--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancServer/Sources/ServerJobs/SplitStudyJob.cpp	Wed Jun 10 20:30:34 2020 +0200
@@ -0,0 +1,351 @@
+/**
+ * Orthanc - A Lightweight, RESTful DICOM Store
+ * Copyright (C) 2012-2016 Sebastien Jodogne, Medical Physics
+ * Department, University Hospital of Liege, Belgium
+ * Copyright (C) 2017-2020 Osimis S.A., Belgium
+ *
+ * This program is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License as
+ * published by the Free Software Foundation, either version 3 of the
+ * License, or (at your option) any later version.
+ *
+ * In addition, as a special exception, the copyright holders of this
+ * program give permission to link the code of its release with the
+ * OpenSSL project's "OpenSSL" library (or with modified versions of it
+ * that use the same license as the "OpenSSL" library), and distribute
+ * the linked executables. You must obey the GNU General Public License
+ * in all respects for all of the code used other than "OpenSSL". If you
+ * modify file(s) with this exception, you may extend this exception to
+ * your version of the file(s), but you are not obligated to do so. If
+ * you do not wish to do so, delete this exception statement from your
+ * version. If you delete this exception statement from all source files
+ * in the program, then also delete it here.
+ * 
+ * This program is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+ * General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ **/
+
+
+#include "SplitStudyJob.h"
+
+#include "../../Core/DicomParsing/FromDcmtkBridge.h"
+#include "../../Core/Logging.h"
+#include "../../Core/SerializationToolbox.h"
+#include "../ServerContext.h"
+
+
+namespace Orthanc
+{
+  void SplitStudyJob::CheckAllowedTag(const DicomTag& tag) const
+  {
+    if (allowedTags_.find(tag) == allowedTags_.end())
+    {
+      throw OrthancException(ErrorCode_ParameterOutOfRange,
+                             "Cannot modify the following tag while splitting a study "
+                             "(not in the patient/study modules): " +
+                             FromDcmtkBridge::GetTagName(tag, "") +
+                             " (" + tag.Format() + ")");
+    }
+  }
+
+  
+  void SplitStudyJob::Setup()
+  {
+    SetPermissive(false);
+    
+    DicomTag::AddTagsForModule(allowedTags_, DicomModule_Patient);
+    DicomTag::AddTagsForModule(allowedTags_, DicomModule_Study);
+    allowedTags_.erase(DICOM_TAG_STUDY_INSTANCE_UID);
+    allowedTags_.erase(DICOM_TAG_SERIES_INSTANCE_UID);
+  }
+
+  
+  bool SplitStudyJob::HandleInstance(const std::string& instance)
+  {
+    if (!HasTrailingStep())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls,
+                             "AddTrailingStep() should have been called after AddSourceSeries()");
+    }
+    
+    /**
+     * Retrieve the DICOM instance to be modified
+     **/
+    
+    std::unique_ptr<ParsedDicomFile> modified;
+
+    try
+    {
+      ServerContext::DicomCacheLocker locker(GetContext(), instance);
+      modified.reset(locker.GetDicom().Clone(true));
+    }
+    catch (OrthancException&)
+    {
+      LOG(WARNING) << "An instance was removed after the job was issued: " << instance;
+      return false;
+    }
+
+
+    /**
+     * Chose the target UIDs
+     **/
+
+    assert(modified->GetHasher().HashStudy() == sourceStudy_);
+
+    std::string series = modified->GetHasher().HashSeries();
+
+    SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series);
+
+    if (targetSeriesUid == seriesUidMap_.end())
+    {
+      throw OrthancException(ErrorCode_BadFileFormat);  // Should never happen
+    }
+
+
+    /**
+     * Apply user-specified modifications
+     **/
+
+    for (std::set<DicomTag>::const_iterator it = removals_.begin();
+         it != removals_.end(); ++it)
+    {
+      modified->Remove(*it);
+    }
+    
+    for (Replacements::const_iterator it = replacements_.begin();
+         it != replacements_.end(); ++it)
+    {
+      modified->ReplacePlainString(it->first, it->second);
+    }
+
+
+    /**
+     * Store the new instance into Orthanc
+     **/
+    
+    modified->ReplacePlainString(DICOM_TAG_STUDY_INSTANCE_UID, targetStudyUid_);
+    modified->ReplacePlainString(DICOM_TAG_SERIES_INSTANCE_UID, targetSeriesUid->second);
+
+    // Fix since Orthanc 1.5.8: Assign new "SOPInstanceUID", as the instance has been modified
+    modified->ReplacePlainString(DICOM_TAG_SOP_INSTANCE_UID, FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Instance));
+
+    if (targetStudy_.empty())
+    {
+      targetStudy_ = modified->GetHasher().HashStudy();
+    }
+    
+    DicomInstanceToStore toStore;
+    toStore.SetOrigin(origin_);
+    toStore.SetParsedDicomFile(*modified);
+
+    std::string modifiedInstance;
+    if (GetContext().Store(modifiedInstance, toStore,
+                           StoreInstanceMode_Default) != StoreStatus_Success)
+    {
+      LOG(ERROR) << "Error while storing a modified instance " << instance;
+      return false;
+    }
+
+    return true;
+  }
+
+  
+  SplitStudyJob::SplitStudyJob(ServerContext& context,
+                               const std::string& sourceStudy) :
+    CleaningInstancesJob(context, false /* by default, remove source instances */),
+    sourceStudy_(sourceStudy),
+    targetStudyUid_(FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Study))
+  {
+    Setup();
+    
+    ResourceType type;
+    
+    if (!GetContext().GetIndex().LookupResourceType(type, sourceStudy) ||
+        type != ResourceType_Study)
+    {
+      throw OrthancException(ErrorCode_UnknownResource,
+                             "Cannot split unknown study " + sourceStudy);
+    }
+  }
+  
+
+  void SplitStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      origin_ = origin;
+    }
+  }
+
+  
+  void SplitStudyJob::SetOrigin(const RestApiCall& call)
+  {
+    SetOrigin(DicomInstanceOrigin::FromRest(call));
+  }
+
+
+  void SplitStudyJob::AddSourceSeries(const std::string& series)
+  {
+    std::string parent;
+
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else if (!GetContext().GetIndex().LookupParent(parent, series, ResourceType_Study) ||
+             parent != sourceStudy_)
+    {
+      throw OrthancException(ErrorCode_UnknownResource,
+                             "This series does not belong to the study to be split: " + series);
+    }
+    else
+    {
+      // Generate a target SeriesInstanceUID for this series
+      seriesUidMap_[series] = FromDcmtkBridge::GenerateUniqueIdentifier(ResourceType_Series);
+
+      // Add all the instances of the series as to be processed
+      std::list<std::string> instances;
+      GetContext().GetIndex().GetChildren(instances, series);
+
+      for (std::list<std::string>::const_iterator
+             it = instances.begin(); it != instances.end(); ++it)
+      {
+        AddInstance(*it);
+      }
+    }    
+  }
+
+
+  bool SplitStudyJob::LookupTargetSeriesUid(std::string& uid,
+                                            const std::string& series) const
+  {
+    SeriesUidMap::const_iterator found = seriesUidMap_.find(series);
+
+    if (found == seriesUidMap_.end())
+    {
+      return false;
+    }
+    else
+    {
+      uid = found->second;
+      return true;
+    }
+  }
+
+
+  void SplitStudyJob::Remove(const DicomTag& tag)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+
+    CheckAllowedTag(tag);
+    removals_.insert(tag);
+  }
+
+  
+  void SplitStudyJob::Replace(const DicomTag& tag,
+                              const std::string& value)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+
+    CheckAllowedTag(tag);
+    replacements_[tag] = value;
+  }
+
+
+  bool SplitStudyJob::LookupReplacement(std::string& value,
+                                        const DicomTag& tag) const
+  {
+    Replacements::const_iterator found = replacements_.find(tag);
+
+    if (found == replacements_.end())
+    {
+      return false;
+    }
+    else
+    {
+      value = found->second;
+      return true;
+    }
+  }
+  
+    
+  void SplitStudyJob::GetPublicContent(Json::Value& value)
+  {
+    CleaningInstancesJob::GetPublicContent(value);
+
+    if (!targetStudy_.empty())
+    {
+      value["TargetStudy"] = targetStudy_;
+    }
+    
+    value["TargetStudyUID"] = targetStudyUid_;
+  }
+
+
+  static const char* SOURCE_STUDY = "SourceStudy";
+  static const char* TARGET_STUDY = "TargetStudy";
+  static const char* TARGET_STUDY_UID = "TargetStudyUID";
+  static const char* SERIES_UID_MAP = "SeriesUIDMap";
+  static const char* ORIGIN = "Origin";
+  static const char* REPLACEMENTS = "Replacements";
+  static const char* REMOVALS = "Removals";
+
+
+  SplitStudyJob::SplitStudyJob(ServerContext& context,
+                               const Json::Value& serialized) :
+    CleaningInstancesJob(context, serialized,
+                         false /* by default, remove source instances */)  // (*)
+  {
+    if (!HasTrailingStep())
+    {
+      // Should have been set by (*)
+      throw OrthancException(ErrorCode_InternalError);
+    }
+
+    Setup();
+
+    sourceStudy_ = SerializationToolbox::ReadString(serialized, SOURCE_STUDY);
+    targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
+    targetStudyUid_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY_UID);
+    SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
+    origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
+    SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
+    SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
+  }
+
+  
+  bool SplitStudyJob::Serialize(Json::Value& target)
+  {
+    if (!CleaningInstancesJob::Serialize(target))
+    {
+      return false;
+    }
+    else
+    {
+      target[SOURCE_STUDY] = sourceStudy_;
+      target[TARGET_STUDY] = targetStudy_;
+      target[TARGET_STUDY_UID] = targetStudyUid_;
+      SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
+      origin_.Serialize(target[ORIGIN]);
+      SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
+      SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
+
+      return true;
+    }
+  }
+}