--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/OrthancServer/Sources/ServerJobs/ResourceModificationJob.cpp	Wed Jun 10 20:30:34 2020 +0200
@@ -0,0 +1,460 @@
+/**
+ * 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 "../PrecompiledHeadersServer.h"
+#include "ResourceModificationJob.h"
+
+#include "../../Core/Logging.h"
+#include "../../Core/SerializationToolbox.h"
+#include "../ServerContext.h"
+
+#include <dcmtk/dcmdata/dcfilefo.h>
+#include <dcmtk/dcmdata/dcdeftag.h>
+#include <cassert>
+
+namespace Orthanc
+{
+  class ResourceModificationJob::Output : public boost::noncopyable
+  {
+  private:
+    ResourceType  level_;
+    bool          isFirst_;
+    std::string   id_;
+    std::string   patientId_;
+
+  public:
+    Output(ResourceType level) :
+      level_(level),
+      isFirst_(true)
+    {
+      if (level_ != ResourceType_Patient &&
+          level_ != ResourceType_Study &&
+          level_ != ResourceType_Series)
+      {
+        throw OrthancException(ErrorCode_ParameterOutOfRange);
+      }            
+    }
+
+    ResourceType GetLevel() const
+    {
+      return level_;
+    }
+    
+
+    void Update(DicomInstanceHasher& hasher)
+    {
+      if (isFirst_)
+      {
+        switch (level_)
+        {
+          case ResourceType_Series:
+            id_ = hasher.HashSeries();
+            break;
+
+          case ResourceType_Study:
+            id_ = hasher.HashStudy();
+            break;
+
+          case ResourceType_Patient:
+            id_ = hasher.HashPatient();
+            break;
+
+          default:
+            throw OrthancException(ErrorCode_InternalError);
+        }
+
+        patientId_ = hasher.HashPatient();
+        isFirst_ = false;
+      }
+    }
+
+
+    bool Format(Json::Value& target)
+    {
+      if (isFirst_)
+      {
+        return false;
+      }
+      else
+      {
+        target = Json::objectValue;
+        target["Type"] = EnumerationToString(level_);
+        target["ID"] = id_;
+        target["Path"] = GetBasePath(level_, id_);
+        target["PatientID"] = patientId_;
+        return true;
+      }
+    }
+
+  
+    bool GetIdentifier(std::string& id)
+    {
+      if (isFirst_)
+      {
+        return false;
+      }
+      else
+      {
+        id = id_;
+        return true;
+      }
+    }
+  };
+    
+
+
+
+  bool ResourceModificationJob::HandleInstance(const std::string& instance)
+  {
+    if (modification_.get() == NULL ||
+        output_.get() == NULL)
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls,
+                             "No modification was provided for this job");
+    }
+
+      
+    LOG(INFO) << "Modifying instance in a job: " << instance;
+
+
+    /**
+     * Retrieve the original instance from the DICOM cache.
+     **/
+    
+    std::unique_ptr<DicomInstanceHasher> originalHasher;
+    std::unique_ptr<ParsedDicomFile> modified;
+
+    try
+    {
+      ServerContext::DicomCacheLocker locker(GetContext(), instance);
+      ParsedDicomFile& original = locker.GetDicom();
+
+      originalHasher.reset(new DicomInstanceHasher(original.GetHasher()));
+      modified.reset(original.Clone(true));
+    }
+    catch (OrthancException& e)
+    {
+      LOG(WARNING) << "An error occurred while executing a Modification job on instance " << instance << ": " << e.GetDetails();
+      return false;
+    }
+
+
+    /**
+     * Compute the resulting DICOM instance.
+     **/
+
+    modification_->Apply(*modified);
+
+    const std::string modifiedUid = IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject());
+    
+    if (transcode_)
+    {
+      std::set<DicomTransferSyntax> syntaxes;
+      syntaxes.insert(transferSyntax_);
+
+      IDicomTranscoder::DicomImage source;
+      source.AcquireParsed(*modified);  // "modified" is invalid below this point
+      
+      IDicomTranscoder::DicomImage transcoded;
+      if (GetContext().Transcode(transcoded, source, syntaxes, true))
+      {
+        modified.reset(transcoded.ReleaseAsParsedDicomFile());
+
+        // Fix the SOP instance UID in order the preserve the
+        // references between instance UIDs in the DICOM hierarchy
+        // (the UID might have changed in the case of lossy transcoding)
+        if (modified.get() == NULL ||
+            modified->GetDcmtkObject().getDataset() == NULL ||
+            !modified->GetDcmtkObject().getDataset()->putAndInsertString(
+              DCM_SOPInstanceUID, modifiedUid.c_str(), OFTrue /* replace */).good())
+        {
+          throw OrthancException(ErrorCode_InternalError);
+        }
+      }
+      else
+      {
+        LOG(WARNING) << "Cannot transcode instance, keeping original transfer syntax: " << instance;
+        modified.reset(source.ReleaseAsParsedDicomFile());
+      }
+    }
+
+    assert(modifiedUid == IDicomTranscoder::GetSopInstanceUid(modified->GetDcmtkObject()));
+
+    DicomInstanceToStore toStore;
+    toStore.SetOrigin(origin_);
+    toStore.SetParsedDicomFile(*modified);
+
+
+    /**
+     * Prepare the metadata information to associate with the
+     * resulting DICOM instance (AnonymizedFrom/ModifiedFrom).
+     **/
+
+    DicomInstanceHasher modifiedHasher = modified->GetHasher();
+      
+    MetadataType metadataType = (isAnonymization_ ?
+                                 MetadataType_AnonymizedFrom :
+                                 MetadataType_ModifiedFrom);
+
+    if (originalHasher->HashSeries() != modifiedHasher.HashSeries())
+    {
+      toStore.AddMetadata(ResourceType_Series, metadataType, originalHasher->HashSeries());
+    }
+
+    if (originalHasher->HashStudy() != modifiedHasher.HashStudy())
+    {
+      toStore.AddMetadata(ResourceType_Study, metadataType, originalHasher->HashStudy());
+    }
+
+    if (originalHasher->HashPatient() != modifiedHasher.HashPatient())
+    {
+      toStore.AddMetadata(ResourceType_Patient, metadataType, originalHasher->HashPatient());
+    }
+
+    assert(instance == originalHasher->HashInstance());
+    toStore.AddMetadata(ResourceType_Instance, metadataType, instance);
+
+
+    /**
+     * Store the resulting DICOM instance into the Orthanc store.
+     **/
+
+    std::string modifiedInstance;
+    if (GetContext().Store(modifiedInstance, toStore,
+                           StoreInstanceMode_Default) != StoreStatus_Success)
+    {
+      throw OrthancException(ErrorCode_CannotStoreInstance,
+                             "Error while storing a modified instance " + instance);
+    }
+
+    /**
+     * The assertion below will fail if automated transcoding to a
+     * lossy transfer syntax is enabled in the Orthanc core, and if
+     * the source instance is not in this transfer syntax.
+     **/
+    // assert(modifiedInstance == modifiedHasher.HashInstance());
+
+    output_->Update(modifiedHasher);
+
+    return true;
+  }
+
+
+  ResourceModificationJob::ResourceModificationJob(ServerContext& context) :
+    CleaningInstancesJob(context, true /* by default, keep source */),
+    modification_(new DicomModification),
+    isAnonymization_(false),
+    transcode_(false)
+  {
+  }
+
+
+  void ResourceModificationJob::SetModification(DicomModification* modification,
+                                                ResourceType level,
+                                                bool isAnonymization)
+  {
+    if (modification == NULL)
+    {
+      throw OrthancException(ErrorCode_NullPointer);
+    }
+    else if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      modification_.reset(modification);
+      output_.reset(new Output(level));
+      isAnonymization_ = isAnonymization;
+    }
+  }
+
+
+  void ResourceModificationJob::SetOrigin(const DicomInstanceOrigin& origin)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      origin_ = origin;
+    }
+  }
+
+  
+  void ResourceModificationJob::SetOrigin(const RestApiCall& call)
+  {
+    SetOrigin(DicomInstanceOrigin::FromRest(call));
+  }
+
+
+  const DicomModification& ResourceModificationJob::GetModification() const
+  {
+    if (modification_.get() == NULL)
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      return *modification_;
+    }
+  }
+
+
+  DicomTransferSyntax ResourceModificationJob::GetTransferSyntax() const
+  {
+    if (transcode_)
+    {
+      return transferSyntax_;
+    }
+    else
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+  }
+  
+
+  void ResourceModificationJob::SetTranscode(DicomTransferSyntax syntax)
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      transcode_ = true;
+      transferSyntax_ = syntax;
+    }    
+  }
+
+
+  void ResourceModificationJob::SetTranscode(const std::string& transferSyntaxUid)
+  {
+    DicomTransferSyntax s;
+    if (LookupTransferSyntax(s, transferSyntaxUid))
+    {
+      SetTranscode(s);
+    }
+    else
+    {
+      throw OrthancException(ErrorCode_BadFileFormat,
+                             "Unknown transfer syntax UID: " + transferSyntaxUid);
+    }
+  }
+
+
+  void ResourceModificationJob::ClearTranscode()
+  {
+    if (IsStarted())
+    {
+      throw OrthancException(ErrorCode_BadSequenceOfCalls);
+    }
+    else
+    {
+      transcode_ = false;
+    }
+  }
+
+
+  void ResourceModificationJob::GetPublicContent(Json::Value& value)
+  {
+    CleaningInstancesJob::GetPublicContent(value);
+
+    value["IsAnonymization"] = isAnonymization_;
+
+    if (output_.get() != NULL)
+    {
+      output_->Format(value);
+    }
+
+    if (transcode_)
+    {
+      value["Transcode"] = GetTransferSyntaxUid(transferSyntax_);
+    }
+  }
+
+
+  static const char* MODIFICATION = "Modification";
+  static const char* ORIGIN = "Origin";
+  static const char* IS_ANONYMIZATION = "IsAnonymization";
+  static const char* TRANSCODE = "Transcode";
+  
+
+  ResourceModificationJob::ResourceModificationJob(ServerContext& context,
+                                                   const Json::Value& serialized) :
+    CleaningInstancesJob(context, serialized, true /* by default, keep source */)
+  {
+    assert(serialized.type() == Json::objectValue);
+
+    isAnonymization_ = SerializationToolbox::ReadBoolean(serialized, IS_ANONYMIZATION);
+    origin_ = DicomInstanceOrigin(serialized[ORIGIN]);
+    modification_.reset(new DicomModification(serialized[MODIFICATION]));
+
+    if (serialized.isMember(TRANSCODE))
+    {
+      SetTranscode(SerializationToolbox::ReadString(serialized, TRANSCODE));
+    }
+    else
+    {
+      transcode_ = false;
+    }
+  }
+  
+  bool ResourceModificationJob::Serialize(Json::Value& value)
+  {
+    if (!CleaningInstancesJob::Serialize(value))
+    {
+      return false;
+    }
+    else
+    {
+      assert(value.type() == Json::objectValue);
+      
+      value[IS_ANONYMIZATION] = isAnonymization_;
+
+      if (transcode_)
+      {
+        value[TRANSCODE] = GetTransferSyntaxUid(transferSyntax_);
+      }
+      
+      origin_.Serialize(value[ORIGIN]);
+      
+      Json::Value tmp;
+      modification_->Serialize(tmp);
+      value[MODIFICATION] = tmp;
+
+      return true;
+    }
+  }
+}