Mercurial > hg > orthanc

annotate OrthancServer/ServerJobs/SplitStudyJob.cpp @ 3768:6110a4995ace

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replacing std::auto_ptr by std::unique_ptr in GDCM sample plugin
author Sebastien Jodogne <s.jodogne@gmail.com>
date Tue, 17 Mar 2020 15:02:23 +0100
parents 2a170a8f1faf
children 023b2a9f3aa1
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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) 2017-2020 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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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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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::unique_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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102
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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 // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified
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129 modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
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130
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131 if (targetStudy_.empty())
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132 {
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133 targetStudy_ = modified->GetHasher().HashStudy();
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134 }
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135
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136 DicomInstanceToStore toStore;
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137 toStore.SetOrigin(origin_);
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138 toStore.SetParsedDicomFile(*modified);
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139
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140 std::string modifiedInstance;
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141 if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success)
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142 {
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143 LOG(ERROR) << "Error while storing a modified instance " << instance;
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144 return false;
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145 }
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146
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147 return true;
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148 }
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149
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150
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151 bool SplitStudyJob::HandleTrailingStep()
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152 {
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153 if (!keepSource_)
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154 {
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155 const size_t n = GetInstancesCount();
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156
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157 for (size_t i = 0; i < n; i++)
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158 {
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159 Json::Value tmp;
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160 context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance);
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161 }
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162 }
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163
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164 return true;
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165 }
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166
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167
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168 SplitStudyJob::SplitStudyJob(ServerContext& context,
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169 const std::string& sourceStudy) :
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170 context_(context),
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171 keepSource_(false),
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172 sourceStudy_(sourceStudy),
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173 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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174 {
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175 Setup();
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176
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177 ResourceType type;
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178
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179 if (!context_.GetIndex().LookupResourceType(type, sourceStudy) ||
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180 type != ResourceType_Study)
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181 {
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182 throw OrthancException(ErrorCode_UnknownResource,
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183 "Cannot split unknown study " + sourceStudy);
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184 }
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185 }
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186
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187
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188 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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189 {
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190 if (IsStarted())
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191 {
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192 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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193 }
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194 else
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195 {
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196 origin_ = origin;
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197 }
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198 }
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199
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200
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201 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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202 {
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203 SetOrigin(DicomInstanceOrigin::FromRest(call));
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204 }
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205
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206
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207 void SplitStudyJob::AddSourceSeries(const std::string& series)
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208 {
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209 std::string parent;
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210
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211 if (IsStarted())
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212 {
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213 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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214 }
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215 else if (!context_.GetIndex().LookupParent(parent, series, ResourceType_Study) ||
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216 parent != sourceStudy_)
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217 {
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218 throw OrthancException(ErrorCode_UnknownResource,
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219 "This series does not belong to the study to be split: " + series);
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220 }
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221 else
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222 {
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223 // Generate a target SeriesInstanceUID for this series
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224 seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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225
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226 // Add all the instances of the series as to be processed
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227 std::list<std::string> instances;
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228 context_.GetIndex().GetChildren(instances, series);
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229
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230 for (std::list<std::string>::const_iterator
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231 it = instances.begin(); it != instances.end(); ++it)
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232 {
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233 AddInstance(*it);
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234 }
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235 }
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236 }
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237
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238
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239 void SplitStudyJob::SetKeepSource(bool keep)
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240 {
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241 if (IsStarted())
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242 {
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243 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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244 }
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245
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246 keepSource_ = keep;
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247 }
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248
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249
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250 bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
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251 const std::string& series) const
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252 {
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253 SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
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254
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255 if (found == seriesUidMap_.end())
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256 {
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257 return false;
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258 }
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259 else
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260 {
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261 uid = found->second;
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262 return true;
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263 }
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264 }
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265
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266
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267 void SplitStudyJob::Remove(const DicomTag& tag)
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268 {
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269 if (IsStarted())
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270 {
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271 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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272 }
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273
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274 CheckAllowedTag(tag);
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275 removals_.insert(tag);
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276 }
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277
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278
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279 void SplitStudyJob::Replace(const DicomTag& tag,
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280 const std::string& value)
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281 {
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282 if (IsStarted())
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283 {
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284 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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285 }
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286
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287 CheckAllowedTag(tag);
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288 replacements_[tag] = value;
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289 }
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290
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291
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292 bool SplitStudyJob::LookupReplacement(std::string& value,
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293 const DicomTag& tag) const
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294 {
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295 Replacements::const_iterator found = replacements_.find(tag);
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296
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297 if (found == replacements_.end())
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298 {
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299 return false;
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300 }
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301 else
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302 {
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303 value = found->second;
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304 return true;
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305 }
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306 }
2844
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307
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308
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309 void SplitStudyJob::GetPublicContent(Json::Value& value)
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310 {
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311 SetOfInstancesJob::GetPublicContent(value);
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312
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313 if (!targetStudy_.empty())
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314 {
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315 value["TargetStudy"] = targetStudy_;
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316 }
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317
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318 value["TargetStudyUID"] = targetStudyUid_;
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319 }
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320
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321
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322 static const char* KEEP_SOURCE = "KeepSource";
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323 static const char* SOURCE_STUDY = "SourceStudy";
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324 static const char* TARGET_STUDY = "TargetStudy";
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325 static const char* TARGET_STUDY_UID = "TargetStudyUID";
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326 static const char* SERIES_UID_MAP = "SeriesUIDMap";
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327 static const char* ORIGIN = "Origin";
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328 static const char* REPLACEMENTS = "Replacements";
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329 static const char* REMOVALS = "Removals";
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330
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diff changeset
331
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332 SplitStudyJob::SplitStudyJob(ServerContext& context,
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333 const Json::Value& serialized) :
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334 SetOfInstancesJob(serialized), // (*)
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335 context_(context)
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336 {
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337 if (!HasTrailingStep())
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338 {
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339 // Should have been set by (*)
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340 throw OrthancException(ErrorCode_InternalError);
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341 }
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diff changeset
342
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diff changeset
343 Setup();
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diff changeset
344
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diff changeset
345 keepSource_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SOURCE);
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diff changeset
346 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
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diff changeset
347 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
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diff changeset
348 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
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349 SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
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diff changeset
350 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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351 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
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352 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
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diff changeset
353 }
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diff changeset
354
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diff changeset
355
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356 bool SplitStudyJob::Serialize(Json::Value& target)
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357 {
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diff changeset
358 if (!SetOfInstancesJob::Serialize(target))
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diff changeset
359 {
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360 return false;
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diff changeset
361 }
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diff changeset
362 else
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diff changeset
363 {
218e2c864d1d serialization of SplitStudyJob
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diff changeset
364 target[KEEP_SOURCE] = keepSource_;
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diff changeset
365 target[SOURCE_STUDY] = sourceStudy_;
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diff changeset
366 target[TARGET_STUDY] = targetStudy_;
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diff changeset
367 target[TARGET_STUDY_UID] = targetStudyUid_;
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diff changeset
368 SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
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diff changeset
369 origin_.Serialize(target[ORIGIN]);
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diff changeset
370 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
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diff changeset
371 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
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diff changeset
372
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diff changeset
373 return true;
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diff changeset
374 }
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375 }
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diff changeset
376 }