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annotate OrthancServer/ServerJobs/SplitStudyJob.cpp @ 2845:218e2c864d1d

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serialization of SplitStudyJob
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 28 Sep 2018 17:59:44 +0200
parents 99863d6245b2
children d386abc18133
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rev   line source
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1 /**
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2 * Orthanc - A Lightweight, RESTful DICOM Store
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3 * Copyright (C) 2012-2016 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 LOG(ERROR) << "Cannot modify the following tag while splitting a study "
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47 << "(not in the patient/study modules): "
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48 << FromDcmtkBridge::GetTagName(tag, "") << " (" << tag.Format() << ")";
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49 throw OrthancException(ErrorCode_ParameterOutOfRange);
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50 }
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51 }
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52
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53
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54 void SplitStudyJob::Setup()
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55 {
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56 SetPermissive(false);
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57
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58 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
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59 DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
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60 allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
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61 allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
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62 }
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63
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64
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65 bool SplitStudyJob::HandleInstance(const std::string& instance)
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66 {
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67 /**
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68 * Retrieve the DICOM instance to be modified
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69 **/
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70
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71 std::auto_ptr<ParsedDicomFile> modified;
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72
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73 try
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74 {
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75 ServerContext::DicomCacheLocker locker(context_, instance);
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76 modified.reset(locker.GetDicom().Clone(true));
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77 }
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78 catch (OrthancException&)
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79 {
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80 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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81 return false;
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82 }
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83
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84
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85 /**
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86 * Chose the target UIDs
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87 **/
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88
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89 std::string series;
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90 if (!modified->GetTagValue(series, DICOM_TAG_SERIES_INSTANCE_UID))
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91 {
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92 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen
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93 }
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94
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95 std::string targetSeriesUid;
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96 SeriesUidMap::const_iterator found = targetSeries_.find(series);
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97
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98 if (found == targetSeries_.end())
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99 {
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100 // Choose a random SeriesInstanceUID for this series
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101 targetSeriesUid = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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102 targetSeries_[series] = targetSeriesUid;
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103 }
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104 else
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105 {
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106 targetSeriesUid = found->second;
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107 }
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108
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109
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110 /**
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111 * Apply user-specified modifications
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112 **/
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113
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114 for (std::set<DicomTag>::const_iterator it = removals_.begin();
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115 it != removals_.end(); ++it)
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116 {
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117 modified->Remove(*it);
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118 }
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119
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120 for (Replacements::const_iterator it = replacements_.begin();
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121 it != replacements_.end(); ++it)
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122 {
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123 modified->ReplacePlainString(it->first, it->second);
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124 }
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125
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126
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127 /**
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128 * Store the new instance into Orthanc
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129 **/
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130
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131 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
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132 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid);
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133
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134 if (targetStudy_.empty())
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135 {
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136 targetStudy_ = modified->GetHasher().HashStudy();
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137 }
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138
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139 DicomInstanceToStore toStore;
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140 toStore.SetOrigin(origin_);
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141 toStore.SetParsedDicomFile(*modified);
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142
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143 std::string modifiedInstance;
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144 if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success)
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145 {
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146 LOG(ERROR) << "Error while storing a modified instance " << instance;
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147 return false;
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148 }
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149
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150 return true;
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151 }
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152
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153
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154 bool SplitStudyJob::HandleTrailingStep()
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155 {
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156 if (!keepSource_)
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157 {
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158 const size_t n = GetInstancesCount();
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159
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160 for (size_t i = 0; i < n; i++)
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161 {
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162 Json::Value tmp;
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163 context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance);
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164 }
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165 }
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166
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167 return true;
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168 }
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169
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170
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171 SplitStudyJob::SplitStudyJob(ServerContext& context,
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172 const std::string& sourceStudy) :
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173 SetOfInstancesJob(true /* with trailing step */),
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174 context_(context),
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175 keepSource_(false),
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176 sourceStudy_(sourceStudy),
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177 targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
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178 {
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179 Setup();
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180
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181 ResourceType type;
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182
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183 if (!context_.GetIndex().LookupResourceType(type, sourceStudy) ||
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184 type != ResourceType_Study)
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185 {
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186 LOG(ERROR) << "Cannot split unknown study: " << sourceStudy;
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187 throw OrthancException(ErrorCode_UnknownResource);
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188 }
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189
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190 std::list<std::string> children;
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191 context_.GetIndex().GetChildren(children, sourceStudy);
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192
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193 for (std::list<std::string>::const_iterator
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194 it = children.begin(); it != children.end(); ++it)
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195 {
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196 sourceSeries_.insert(*it);
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197 }
2844
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198 }
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199
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200
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201 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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202 {
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203 if (IsStarted())
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204 {
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205 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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206 }
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207 else
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208 {
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209 origin_ = origin;
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210 }
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211 }
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212
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213
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214 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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215 {
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216 SetOrigin(DicomInstanceOrigin::FromRest(call));
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217 }
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218
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219
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220 void SplitStudyJob::AddSourceSeries(const std::string& series)
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221 {
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diff changeset
222 if (IsStarted())
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223 {
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224 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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225 }
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226 else if (sourceSeries_.find(series) == sourceSeries_.end())
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227 {
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228 LOG(ERROR) << "This series does not belong to the study to be split: " << series;
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229 throw OrthancException(ErrorCode_UnknownResource);
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diff changeset
230 }
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diff changeset
231 else
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232 {
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233 // Add all the instances of the series as to be processed
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diff changeset
234 std::list<std::string> instances;
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diff changeset
235 context_.GetIndex().GetChildren(instances, series);
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236
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diff changeset
237 for (std::list<std::string>::const_iterator
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diff changeset
238 it = instances.begin(); it != instances.end(); ++it)
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239 {
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diff changeset
240 AddInstance(*it);
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diff changeset
241 }
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242 }
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diff changeset
243 }
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parents:
diff changeset
244
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245
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246 void SplitStudyJob::SetKeepSource(bool keep)
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247 {
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diff changeset
248 if (IsStarted())
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diff changeset
249 {
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250 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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diff changeset
251 }
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252
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253 keepSource_ = keep;
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254 }
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255
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256
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257 void SplitStudyJob::Remove(const DicomTag& tag)
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258 {
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259 if (IsStarted())
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260 {
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261 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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262 }
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263
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264 CheckAllowedTag(tag);
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265 removals_.insert(tag);
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266 }
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267
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268
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269 void SplitStudyJob::Replace(const DicomTag& tag,
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270 const std::string& value)
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271 {
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272 if (IsStarted())
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273 {
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274 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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275 }
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276
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277 CheckAllowedTag(tag);
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278 replacements_[tag] = value;
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279 }
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280
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281
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282 void SplitStudyJob::GetPublicContent(Json::Value& value)
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283 {
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284 SetOfInstancesJob::GetPublicContent(value);
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285
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286 if (!targetStudy_.empty())
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287 {
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288 value["TargetStudy"] = targetStudy_;
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289 }
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290
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291 value["TargetStudyUID"] = targetStudyUid_;
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292 }
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293
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294
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295 static const char* SOURCE_STUDY = "SourceStudy";
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296 static const char* SOURCE_SERIES = "SourceSeries";
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297 static const char* KEEP_SOURCE = "KeepSource";
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298 static const char* TARGET_STUDY = "TargetStudy";
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299 static const char* TARGET_STUDY_UID = "TargetStudyUID";
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300 static const char* TARGET_SERIES = "TargetSeries";
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301 static const char* ORIGIN = "Origin";
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302 static const char* REPLACEMENTS = "Replacements";
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303 static const char* REMOVALS = "Removals";
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304
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305
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306 SplitStudyJob::SplitStudyJob(ServerContext& context,
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307 const Json::Value& serialized) :
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308 SetOfInstancesJob(serialized), // (*)
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309 context_(context)
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310 {
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311 if (!HasTrailingStep())
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312 {
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313 // Should have been set by (*)
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314 throw OrthancException(ErrorCode_InternalError);
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315 }
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316
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317 Setup();
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318
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319 keepSource_ = SerializationToolbox::ReadBoolean(serialized, KEEP_SOURCE);
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320 sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
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321 SerializationToolbox::ReadSetOfStrings(sourceSeries_, serialized, SOURCE_SERIES);
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322 targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
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323 targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
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324 SerializationToolbox::ReadMapOfStrings(targetSeries_, serialized, TARGET_SERIES);
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325 origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
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326 SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
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327 SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
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328 }
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329
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330
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331 bool SplitStudyJob::Serialize(Json::Value& target)
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332 {
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333 if (!SetOfInstancesJob::Serialize(target))
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334 {
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335 return false;
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336 }
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337 else
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338 {
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339 target[KEEP_SOURCE] = keepSource_;
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340 target[SOURCE_STUDY] = sourceStudy_;
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341 SerializationToolbox::WriteSetOfStrings(target, sourceSeries_, SOURCE_SERIES);
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342 target[TARGET_STUDY] = targetStudy_;
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343 target[TARGET_STUDY_UID] = targetStudyUid_;
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344 SerializationToolbox::WriteMapOfStrings(target, targetSeries_, TARGET_SERIES);
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345 origin_.Serialize(target[ORIGIN]);
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346 SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
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347 SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
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348
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349 return true;
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350 }
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351 }
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352 }