--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancServer/Sources/ServerJobs/MergeStudyJob.cpp	Wed Jun 10 20:30:34 2020 +0200
@@ -0,0 +1,375 @@
+/**
+ * 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 "MergeStudyJob.h"
+
+#include "../../Core/DicomParsing/FromDcmtkBridge.h"
+#include "../../Core/Logging.h"
+#include "../../Core/SerializationToolbox.h"
+#include "../ServerContext.h"
+
+
+namespace Orthanc
+{
+  void MergeStudyJob::AddSourceSeriesInternal(const std::string& series)
+  {
+    // 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);
+    }
+  }
+
+
+  void MergeStudyJob::AddSourceStudyInternal(const std::string& study)
+  {
+    if (study == targetStudy_)
+    {
+      throw OrthancException(ErrorCode_UnknownResource,
+                             "Cannot merge a study into the same study: " + study);
+    }
+    else
+    {
+      std::list<std::string> series;
+      GetContext().GetIndex().GetChildren(series, study);
+
+      for (std::list<std::string>::const_iterator
+             it = series.begin(); it != series.end(); ++it)
+      {
+        AddSourceSeriesInternal(*it);
+      }
+    }
+  }
+
+
+  bool MergeStudyJob::HandleInstance(const std::string& instance)
+  {
+    if (!HasTrailingStep())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls,
+                             "AddTrailingStep() should have been called after AddSourceXXX()");
+    }
+    
+    /**
+     * 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
+     **/
+
+    std::string series = modified->GetHasher().HashSeries();
+
+    SeriesUidMap::const_iterator targetSeriesUid = seriesUidMap_.find(series);
+
+    if (targetSeriesUid == seriesUidMap_.end())
+    {
+      throw OrthancException(ErrorCode_BadFileFormat);  // Should never happen
+    }
+
+
+    /**
+     * Copy the tags from the "Patient Module Attributes" and "General
+     * Study Module Attributes" modules of the target study
+     **/
+
+    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_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));
+
+    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;
+  }
+
+  
+  MergeStudyJob::MergeStudyJob(ServerContext& context,
+                               const std::string& targetStudy) :
+    CleaningInstancesJob(context, false /* by default, remove source instances */),
+    targetStudy_(targetStudy)
+  {
+    /**
+     * Check the validity of the input ID
+     **/
+    
+    ResourceType type;
+
+    if (!GetContext().GetIndex().LookupResourceType(type, targetStudy) ||
+        type != ResourceType_Study)
+    {
+      throw OrthancException(ErrorCode_UnknownResource,
+                             "Cannot merge into an unknown study: " + targetStudy);
+    }
+
+
+    /**
+     * Detect the tags to be removed/replaced by parsing one child
+     * instance of the study
+     **/
+
+    DicomTag::AddTagsForModule(removals_, DicomModule_Patient);
+    DicomTag::AddTagsForModule(removals_, DicomModule_Study);
+    
+    std::list<std::string> instances;
+    GetContext().GetIndex().GetChildInstances(instances, targetStudy);
+    
+    if (instances.empty())
+    {
+      throw OrthancException(ErrorCode_UnknownResource);
+    }
+
+    DicomMap dicom;
+
+    {
+      ServerContext::DicomCacheLocker locker(GetContext(), instances.front());
+      locker.GetDicom().ExtractDicomSummary(dicom);
+    }
+
+    const std::set<DicomTag> moduleTags = removals_;
+    for (std::set<DicomTag>::const_iterator it = moduleTags.begin();
+         it != moduleTags.end(); ++it)
+    {
+      const DicomValue* value = dicom.TestAndGetValue(*it);
+      std::string str;
+      
+      if (value != NULL &&
+          value->CopyToString(str, false))
+      {
+        removals_.erase(*it);
+        replacements_.insert(std::make_pair(*it, str));
+      }
+    }
+  }
+  
+
+  void MergeStudyJob::SetOrigin(const DicomInstanceOrigin& origin)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      origin_ = origin;
+    }
+  }
+
+  
+  void MergeStudyJob::SetOrigin(const RestApiCall& call)
+  {
+    SetOrigin(DicomInstanceOrigin::FromRest(call));
+  }
+
+
+  void MergeStudyJob::AddSource(const std::string& studyOrSeries)
+  {
+    ResourceType level;
+    
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else if (!GetContext().GetIndex().LookupResourceType(level, studyOrSeries))
+    {
+      throw OrthancException(ErrorCode_UnknownResource,
+                             "Cannot find this resource: " + studyOrSeries);
+    }
+    else
+    {
+      switch (level)
+      {
+        case ResourceType_Study:
+          AddSourceStudyInternal(studyOrSeries);
+          break;
+          
+        case ResourceType_Series:
+          AddSourceSeries(studyOrSeries);
+          break;
+          
+        default:
+          throw OrthancException(ErrorCode_UnknownResource,
+                                 "This resource is neither a study, nor a series: " +
+                                 studyOrSeries + " is a " +
+                                 std::string(EnumerationToString(level)));
+      }
+    }    
+  }
+  
+
+  void MergeStudyJob::AddSourceSeries(const std::string& series)
+  {
+    std::string parent;
+
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else if (!GetContext().GetIndex().LookupParent(parent, series, ResourceType_Study))
+    {
+      throw OrthancException(ErrorCode_UnknownResource,
+                             "This resource is not a series: " + series);
+    }
+    else if (parent == targetStudy_)
+    {
+      throw OrthancException(ErrorCode_UnknownResource,
+                             "Cannot merge series " + series +
+                             " into its parent study " + targetStudy_);
+    }
+    else
+    {
+      AddSourceSeriesInternal(series);
+    }    
+  }
+
+
+  void MergeStudyJob::AddSourceStudy(const std::string& study)
+  {
+    ResourceType actualLevel;
+
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else if (!GetContext().GetIndex().LookupResourceType(actualLevel, study) ||
+             actualLevel != ResourceType_Study)
+    {
+      throw OrthancException(ErrorCode_UnknownResource,
+                             "This resource is not a study: " + study);
+    }
+    else
+    {
+      AddSourceStudyInternal(study);
+    }    
+  }
+
+
+  void MergeStudyJob::GetPublicContent(Json::Value& value)
+  {
+    CleaningInstancesJob::GetPublicContent(value);
+    value["TargetStudy"] = targetStudy_;
+  }
+
+
+  static const char* TARGET_STUDY = "TargetStudy";
+  static const char* REPLACEMENTS = "Replacements";
+  static const char* REMOVALS = "Removals";
+  static const char* SERIES_UID_MAP = "SeriesUIDMap";
+  static const char* ORIGIN = "Origin";
+
+
+  MergeStudyJob::MergeStudyJob(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);
+    }
+
+    targetStudy_ = SerializationToolbox::ReadString(serialized, TARGET_STUDY);
+    SerializationToolbox::ReadMapOfTags(replacements_, serialized, REPLACEMENTS);
+    SerializationToolbox::ReadSetOfTags(removals_, serialized, REMOVALS);
+    SerializationToolbox::ReadMapOfStrings(seriesUidMap_, serialized, SERIES_UID_MAP);
+    origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
+  }
+
+  
+  bool MergeStudyJob::Serialize(Json::Value& target)
+  {
+    if (!CleaningInstancesJob::Serialize(target))
+    {
+      return false;
+    }
+    else
+    {
+      target[TARGET_STUDY] = targetStudy_;
+      SerializationToolbox::WriteMapOfTags(target, replacements_, REPLACEMENTS);
+      SerializationToolbox::WriteSetOfTags(target, removals_, REMOVALS);
+      SerializationToolbox::WriteMapOfStrings(target, seriesUidMap_, SERIES_UID_MAP);
+      origin_.Serialize(target[ORIGIN]);
+
+      return true;
+    }
+  }
+}