyJob::Serialize(Json::Value& target)
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354 {
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355 if (!SetOfInstancesJob::Serialize(target))
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356 {
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357 return false;
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358 }
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359 else
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360 {
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361 target[KEEP_SOURCE] = keepSource_;
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362 target[SOURCE_STUDY] = sourceStudy_;
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363 target[TARGET_STUDY] = targetStudy_;
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364 target[TARGET_STUDY_UID] = targetStudyUid_;
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365 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
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diff changeset
366 origin_.Serialize(target[ORIGIN]);
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367 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
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368 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
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diff changeset
369
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370 return true;
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diff changeset
371 }
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372 }
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373 }