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annotate OrthancServer/ServerJobs/SplitStudyJob.cpp @ 2844:99863d6245b2

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New URI: "/studies/.../split" to split a study
author Sebastien Jodogne <s.jodogne@gmail.com>
date Fri, 28 Sep 2018 16:48:43 +0200
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children 218e2c864d1d
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2844
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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/Logging.h"
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37 #include "../../Core/DicomParsing/FromDcmtkBridge.h"
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38
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39 namespace Orthanc
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40 {
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41 void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
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42 {
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43 if (allowedTags_.find(tag) == allowedTags_.end())
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44 {
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45 LOG(ERROR) << "Cannot modify the following tag while splitting a study "
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46 << "(not in the patient/study modules): "
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47 << FromDcmtkBridge::GetTagName(tag, "") << " (" << tag.Format() << ")";
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48 throw OrthancException(ErrorCode_ParameterOutOfRange);
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49 }
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50 }
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51
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52
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53 void SplitStudyJob::Setup(const std::string& sourceStudy)
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54 {
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55 SetPermissive(false);
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56
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57 keepSource_ = false;
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58 sourceStudy_ = sourceStudy;
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59 targetStudyUid_ = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study);
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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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66 ResourceType type;
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67
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68 if (!context_.GetIndex().LookupResourceType(type, sourceStudy) ||
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69 type != ResourceType_Study)
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70 {
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71 LOG(ERROR) << "Cannot split unknown study: " << sourceStudy;
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72 throw OrthancException(ErrorCode_UnknownResource);
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73 }
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74
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75 std::list<std::string> children;
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76 context_.GetIndex().GetChildren(children, sourceStudy);
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77
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78 for (std::list<std::string>::const_iterator
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79 it = children.begin(); it != children.end(); ++it)
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80 {
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81 sourceSeries_.insert(*it);
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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 bool SplitStudyJob::HandleInstance(const std::string& instance)
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87 {
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88 /**
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89 * Retrieve the DICOM instance to be modified
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90 **/
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91
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92 std::auto_ptr<ParsedDicomFile> modified;
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93
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94 try
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95 {
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96 ServerContext::DicomCacheLocker locker(context_, instance);
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97 modified.reset(locker.GetDicom().Clone(true));
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98 }
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99 catch (OrthancException&)
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100 {
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101 LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
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102 return false;
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103 }
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104
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105
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106 /**
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107 * Chose the target UIDs
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108 **/
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109
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110 std::string series;
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111 if (!modified->GetTagValue(series, DICOM_TAG_SERIES_INSTANCE_UID))
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112 {
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113 throw OrthancException(ErrorCode_BadFileFormat); // Should never happen
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114 }
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115
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116 std::string targetSeriesUid;
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117 SeriesUidMap::const_iterator found = targetSeries_.find(series);
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118
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119 if (found == targetSeries_.end())
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120 {
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121 // Choose a random SeriesInstanceUID for this series
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122 targetSeriesUid = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
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123 targetSeries_[series] = targetSeriesUid;
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124 }
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125 else
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126 {
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127 targetSeriesUid = found->second;
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128 }
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129
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130
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131 /**
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132 * Apply user-specified modifications
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133 **/
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134
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135 for (Removals::const_iterator it = removals_.begin();
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136 it != removals_.end(); ++it)
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137 {
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138 modified->Remove(*it);
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139 }
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140
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141 for (Replacements::const_iterator it = replacements_.begin();
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142 it != replacements_.end(); ++it)
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143 {
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144 modified->ReplacePlainString(it->first, it->second);
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145 }
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146
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147
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148 /**
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149 * Store the new instance into Orthanc
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150 **/
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151
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152 modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
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153 modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid);
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154
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155 if (targetStudy_.empty())
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156 {
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157 targetStudy_ = modified->GetHasher().HashStudy();
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158 }
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159
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160 DicomInstanceToStore toStore;
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161 toStore.SetOrigin(origin_);
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162 toStore.SetParsedDicomFile(*modified);
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163
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164 std::string modifiedInstance;
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165 if (context_.Store(modifiedInstance, toStore) != StoreStatus_Success)
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166 {
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167 LOG(ERROR) << "Error while storing a modified instance " << instance;
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168 return false;
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169 }
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170
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171 return true;
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172 }
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173
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174
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175 bool SplitStudyJob::HandleTrailingStep()
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176 {
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177 if (!keepSource_)
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178 {
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179 const size_t n = GetInstancesCount();
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180
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181 for (size_t i = 0; i < n; i++)
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182 {
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183 Json::Value tmp;
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diff changeset
184 context_.DeleteResource(tmp, GetInstance(i), ResourceType_Instance);
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185 }
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186 }
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187
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188 return true;
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189 }
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parents:
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190
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parents:
diff changeset
191
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diff changeset
192 SplitStudyJob::SplitStudyJob(ServerContext& context,
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193 const std::string& sourceStudy) :
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194 SetOfInstancesJob(true /* with trailing step */),
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195 context_(context)
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196 {
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diff changeset
197 Setup(sourceStudy);
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198 }
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199
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parents:
diff changeset
200
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parents:
diff changeset
201 SplitStudyJob::SplitStudyJob(ServerContext& context,
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202 const Json::Value& serialized) :
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diff changeset
203 SetOfInstancesJob(serialized),
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diff changeset
204 context_(context)
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diff changeset
205 {
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diff changeset
206 //assert(HasTrailingStep());
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diff changeset
207 //Setup();
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diff changeset
208 }
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parents:
diff changeset
209
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parents:
diff changeset
210
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parents:
diff changeset
211 void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
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parents:
diff changeset
212 {
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diff changeset
213 if (IsStarted())
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diff changeset
214 {
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diff changeset
215 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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216 }
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diff changeset
217 else
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diff changeset
218 {
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diff changeset
219 origin_ = origin;
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diff changeset
220 }
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parents:
diff changeset
221 }
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parents:
diff changeset
222
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parents:
diff changeset
223
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parents:
diff changeset
224 void SplitStudyJob::SetOrigin(const RestApiCall& call)
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diff changeset
225 {
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diff changeset
226 SetOrigin(DicomInstanceOrigin::FromRest(call));
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diff changeset
227 }
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diff changeset
228
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diff changeset
229
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parents:
diff changeset
230 void SplitStudyJob::AddSourceSeries(const std::string& series)
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parents:
diff changeset
231 {
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parents:
diff changeset
232 if (IsStarted())
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parents:
diff changeset
233 {
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diff changeset
234 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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diff changeset
235 }
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parents:
diff changeset
236 else if (sourceSeries_.find(series) == sourceSeries_.end())
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parents:
diff changeset
237 {
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parents:
diff changeset
238 LOG(ERROR) << "This series does not belong to the study to be split: " << series;
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parents:
diff changeset
239 throw OrthancException(ErrorCode_UnknownResource);
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parents:
diff changeset
240 }
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parents:
diff changeset
241 else
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parents:
diff changeset
242 {
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diff changeset
243 // Add all the instances of the series as to be processed
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parents:
diff changeset
244 std::list<std::string> instances;
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parents:
diff changeset
245 context_.GetIndex().GetChildren(instances, series);
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parents:
diff changeset
246
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parents:
diff changeset
247 for (std::list<std::string>::const_iterator
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parents:
diff changeset
248 it = instances.begin(); it != instances.end(); ++it)
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diff changeset
249 {
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250 AddInstance(*it);
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251 }
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252 }
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253 }
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254
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255
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256 void SplitStudyJob::SetKeepSource(bool keep)
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257 {
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258 if (IsStarted())
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259 {
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260 throw OrthancException(ErrorCode_BadSequenceOfCalls);
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261 }
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262
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263 keepSource_ = keep;
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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 void SplitStudyJob::GetPublicContent(Json::Value& value)
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293 {
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294 SetOfInstancesJob::GetPublicContent(value);
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295
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296 if (!targetStudy_.empty())
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297 {
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298 value["TargetStudy"] = targetStudy_;
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299 }
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300
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301 value["TargetStudyUID"] = targetStudyUid_;
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302 }
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303
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304
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305 bool SplitStudyJob::Serialize(Json::Value& target)
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306 {
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307 return true;
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308 }
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309 }